Complex_Diet Data Analysis

Complex_Protein Report

This report is dived in two parts, first is all the metagenomics statistical analysis. Just to remeber, here we already have done all the bioinformatics part. Which are: Remove low quality reads, remove host contamination, put taxonomic with kraken2 and calculate the total or relative abundace of reads for each taxonomic unit. Now we will load all the files in R and the metadata.

Load packages

library(tidyverse)
library(BiocManager)
library(phyloseq)
library(labdsv)
library(ape)
library(Maaslin2)
library(ggplot2)
library(dplyr)
library(forcats)
library(viridis)
library(vegan)
library(knitr)
library(mixOmics)
library(ALDEx2)
library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)
library(ANCOMBC)
library(Biostrings)
library(scater)
library(TreeSummarizedExperiment)
library(mia)
library(metagMisc)
library(devtools)
library(pairwiseAdonis)
library(ggpubr)
library(openxlsx)
library(maaslin3)
library(patchwork)

Load data

#| label: load-bracken-data

# Load all taxonomic levels
domain_raw <- read.delim("merged_D_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
phylum_raw <- read.delim("merged_P_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
class_raw <- read.delim("merged_C_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
order_raw <- read.delim("merged_O_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
family_raw <- read.delim("merged_F_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
genus_raw <- read.delim("merged_G_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)
species_raw <- read.delim("merged_S_abundance.txt", header = TRUE, row.names = 1, check.names = FALSE)

# Load metadata
meta_tab <- read.csv("meta.csv", row.names = 1)

Separate counts and fractions (using species as example - repeat for other levels)

# Get column names
all_cols <- colnames(species_raw)

# Identify count columns (end with _num) and fraction columns (end with _frac)
num_cols <- grep("_num$", all_cols, value = TRUE)
frac_cols <- grep("_frac$", all_cols, value = TRUE)

# Create clean sample names (remove .bracken_num suffix)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

# Extract counts matrix
species_counts <- species_raw[, num_cols]
colnames(species_counts) <- sample_names
species_counts <- as.matrix(species_counts)
storage.mode(species_counts) <- "numeric"

# Extract fractions matrix  
species_frac <- species_raw[, frac_cols]
colnames(species_frac) <- sample_names
species_frac <- as.matrix(species_frac)
storage.mode(species_frac) <- "numeric"

# Check dimensions
dim(species_counts)

[1] 2671   29

dim(species_frac)

[1] 2671   29

Repeat for all taxonomic levels:

#| label: process-all-levels

# Domain
num_cols <- grep("_num$", colnames(domain_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(domain_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

domain_counts <- as.matrix(domain_raw[, num_cols])
colnames(domain_counts) <- sample_names
storage.mode(domain_counts) <- "numeric"

domain_frac <- as.matrix(domain_raw[, frac_cols])
colnames(domain_frac) <- sample_names
storage.mode(domain_frac) <- "numeric"

# Phylum
num_cols <- grep("_num$", colnames(phylum_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(phylum_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

phylum_counts <- as.matrix(phylum_raw[, num_cols])
colnames(phylum_counts) <- sample_names
storage.mode(phylum_counts) <- "numeric"

phylum_frac <- as.matrix(phylum_raw[, frac_cols])
colnames(phylum_frac) <- sample_names
storage.mode(phylum_frac) <- "numeric"

# Class
num_cols <- grep("_num$", colnames(class_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(class_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

class_counts <- as.matrix(class_raw[, num_cols])
colnames(class_counts) <- sample_names
storage.mode(class_counts) <- "numeric"

class_frac <- as.matrix(class_raw[, frac_cols])
colnames(class_frac) <- sample_names
storage.mode(class_frac) <- "numeric"

# Order
num_cols <- grep("_num$", colnames(order_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(order_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

order_counts <- as.matrix(order_raw[, num_cols])
colnames(order_counts) <- sample_names
storage.mode(order_counts) <- "numeric"

order_frac <- as.matrix(order_raw[, frac_cols])
colnames(order_frac) <- sample_names
storage.mode(order_frac) <- "numeric"

# Family
num_cols <- grep("_num$", colnames(family_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(family_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

family_counts <- as.matrix(family_raw[, num_cols])
colnames(family_counts) <- sample_names
storage.mode(family_counts) <- "numeric"

family_frac <- as.matrix(family_raw[, frac_cols])
colnames(family_frac) <- sample_names
storage.mode(family_frac) <- "numeric"

# Genus
num_cols <- grep("_num$", colnames(genus_raw), value = TRUE)
frac_cols <- grep("_frac$", colnames(genus_raw), value = TRUE)
sample_names <- gsub("\\.bracken_num$", "", num_cols)

genus_counts <- as.matrix(genus_raw[, num_cols])
colnames(genus_counts) <- sample_names
storage.mode(genus_counts) <- "numeric"

genus_frac <- as.matrix(genus_raw[, frac_cols])
colnames(genus_frac) <- sample_names
storage.mode(genus_frac) <- "numeric"

Align samples between data and metadata:

# Find common samples between data and metadata
common_samples <- intersect(colnames(species_counts), rownames(meta_tab))
length(common_samples)

[1] 29

# Subset and reorder all matrices and metadata
meta_tab <- meta_tab[common_samples, ]

domain_counts <- domain_counts[, common_samples]
domain_frac <- domain_frac[, common_samples]

phylum_counts <- phylum_counts[, common_samples]
phylum_frac <- phylum_frac[, common_samples]

class_counts <- class_counts[, common_samples]
class_frac <- class_frac[, common_samples]

order_counts <- order_counts[, common_samples]
order_frac <- order_frac[, common_samples]

family_counts <- family_counts[, common_samples]
family_frac <- family_frac[, common_samples]

genus_counts <- genus_counts[, common_samples]
genus_frac <- genus_frac[, common_samples]

species_counts <- species_counts[, common_samples]
species_frac <- species_frac[, common_samples]

Set up factors and colorblind-friendly palette:

# Convert metadata columns to factors
meta_tab$complex <- factor(meta_tab$complex, levels = c("low", "medium", "high"))
meta_tab$protease <- factor(meta_tab$protease, levels = c("cont", "prot"))
meta_tab$interaction <- factor(meta_tab$interaction)

# Colorblind-friendly palette (Wong, 2011 - Nature Methods)
cb_palette <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", 
                "#0072B2", "#D55E00", "#CC79A7", "#999999")

# Assign consistent colors to your treatment groups
complex_colors <- c("low" = "#56B4E9", "medium" = "#E69F00", "high" = "#009E73")
protease_colors <- c("cont" = "#0072B2", "prot" = "#D55E00")

# Publication-ready theme for ggplot
theme_publication <- theme_bw(base_size = 12) +
  theme(
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.border = element_rect(color = "black", linewidth = 1),
    axis.text = element_text(color = "black"),
    axis.title = element_text(face = "bold"),
    legend.background = element_rect(color = "black", linewidth = 0.5),
    legend.title = element_text(face = "bold"),
    strip.background = element_rect(fill = "grey90", color = "black"),
    strip.text = element_text(face = "bold"),
    plot.title = element_text(hjust = 0.5, face = "bold")
  )

Quick data summary:

# Summary of taxa per level
data.frame(
  Level = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  N_Taxa = c(nrow(domain_counts), nrow(phylum_counts), nrow(class_counts),
             nrow(order_counts), nrow(family_counts), nrow(genus_counts), 
             nrow(species_counts)),
  N_Samples = ncol(species_counts)
)

    Level N_Taxa N_Samples
1  Domain      4        29
2  Phylum     44        29
3   Class     88        29
4   Order    192        29
5  Family    440        29
6   Genus   1267        29
7 Species   2671        29

Alpha Diversity

Calculate alpha diversity metrics:

Bruno, a diversidade alpha é feito sobre a relativa abundance. Se vc somar a relativa abudancia de todas as especies dentro uma amostra tem que dar um ou bem proximo de 1. Faz sentido? Diversidade alpha tem varias metricas, aqui eu coloquei as principais. Entretento, a metrica CHAO1, tem que ser feito sobre o numero de counts e nao abundancia relativa. Obseerva que as tabelas tem o nome diferente “_counts”.

# Transpose matrix (vegan needs samples as rows)
species_frac_t <- t(species_frac)
species_count_t <- t(species_counts)


library(vegan)

# Calculate alpha diversity metrics
alpha_div <- data.frame(
  sample    = rownames(species_frac_t),
  observed  = specnumber(species_frac_t),
  shannon   = diversity(species_frac_t, index = "shannon"),
  simpson   = diversity(species_frac_t, index = "simpson"),
  invsimpson = diversity(species_frac_t, index = "invsimpson")
)


# Add Chao1 (needs integer counts)
chao1_values <- estimateR(round(species_count_t))
alpha_div$chao1 <- chao1_values["S.chao1", ]

# Add Pielou's evenness (J = H / ln(S))
alpha_div$pielou <- alpha_div$shannon / log(alpha_div$observed)

# Merge with metadata
alpha_div <- merge(alpha_div, meta_tab, by.x = "sample", by.y = "row.names")

head(alpha_div)

  sample observed  shannon   simpson invsimpson chao1    pielou code tag weight
1   2827      579 3.244500 0.8926665   9.316758   579 0.5100371    3 815  32.00
2   2828      459 2.360992 0.7056383   3.397181   459 0.3852133    4 867  32.60
3   2830      799 3.629339 0.8813789   8.430207   799 0.5430411    6 911  33.80
4   2831      732 3.274195 0.8290662   5.850216   732 0.4964075    7 762  33.45
5   2832     1107 3.645070 0.8277069   5.804064  1107 0.5200253    8 773  29.75
6   2833     1558 4.092507 0.9268360  13.667922  1558 0.5567159    9 791  30.90
  pen trt complex protease interaction
1  41   3     low     prot        BCCP
2  31   4    high     cont        ACSP
3  29   6     low     cont        BCSP
4  42   5  medium     cont        MCSP
5  14   3     low     prot        BCCP
6  13   5  medium     cont        MCSP

Statistical tests for Complex factor:

# Kruskal-Wallis test for each metric (complex has 3 levels)
kruskal_observed_complex <- kruskal.test(observed ~ complex, data = alpha_div)
kruskal_shannon_complex <- kruskal.test(shannon ~ complex, data = alpha_div)
kruskal_simpson_complex <- kruskal.test(simpson ~ complex, data = alpha_div)
kruskal_invsimpson_complex <- kruskal.test(invsimpson ~ complex, data = alpha_div)
kruskal_chao1_complex <- kruskal.test(chao1 ~ complex, data = alpha_div)
kruskal_pielou_complex <- kruskal.test(pielou ~ complex, data = alpha_div)

# Summary table
stats_complex <- data.frame(
  Metric = c("Observed", "Shannon", "Simpson", "InvSimpson", "Chao1", "Pielou"),
  Chi_squared = c(kruskal_observed_complex$statistic,
                  kruskal_shannon_complex$statistic,
                  kruskal_simpson_complex$statistic,
                  kruskal_invsimpson_complex$statistic,
                  kruskal_chao1_complex$statistic,
                  kruskal_pielou_complex$statistic),
  p_value = c(kruskal_observed_complex$p.value,
              kruskal_shannon_complex$p.value,
              kruskal_simpson_complex$p.value,
              kruskal_invsimpson_complex$p.value,
              kruskal_chao1_complex$p.value,
              kruskal_pielou_complex$p.value)
)

stats_complex$p_adj <- p.adjust(stats_complex$p_value, method = "BH")
stats_complex$significance <- ifelse(stats_complex$p_adj < 0.001, "***",
                              ifelse(stats_complex$p_adj < 0.01, "**",
                              ifelse(stats_complex$p_adj < 0.05, "*", "ns")))

kable(stats_complex, digits = 4, caption = "Kruskal-Wallis test: Alpha diversity ~ Complex")

Kruskal-Wallis test: Alpha diversity ~ Complex

Metric	Chi_squared	p_value	p_adj	significance
Observed	3.5252	0.1716	0.3641	ns
Shannon	3.4070	0.1820	0.3641	ns
Simpson	0.6889	0.7086	0.7086	ns
InvSimpson	0.6889	0.7086	0.7086	ns
Chao1	3.5252	0.1716	0.3641	ns
Pielou	1.7781	0.4110	0.6166	ns

Statistical tests for Protease factor:

# Wilcoxon test for each metric (protease has 2 levels)
wilcox_observed_prot <- wilcox.test(observed ~ protease, data = alpha_div)
wilcox_shannon_prot <- wilcox.test(shannon ~ protease, data = alpha_div)
wilcox_simpson_prot <- wilcox.test(simpson ~ protease, data = alpha_div)
wilcox_invsimpson_prot <- wilcox.test(invsimpson ~ protease, data = alpha_div)
wilcox_chao1_prot <- wilcox.test(chao1 ~ protease, data = alpha_div)
wilcox_pielou_prot <- wilcox.test(pielou ~ protease, data = alpha_div)

# Summary table
stats_protease <- data.frame(
  Metric = c("Observed", "Shannon", "Simpson", "InvSimpson", "Chao1", "Pielou"),
  W_statistic = c(wilcox_observed_prot$statistic,
                  wilcox_shannon_prot$statistic,
                  wilcox_simpson_prot$statistic,
                  wilcox_invsimpson_prot$statistic,
                  wilcox_chao1_prot$statistic,
                  wilcox_pielou_prot$statistic),
  p_value = c(wilcox_observed_prot$p.value,
              wilcox_shannon_prot$p.value,
              wilcox_simpson_prot$p.value,
              wilcox_invsimpson_prot$p.value,
              wilcox_chao1_prot$p.value,
              wilcox_pielou_prot$p.value)
)

stats_protease$p_adj <- p.adjust(stats_protease$p_value, method = "BH")
stats_protease$significance <- ifelse(stats_protease$p_adj < 0.001, "***",
                               ifelse(stats_protease$p_adj < 0.01, "**",
                               ifelse(stats_protease$p_adj < 0.05, "*", "ns")))

kable(stats_protease, digits = 4, caption = "Wilcoxon test: Alpha diversity ~ Protease")

Wilcoxon test: Alpha diversity ~ Protease

Metric	W_statistic	p_value	p_adj	significance
Observed	122	0.4713	0.4713	ns
Shannon	84	0.3766	0.4713	ns
Simpson	79	0.2703	0.4713	ns
InvSimpson	79	0.2703	0.4713	ns
Chao1	122	0.4713	0.4713	ns
Pielou	84	0.3766	0.4713	ns

Plot alpha diversity by Complex:

# Pairwise comparisons for complex
comparisons_complex <- list(c("low", "medium"), c("low", "high"), c("medium", "high"))

# Observed richness
p1 <- ggplot(alpha_div, aes(x = complex, y = observed, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$observed) * 1.1) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Observed Species", title = "Observed Richness") +
  theme_publication +
  theme(legend.position = "none")

# Shannon
p2 <- ggplot(alpha_div, aes(x = complex, y = shannon, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$shannon) * 1.1) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Shannon Index", title = "Shannon Diversity") +
  theme_publication +
  theme(legend.position = "none")

# Simpson
p3 <- ggplot(alpha_div, aes(x = complex, y = simpson, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$simpson) * 1.05) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Simpson Index", title = "Simpson Diversity") +
  theme_publication +
  theme(legend.position = "none")

# Inverse Simpson
p4 <- ggplot(alpha_div, aes(x = complex, y = invsimpson, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$invsimpson) * 1.1) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Inverse Simpson", title = "Inverse Simpson") +
  theme_publication +
  theme(legend.position = "none")

# Chao1
p5 <- ggplot(alpha_div, aes(x = complex, y = chao1, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$chao1) * 1.1) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Chao1 Index", title = "Chao1 Richness") +
  theme_publication +
  theme(legend.position = "none")

# Pielou evenness
p6 <- ggplot(alpha_div, aes(x = complex, y = pielou, fill = complex)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = complex_colors) +
  stat_compare_means(method = "kruskal.test", label.x = 1.5, label.y = max(alpha_div$pielou, na.rm = TRUE) * 1.05) +
  stat_compare_means(comparisons = comparisons_complex, method = "wilcox.test", 
                     label = "p.signif", hide.ns = TRUE) +
  labs(x = "Complex", y = "Pielou's Evenness", title = "Pielou Evenness") +
  theme_publication +
  theme(legend.position = "none")

# Combine plots
(p1 | p2 | p3) / (p4 | p5 | p6) +
  plot_annotation(title = "Alpha Diversity by Diet Complexity",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Plot alpha diversity by Protease:

# Observed richness
p1 <- ggplot(alpha_div, aes(x = protease, y = observed, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$observed) * 1.1) +
  labs(x = "Protease", y = "Observed Species", title = "Observed Richness") +
  theme_publication +
  theme(legend.position = "none")

# Shannon
p2 <- ggplot(alpha_div, aes(x = protease, y = shannon, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$shannon) * 1.1) +
  labs(x = "Protease", y = "Shannon Index", title = "Shannon Diversity") +
  theme_publication +
  theme(legend.position = "none")

# Simpson
p3 <- ggplot(alpha_div, aes(x = protease, y = simpson, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$simpson) * 1.05) +
  labs(x = "Protease", y = "Simpson Index", title = "Simpson Diversity") +
  theme_publication +
  theme(legend.position = "none")

# Inverse Simpson
p4 <- ggplot(alpha_div, aes(x = protease, y = invsimpson, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$invsimpson) * 1.1) +
  labs(x = "Protease", y = "Inverse Simpson", title = "Inverse Simpson") +
  theme_publication +
  theme(legend.position = "none")

# Chao1
p5 <- ggplot(alpha_div, aes(x = protease, y = chao1, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$chao1) * 1.1) +
  labs(x = "Protease", y = "Chao1 Index", title = "Chao1 Richness") +
  theme_publication +
  theme(legend.position = "none")

# Pielou evenness
p6 <- ggplot(alpha_div, aes(x = protease, y = pielou, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  stat_compare_means(method = "wilcox.test", label.x = 1.3, label.y = max(alpha_div$pielou, na.rm = TRUE) * 1.05) +
  labs(x = "Protease", y = "Pielou's Evenness", title = "Pielou Evenness") +
  theme_publication +
  theme(legend.position = "none")

# Combine plots
(p1 | p2 | p3) / (p4 | p5 | p6) +
  plot_annotation(title = "Alpha Diversity by Protease Treatment",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Interaction plot (Complex x Protease):

# Shannon by both factors
p1 <- ggplot(alpha_div, aes(x = complex, y = shannon, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_point(position = position_jitterdodge(jitter.width = 0.2), size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  labs(x = "Complex", y = "Shannon Index", fill = "Protease", title = "Shannon Diversity") +
  theme_publication

# Observed by both factors
p2 <- ggplot(alpha_div, aes(x = complex, y = observed, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_point(position = position_jitterdodge(jitter.width = 0.2), size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  labs(x = "Complex", y = "Observed Species", fill = "Protease", title = "Observed Richness") +
  theme_publication

# Chao1 by both factors
p3 <- ggplot(alpha_div, aes(x = complex, y = simpson, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_point(position = position_jitterdodge(jitter.width = 0.2), size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  labs(x = "Complex", y = "Simpson Index", fill = "Protease", title = "Simpson Diversity") +
  theme_publication

# Inverse Simpson by both factors
p4 <- ggplot(alpha_div, aes(x = complex, y = invsimpson, fill = protease)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_point(position = position_jitterdodge(jitter.width = 0.2), size = 2, alpha = 0.6) +
  scale_fill_manual(values = protease_colors) +
  labs(x = "Complex", y = "Inverse Simpson", fill = "Protease", title = "Inverse Simpson") +
  theme_publication

(p1 | p2) / (p3 | p4) +
  plot_annotation(title = "Alpha Diversity: Complex × Protease Interaction",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Two-way ANOVA for interaction effects:

Bruno, aqui tem um coisa para vc decidir e ver em que situação faz mais sentido quando compara com o resultado das outras variaveis do paper (Imuno, desempenho, etc…). Quando a gente usa anova para comparar os tratamentos da significavo, principalmente no Shannon, Simpson index. Onde o grupo protease e complex diet teve maior diversidade que o grupo sem protease e dieta complexa. Mas quando usa o test no-parametrico e com ajuste para false discovery rate, não da significativo. Como estatistico, eu ia para falar que não é diferente. Mas tudo depende do contexto e talvez tem espaço para especular.

# Two-way ANOVA for Shannon
anova_shannon <- aov(shannon ~ complex * protease, data = alpha_div)
summary(anova_shannon)

                 Df Sum Sq Mean Sq F value Pr(>F)  
complex           2 0.8956  0.4478   3.400 0.0509 .
protease          1 0.1626  0.1626   1.235 0.2780  
complex:protease  2 1.3666  0.6833   5.188 0.0138 *
Residuals        23 3.0294  0.1317                 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

# Two-way ANOVA for Observed
anova_observed <- aov(observed ~ complex * protease, data = alpha_div)
summary(anova_observed)

                 Df  Sum Sq Mean Sq F value Pr(>F)
complex           2  162028   81014   1.290  0.294
protease          1   79765   79765   1.270  0.271
complex:protease  2   20733   10367   0.165  0.849
Residuals        23 1444460   62803               

# Two-way ANOVA for simpson
anova_simpson <- aov(simpson ~ complex * protease, data = alpha_div)
summary(anova_simpson)

                 Df  Sum Sq Mean Sq F value  Pr(>F)   
complex           2 0.02484 0.01242   2.673 0.09039 . 
protease          1 0.01943 0.01943   4.182 0.05246 . 
complex:protease  2 0.07212 0.03606   7.762 0.00265 **
Residuals        23 0.10685 0.00465                   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

# Two-way ANOVA for Inverse Simpson
anova_invsimpson <- aov(invsimpson ~ complex * protease, data = alpha_div)
summary(anova_invsimpson)

                 Df Sum Sq Mean Sq F value Pr(>F)  
complex           2    4.5    2.24   0.132 0.8772  
protease          1   27.0   27.02   1.593 0.2196  
complex:protease  2  127.9   63.96   3.771 0.0383 *
Residuals        23  390.2   16.96                 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

# Summary table of interaction effects
interaction_pvalues <- data.frame(
  Metric = c("Shannon", "Observed", "Chao1", "InvSimpson"),
  Complex_p = c(summary(anova_shannon)[[1]]["complex", "Pr(>F)"],
                summary(anova_observed)[[1]]["complex", "Pr(>F)"],
                summary(anova_simpson)[[1]]["complex", "Pr(>F)"],
                summary(anova_invsimpson)[[1]]["complex", "Pr(>F)"]),
  Protease_p = c(summary(anova_shannon)[[1]]["protease", "Pr(>F)"],
                 summary(anova_observed)[[1]]["protease", "Pr(>F)"],
                 summary(anova_simpson)[[1]]["protease", "Pr(>F)"],
                 summary(anova_invsimpson)[[1]]["protease", "Pr(>F)"]),
  Interaction_p = c(summary(anova_shannon)[[1]]["complex:protease", "Pr(>F)"],
                    summary(anova_observed)[[1]]["complex:protease", "Pr(>F)"],
                    summary(anova_simpson)[[1]]["complex:protease", "Pr(>F)"],
                    summary(anova_invsimpson)[[1]]["complex:protease", "Pr(>F)"])
)

kable(interaction_pvalues, digits = 4, caption = "Two-way ANOVA: Complex × Protease effects on Alpha Diversity")

Two-way ANOVA: Complex × Protease effects on Alpha Diversity

Metric	Complex_p	Protease_p	Interaction_p
Shannon	NA	0.2780	0.0138
Observed	NA	0.2714	0.8488
Chao1	NA	0.0525	0.0027
InvSimpson	NA	0.2196	0.0383

Pairwise comparisons for interaction groups:

# Pairwise Wilcoxon tests for Shannon
pairwise_shannon <- pairwise.wilcox.test(alpha_div$shannon, 
                                          alpha_div$interaction_group,
                                          p.adjust.method = "BH")

# Pairwise Wilcoxon tests for Observed
pairwise_observed <- pairwise.wilcox.test(alpha_div$observed, 
                                           alpha_div$interaction_group,
                                           p.adjust.method = "BH")

# Pairwise Wilcoxon tests for Simpson
pairwise_simpson <- pairwise.wilcox.test(alpha_div$simpson, 
                                        alpha_div$interaction_group,
                                        p.adjust.method = "BH")

# Pairwise Wilcoxon tests for Inverse Simpson
pairwise_invsimpson <- pairwise.wilcox.test(alpha_div$invsimpson, 
                                             alpha_div$interaction_group,
                                             p.adjust.method = "BH")

# Display results
kable(round(pairwise_shannon$p.value, 4), caption = "Pairwise Wilcoxon: Shannon (BH adjusted)")

Table: Pairwise Wilcoxon: Shannon (BH adjusted)

kable(round(pairwise_observed$p.value, 4), caption = "Pairwise Wilcoxon: Observed (BH adjusted)")

Table: Pairwise Wilcoxon: Observed (BH adjusted)

kable(round(pairwise_simpson$p.value, 4), caption = "Pairwise Wilcoxon: Pairwise_simpson (BH adjusted)")

Table: Pairwise Wilcoxon: Pairwise_simpson (BH adjusted)

kable(round(pairwise_invsimpson$p.value, 4), caption = "Pairwise Wilcoxon: Inverse Simpson (BH adjusted)")

Table: Pairwise Wilcoxon: Inverse Simpson (BH adjusted)

Plot with interaction groups and pairwise p-values:

alpha_div$interaction_group <- interaction(alpha_div$complex, alpha_div$protease, sep = "_")

# Colors for interaction groups
interaction_colors <- c(
  "low_cont" = "#0072B2",
  "low_prot" = "#56B4E9",
  "medium_cont" = "#D55E00",
  "medium_prot" = "#E69F00",
  "high_cont" = "#009E73",
  "high_prot" = "#66CC99"
)

# Shannon
p1 <- ggplot(alpha_div, aes(x = interaction_group, y = shannon, fill = interaction_group)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = interaction_colors) +
  stat_compare_means(method = "kruskal.test", label.y = max(alpha_div$shannon) * 1.15) +
  labs(x = "Treatment Group", y = "Shannon Index", title = "Shannon Diversity") +
  theme_publication +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, hjust = 1))

# Observed
p2 <- ggplot(alpha_div, aes(x = interaction_group, y = observed, fill = interaction_group)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = interaction_colors) +
  stat_compare_means(method = "kruskal.test", label.y = max(alpha_div$observed) * 1.15) +
  labs(x = "Treatment Group", y = "Observed Species", title = "Observed Richness") +
  theme_publication +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, hjust = 1))

# Chao1
p3 <- ggplot(alpha_div, aes(x = interaction_group, y = chao1, fill = interaction_group)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = interaction_colors) +
  stat_compare_means(method = "kruskal.test", label.y = max(alpha_div$chao1) * 1.15) +
  labs(x = "Treatment Group", y = "Chao1 Index", title = "Chao1 Richness") +
  theme_publication +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, hjust = 1))

# Inverse Simpson
p4 <- ggplot(alpha_div, aes(x = interaction_group, y = invsimpson, fill = interaction_group)) +
  geom_boxplot(outlier.shape = NA, alpha = 0.7) +
  geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
  scale_fill_manual(values = interaction_colors) +
  stat_compare_means(method = "kruskal.test", label.y = max(alpha_div$invsimpson) * 1.15) +
  labs(x = "Treatment Group", y = "Inverse Simpson", title = "Inverse Simpson") +
  theme_publication +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, hjust = 1))

(p1 | p2) / (p3 | p4) +
  plot_annotation(title = "Alpha Diversity by Interaction Groups (Complex × Protease)",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Beta Diversity Analysis

Calculate distance matrices:

# Transpose matrix (vegan needs samples as rows)
species_counts_t <- t(species_counts)

# Bray-Curtis distance (abundance-based)
dist_bray <- vegdist(species_counts_t, method = "bray")

# Jaccard distance (presence/absence)
dist_jaccard <- vegdist(species_counts_t, method = "jaccard", binary = TRUE)

# Aitchison distance (compositional - recommended for microbiome)
# Add pseudocount to handle zeros, then CLR transform
species_pseudo <- species_counts_t + 1
species_clr <- log(species_pseudo) - rowMeans(log(species_pseudo))
dist_aitchison <- vegdist(species_clr, method = "euclidean")

PERMANOVA - Main effects Complex:

# Bray-Curtis PERMANOVA
set.seed(123)
permanova_bray_complex <- adonis2(dist_bray ~ complex, 
                          data = meta_tab, 
                          permutations = 999)

# Jaccard PERMANOVA
set.seed(123)
permanova_jaccard_complex <- adonis2(dist_jaccard ~ complex, 
                             data = meta_tab, 
                             permutations = 999)

# Aitchison PERMANOVA
set.seed(123)
permanova_aitchison_complex <- adonis2(dist_aitchison ~ complex, 
                               data = meta_tab, 
                               permutations = 999)

# Display results
kable(permanova_bray_complex, digits = 4, caption = "PERMANOVA: Bray-Curtis Distance")

PERMANOVA: Bray-Curtis Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	2	0.1687	0.052	0.7134	0.752
Residual	26	3.0740	0.948	NA	NA
Total	28	3.2427	1.000	NA	NA

kable(permanova_jaccard_complex, digits = 4, caption = "PERMANOVA: Jaccard Distance")

PERMANOVA: Jaccard Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	2	0.2946	0.0844	1.1979	0.186
Residual	26	3.1968	0.9156	NA	NA
Total	28	3.4913	1.0000	NA	NA

kable(permanova_aitchison_complex, digits = 4, caption = "PERMANOVA: Aitchison Distance")

PERMANOVA: Aitchison Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	2	6124.551	0.074	1.0396	0.325
Residual	26	76583.809	0.926	NA	NA
Total	28	82708.360	1.000	NA	NA

PERMANOVA - Main effects Protease:

# Bray-Curtis PERMANOVA
set.seed(123)
permanova_bray_protease <- adonis2(dist_bray ~  protease, 
                          data = meta_tab, 
                          permutations = 999)

# Jaccard PERMANOVA
set.seed(123)
permanova_jaccard_protease <- adonis2(dist_jaccard ~ protease, 
                             data = meta_tab, 
                             permutations = 999)

# Aitchison PERMANOVA
set.seed(123)
permanova_aitchison_protease <- adonis2(dist_aitchison ~ protease, 
                               data = meta_tab, 
                               permutations = 999)

# Display results
kable(permanova_bray_protease, digits = 4, caption = "PERMANOVA: Bray-Curtis Distance")

PERMANOVA: Bray-Curtis Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	1	0.1223	0.0377	1.0585	0.338
Residual	27	3.1204	0.9623	NA	NA
Total	28	3.2427	1.0000	NA	NA

kable(permanova_jaccard_protease, digits = 4, caption = "PERMANOVA: Jaccard Distance")

PERMANOVA: Jaccard Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	1	0.1070	0.0307	0.8537	0.618
Residual	27	3.3843	0.9693	NA	NA
Total	28	3.4913	1.0000	NA	NA

kable(permanova_aitchison_protease, digits = 4, caption = "PERMANOVA: Aitchison Distance")

PERMANOVA: Aitchison Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	1	2550.817	0.0308	0.8592	0.678
Residual	27	80157.543	0.9692	NA	NA
Total	28	82708.360	1.0000	NA	NA

PERMANOVA - Interaction:

# Bray-Curtis PERMANOVA
set.seed(123)
permanova_bray_interaction <- adonis2(dist_bray ~ complex * protease, 
                          data = meta_tab, 
                          permutations = 999)

# Jaccard PERMANOVA
set.seed(123)
permanova_jaccard_interaction <- adonis2(dist_jaccard ~ complex * protease, 
                             data = meta_tab, 
                             permutations = 999)

# Aitchison PERMANOVA
set.seed(123)
permanova_aitchison_interaction <- adonis2(dist_aitchison ~ complex * protease, 
                               data = meta_tab, 
                               permutations = 999)

# Display results
kable(permanova_bray_interaction, digits = 4, caption = "PERMANOVA: Bray-Curtis Distance")

PERMANOVA: Bray-Curtis Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	5	0.6279	0.1936	1.1047	0.315
Residual	23	2.6148	0.8064	NA	NA
Total	28	3.2427	1.0000	NA	NA

kable(permanova_jaccard_interaction, digits = 4, caption = "PERMANOVA: Jaccard Distance")

PERMANOVA: Jaccard Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	5	0.7293	0.2089	1.2146	0.094
Residual	23	2.7621	0.7911	NA	NA
Total	28	3.4913	1.0000	NA	NA

kable(permanova_aitchison_interaction, digits = 4, caption = "PERMANOVA: Aitchison Distance")

PERMANOVA: Aitchison Distance

	Df	SumOfSqs	R2	F	Pr(>F)
Model	5	16513.65	0.1997	1.1476	0.11
Residual	23	66194.71	0.8003	NA	NA
Total	28	82708.36	1.0000	NA	NA

Pairwise PERMANOVA for Complex:

# Pairwise PERMANOVA for complex (Bray-Curtis)
set.seed(123)
pairwise_complex_bray <- pairwise.adonis(dist_bray, 
                                          factors = meta_tab$complex,
                                          p.adjust.m = "BH",
                                          perm = 999)

# Pairwise PERMANOVA for complex (Jaccard)
set.seed(123)
pairwise_complex_jaccard <- pairwise.adonis(dist_jaccard, 
                                             factors = meta_tab$complex,
                                             p.adjust.m = "BH",
                                             perm = 999)

# Pairwise PERMANOVA for complex (Aitchison)
set.seed(123)
pairwise_complex_aitchison <- pairwise.adonis(dist_aitchison, 
                                               factors = meta_tab$complex,
                                               p.adjust.m = "BH",
                                               perm = 999)

kable(pairwise_complex_bray, digits = 4, caption = "Pairwise PERMANOVA (Bray-Curtis): Complex")

Pairwise PERMANOVA (Bray-Curtis): Complex

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low vs high	1	0.0778	0.6172	0.0350	0.717	0.717
low vs medium	1	0.0852	0.7355	0.0415	0.625	0.717
high vs medium	1	0.0897	0.7937	0.0422	0.581	0.717

kable(pairwise_complex_jaccard, digits = 4, caption = "Pairwise PERMANOVA (Jaccard): Complex")

Pairwise PERMANOVA (Jaccard): Complex

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low vs high	1	0.1781	1.4958	0.0809	0.085	0.255
low vs medium	1	0.1603	1.1805	0.0649	0.238	0.357
high vs medium	1	0.1056	0.9226	0.0488	0.491	0.491

kable(pairwise_complex_aitchison, digits = 4, caption = "Pairwise PERMANOVA (Aitchison): Complex")

Pairwise PERMANOVA (Aitchison): Complex

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low vs high	1	3140.138	1.0691	0.0592	0.296	0.444
low vs medium	1	3638.287	1.1352	0.0626	0.223	0.444
high vs medium	1	2441.095	0.9013	0.0477	0.574	0.574

Pairwise PERMANOVA for Interaction groups:

Aqui mais uma vez, nao deu significativo quando ajusta para fdr mas é significativo só com o p value.

# Create interaction group
meta_tab$interaction_group <- interaction(meta_tab$complex, meta_tab$protease, sep = "_")

# Pairwise PERMANOVA for interaction (Bray-Curtis)
set.seed(123)
pairwise_interaction_bray <- pairwise.adonis(dist_bray, 
                                              factors = meta_tab$interaction_group,
                                              p.adjust.m = "BH",
                                              perm = 999)

# Pairwise PERMANOVA for interaction (Aitchison)
set.seed(123)
pairwise_interaction_aitchison <- pairwise.adonis(dist_aitchison, 
                                                   factors = meta_tab$interaction_group,
                                                   p.adjust.m = "BH",
                                                   perm = 999)

# Pairwise PERMANOVA for interaction (jaccard)
set.seed(123)
pairwise_interaction_jaccard <- pairwise.adonis(dist_jaccard, 
                                                   factors = meta_tab$interaction_group,
                                                   p.adjust.m = "BH",
                                                   perm = 999)

kable(pairwise_interaction_bray, digits = 4, caption = "Pairwise PERMANOVA (Bray-Curtis): Interaction Groups")

Pairwise PERMANOVA (Bray-Curtis): Interaction Groups

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low_prot vs high_cont	1	0.2204	1.5607	0.1632	0.164	0.5250
low_prot vs low_cont	1	0.0885	0.6517	0.0852	0.637	0.7962
low_prot vs medium_cont	1	0.0590	0.3904	0.0465	0.970	0.9700
low_prot vs high_prot	1	0.0805	0.5387	0.0631	0.837	0.8968
low_prot vs medium_prot	1	0.1313	0.9259	0.1037	0.475	0.7800
high_cont vs low_cont	1	0.0669	0.8083	0.1035	0.540	0.7800
high_cont vs medium_cont	1	0.2043	1.9548	0.1964	0.106	0.5250
high_cont vs high_prot	1	0.2808	2.7288	0.2543	0.063	0.5250
high_cont vs medium_prot	1	0.0830	0.8712	0.0982	0.566	0.7800
low_cont vs medium_cont	1	0.0912	0.9708	0.1218	0.379	0.7800
low_cont vs high_prot	1	0.1423	1.5451	0.1808	0.175	0.5250
low_cont vs medium_prot	1	0.0657	0.7883	0.1012	0.572	0.7800
medium_cont vs high_prot	1	0.0875	0.7761	0.0884	0.707	0.8158
medium_cont vs medium_prot	1	0.0899	0.8558	0.0966	0.539	0.7800
high_prot vs medium_prot	1	0.1753	1.6948	0.1748	0.112	0.5250

kable(pairwise_interaction_aitchison, digits = 4, caption = "Pairwise PERMANOVA (Aitchison): Interaction Groups")

Pairwise PERMANOVA (Aitchison): Interaction Groups

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low_prot vs high_cont	1	3967.394	1.2938	0.1392	0.149	0.2794
low_prot vs low_cont	1	3131.294	0.8873	0.1125	0.629	0.7862
low_prot vs medium_cont	1	2896.079	0.8147	0.0924	0.735	0.8481
low_prot vs high_prot	1	2285.441	0.7395	0.0846	0.888	0.8880
low_prot vs medium_prot	1	3825.103	1.2344	0.1337	0.171	0.2850
high_cont vs low_cont	1	3411.929	1.2746	0.1540	0.131	0.2794
high_cont vs medium_cont	1	4005.985	1.4260	0.1513	0.090	0.2794
high_cont vs high_prot	1	3338.691	1.4239	0.1511	0.118	0.2794
high_cont vs medium_prot	1	2104.903	0.8945	0.1006	0.595	0.7862
low_cont vs medium_cont	1	3824.584	1.1822	0.1445	0.116	0.2794
low_cont vs high_prot	1	3087.564	1.1417	0.1402	0.191	0.2865
low_cont vs medium_prot	1	3786.593	1.3953	0.1662	0.070	0.2794
medium_cont vs high_prot	1	2465.594	0.8702	0.0981	0.802	0.8593
medium_cont vs medium_prot	1	3919.112	1.3792	0.1470	0.056	0.2794
high_prot vs medium_prot	1	3563.510	1.4991	0.1578	0.064	0.2794

kable(pairwise_interaction_jaccard, digits = 4, caption = "Pairwise PERMANOVA (Jaccard): Interaction Groups")

Pairwise PERMANOVA (Jaccard): Interaction Groups

pairs	Df	SumsOfSqs	F.Model	R2	p.value	p.adjusted	sig
low_prot vs high_cont	1	0.1714	1.3512	0.1445	0.182	0.3412
low_prot vs low_cont	1	0.1342	0.9374	0.1181	0.473	0.6450
low_prot vs medium_cont	1	0.1264	0.7531	0.0860	0.726	0.7260
low_prot vs high_prot	1	0.1210	0.9035	0.1015	0.579	0.7237
low_prot vs medium_prot	1	0.1678	1.3521	0.1446	0.147	0.3412
high_cont vs low_cont	1	0.1490	1.5206	0.1785	0.096	0.3412
high_cont vs medium_cont	1	0.1532	1.1941	0.1299	0.222	0.3700
high_cont vs high_prot	1	0.1321	1.3982	0.1488	0.159	0.3412
high_cont vs medium_prot	1	0.0716	0.8458	0.0956	0.686	0.7260
low_cont vs medium_cont	1	0.1741	1.2022	0.1466	0.258	0.3870
low_cont vs high_prot	1	0.1832	1.7262	0.1978	0.024	0.2700
low_cont vs medium_prot	1	0.1551	1.6352	0.1894	0.054	0.2700
medium_cont vs high_prot	1	0.1182	0.8725	0.0983	0.646	0.7260
medium_cont vs medium_prot	1	0.1685	1.3418	0.1436	0.179	0.3412
high_prot vs medium_prot	1	0.1689	1.8414	0.1871	0.038	0.2700

Betadisper - Test for homogeneity of dispersions:

# Betadisper for Complex (Bray-Curtis)
betadisp_complex_bray <- betadisper(dist_bray, meta_tab$complex)
permutest_complex_bray <- permutest(betadisp_complex_bray, pairwise = TRUE, permutations = 999)

# Betadisper for Protease (Bray-Curtis)
betadisp_protease_bray <- betadisper(dist_bray, meta_tab$protease)
permutest_protease_bray <- permutest(betadisp_protease_bray, pairwise = TRUE, permutations = 999)

# Betadisper for Interaction (Bray-Curtis)
betadisp_interaction_bray <- betadisper(dist_bray, meta_tab$interaction_group)
permutest_interaction_bray <- permutest(betadisp_interaction_bray, pairwise = TRUE, permutations = 999)

# Display results
print("Betadisper - Complex (Bray-Curtis):")

[1] "Betadisper - Complex (Bray-Curtis):"

permutest_complex_bray

Permutation test for homogeneity of multivariate dispersions
Permutation: free
Number of permutations: 999

Response: Distances
          Df  Sum Sq   Mean Sq     F N.Perm Pr(>F)
Groups     2 0.00250 0.0012500 0.129    999  0.885
Residuals 26 0.25201 0.0096926                    

Pairwise comparisons:
(Observed p-value below diagonal, permuted p-value above diagonal)
           low  medium  high
low            0.66700 0.991
medium 0.65814         0.595
high   0.98528 0.61037      

print("Betadisper - Protease (Bray-Curtis):")

[1] "Betadisper - Protease (Bray-Curtis):"

permutest_protease_bray

Permutation test for homogeneity of multivariate dispersions
Permutation: free
Number of permutations: 999

Response: Distances
          Df   Sum Sq   Mean Sq      F N.Perm Pr(>F)
Groups     1 0.017266 0.0172655 2.1828    999  0.149
Residuals 27 0.213563 0.0079097                     

Pairwise comparisons:
(Observed p-value below diagonal, permuted p-value above diagonal)
        cont  prot
cont         0.145
prot 0.15113      

print("Betadisper - Interaction (Bray-Curtis):")

[1] "Betadisper - Interaction (Bray-Curtis):"

permutest_interaction_bray

Permutation test for homogeneity of multivariate dispersions
Permutation: free
Number of permutations: 999

Response: Distances
          Df   Sum Sq  Mean Sq      F N.Perm Pr(>F)
Groups     5 0.071232 0.014246 1.3838    999  0.261
Residuals 23 0.236783 0.010295                     

Pairwise comparisons:
(Observed p-value below diagonal, permuted p-value above diagonal)
            low_cont medium_cont high_cont low_prot medium_prot high_prot
low_cont                0.109000  0.756000 0.023000    0.386000     0.244
medium_cont 0.102469              0.523000 0.193000    0.588000     0.907
high_cont   0.744547    0.526898           0.139000    0.799000     0.629
low_prot    0.028352    0.181411  0.149135             0.109000     0.198
medium_prot 0.392253    0.579271  0.811412 0.111140                 0.730
high_prot   0.246693    0.888172  0.622215 0.199405    0.726144          

PCoA ordination:

# PCoA on Bray-Curtis
pcoa_bray <- cmdscale(dist_bray, k = 3, eig = TRUE)

# Calculate variance explained
var_explained_bray <- round(pcoa_bray$eig / sum(pcoa_bray$eig) * 100, 2)

# Create data frame for plotting
pcoa_bray_df <- data.frame(
  sample = rownames(pcoa_bray$points),
  PC1 = pcoa_bray$points[, 1],
  PC2 = pcoa_bray$points[, 2],
  PC3 = pcoa_bray$points[, 3]
)
pcoa_bray_df <- merge(pcoa_bray_df, meta_tab, by.x = "sample", by.y = "row.names")

# PCoA on Aitchison
pcoa_aitchison <- cmdscale(dist_aitchison, k = 3, eig = TRUE)
var_explained_aitchison <- round(pcoa_aitchison$eig / sum(pcoa_aitchison$eig) * 100, 2)

pcoa_aitchison_df <- data.frame(
  sample = rownames(pcoa_aitchison$points),
  PC1 = pcoa_aitchison$points[, 1],
  PC2 = pcoa_aitchison$points[, 2],
  PC3 = pcoa_aitchison$points[, 3]
)
pcoa_aitchison_df <- merge(pcoa_aitchison_df, meta_tab, by.x = "sample", by.y = "row.names")

PCoA plot by Complex:

# Extract PERMANOVA stats for annotation
r2_complex_bray <- round(permanova_bray_complex["Model", "R2"], 3)
p_complex_bray <- permanova_bray_complex["Model", "Pr(>F)"]
p_label_bray <- ifelse(p_complex_bray < 0.001, "p < 0.001", paste0("p = ", round(p_complex_bray, 3)))

r2_complex_aitchison <- round(permanova_aitchison_complex["Model", "R2"], 3)
p_complex_aitchison <- permanova_aitchison_complex["Model", "Pr(>F)"]
p_label_aitchison <- ifelse(p_complex_aitchison < 0.001, "p < 0.001", paste0("p = ", round(p_complex_aitchison, 3)))

# Bray-Curtis PCoA
p1 <- ggplot(pcoa_bray_df, aes(x = PC1, y = PC2, color = complex, shape = complex)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = complex_colors) +
  labs(
    x = paste0("PCoA1 (", var_explained_bray[1], "%)"),
    y = paste0("PCoA2 (", var_explained_bray[2], "%)"),
    color = "Complex",
    shape = "Complex",
    title = "Bray-Curtis Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("R² = ", r2_complex_bray, "\n", p_label_bray),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

# Aitchison PCoA
p2 <- ggplot(pcoa_aitchison_df, aes(x = PC1, y = PC2, color = complex, shape = complex)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = complex_colors) +
  labs(
    x = paste0("PCoA1 (", var_explained_aitchison[1], "%)"),
    y = paste0("PCoA2 (", var_explained_aitchison[2], "%)"),
    color = "Complex",
    shape = "Complex",
    title = "Aitchison Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("R² = ", r2_complex_aitchison, "\n", p_label_aitchison),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

p1 + p2 +
  plot_annotation(title = "PCoA: Beta Diversity by Diet Complexity",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

PCoA plot by Protease:

# Extract PERMANOVA stats
r2_protease_bray <- round(permanova_bray_protease["Model", "R2"], 3)
p_protease_bray <- permanova_bray_protease["Model", "Pr(>F)"]
p_label_bray <- ifelse(p_protease_bray < 0.001, "p < 0.001", paste0("p = ", round(p_protease_bray, 3)))

r2_protease_aitchison <- round(permanova_aitchison_protease["Model", "R2"], 3)
p_protease_aitchison <- permanova_aitchison_protease["Model", "Pr(>F)"]
p_label_aitchison <- ifelse(p_protease_aitchison < 0.001, "p < 0.001", paste0("p = ", round(p_protease_aitchison, 3)))

# Bray-Curtis PCoA
p1 <- ggplot(pcoa_bray_df, aes(x = PC1, y = PC2, color = protease, shape = protease)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = protease_colors) +
  labs(
    x = paste0("PC1 (", var_explained_bray[1], "%)"),
    y = paste0("PC2 (", var_explained_bray[2], "%)"),
    color = "Protease",
    shape = "Protease",
    title = "Bray-Curtis Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("R² = ", r2_protease_bray, "\n", p_label_bray),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

# Aitchison PCoA
p2 <- ggplot(pcoa_aitchison_df, aes(x = PC1, y = PC2, color = protease, shape = protease)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = protease_colors) +
  labs(
    x = paste0("PC1 (", var_explained_aitchison[1], "%)"),
    y = paste0("PC2 (", var_explained_aitchison[2], "%)"),
    color = "Protease",
    shape = "Protease",
    title = "Aitchison Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("R² = ", r2_protease_aitchison, "\n", p_label_aitchison),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

p1 + p2 +
  plot_annotation(title = "PCoA: Beta Diversity by Protease Treatment",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

PCoA plot by Interaction (Complex x Protease):

# Extract interaction PERMANOVA stats
r2_interaction_bray <- round(permanova_bray_interaction["Model", "R2"], 3)
p_interaction_bray <- permanova_bray_interaction["Model", "Pr(>F)"]
p_label_bray <- ifelse(p_interaction_bray < 0.001, "p < 0.001", paste0("p = ", round(p_interaction_bray, 3)))

r2_interaction_aitchison <- round(permanova_aitchison_interaction["Model", "R2"], 3)
p_interaction_aitchison <- permanova_aitchison_interaction["Model", "Pr(>F)"]
p_label_aitchison <- ifelse(p_interaction_aitchison < 0.001, "p < 0.001", paste0("p = ", round(p_interaction_aitchison, 3)))

# Colors for interaction groups
interaction_colors <- c(
  "low_cont" = "#0072B2",
  "low_prot" = "#56B4E9",
  "medium_cont" = "#D55E00",
  "medium_prot" = "#E69F00",
  "high_cont" = "#009E73",
  "high_prot" = "#66CC99"
)

# Create interaction variable in pcoa dataframes
pcoa_bray_df$interaction_group <- interaction(pcoa_bray_df$complex, pcoa_bray_df$protease, sep = "_")
pcoa_aitchison_df$interaction_group <- interaction(pcoa_aitchison_df$complex, pcoa_aitchison_df$protease, sep = "_")

# Bray-Curtis PCoA
p1 <- ggplot(pcoa_bray_df, aes(x = PC1, y = PC2, color = interaction_group, shape = complex)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(aes(group = interaction_group), level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = interaction_colors) +
  labs(
    x = paste0("PC1 (", var_explained_bray[1], "%)"),
    y = paste0("PC2 (", var_explained_bray[2], "%)"),
    color = "Interaction",
    shape = "Complex",
    title = "Bray-Curtis Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("Interaction R² = ", r2_interaction_bray, "\n", p_label_bray),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

# Aitchison PCoA
p2 <- ggplot(pcoa_aitchison_df, aes(x = PC1, y = PC2, color = interaction_group, shape = complex)) +
  geom_point(size = 4, alpha = 0.8) +
  stat_ellipse(aes(group = interaction_group), level = 0.95, linetype = "dashed", linewidth = 1) +
  scale_color_manual(values = interaction_colors) +
  labs(
    x = paste0("PC1 (", var_explained_aitchison[1], "%)"),
    y = paste0("PC2 (", var_explained_aitchison[2], "%)"),
    color = "Interaction",
    shape = "Complex",
    title = "Aitchison Distance"
  ) +
  annotate("text", x = Inf, y = Inf, 
           label = paste0("Interaction R² = ", r2_interaction_aitchison, "\n", p_label_aitchison),
           hjust = 1.1, vjust = 1.5, size = 4, fontface = "bold") +
  theme_publication

p1 + p2 +
  plot_annotation(title = "PCoA: Beta Diversity by Interaction Groups (Complex × Protease)",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Combined PCoA plot (all factors in one figure):

# Combined plot with color = complex, shape = protease
p_combined <- ggplot(pcoa_bray_df, aes(x = PC1, y = PC2, color = complex, shape = protease)) +
  geom_point(size = 5, alpha = 0.8) +
  stat_ellipse(aes(group = complex, linetype = complex), level = 0.95, linewidth = 1) +
  scale_color_manual(values = complex_colors) +
  scale_shape_manual(values = c("cont" = 16, "prot" = 17)) +
  labs(
    x = paste0("PC1 (", var_explained_bray[1], "%)"),
    y = paste0("PC2 (", var_explained_bray[2], "%)"),
    color = "Complex",
    shape = "Protease",
    linetype = "Complex",
    title = "PCoA: Bray-Curtis Distance",
    subtitle = paste0("Complex: R² = ", r2_complex_bray, ", ", 
                      ifelse(p_complex_bray < 0.001, "p < 0.001", paste0("p = ", round(p_complex_bray, 3))),
                      " | Protease: R² = ", r2_protease_bray, ", ",
                      ifelse(p_protease_bray < 0.001, "p < 0.001", paste0("p = ", round(p_protease_bray, 3))))
  ) +
  theme_publication +
  theme(
    plot.subtitle = element_text(hjust = 0.5, size = 10),
    legend.position = "right"
  )

p_combined

Summary table of PERMANOVA results:

# Create summary table
permanova_summary <- data.frame(
  Distance = rep(c("Bray-Curtis", "Jaccard", "Aitchison"), each = 3),
  Factor = rep(c("Complex", "Protease", "Complex:Protease"), 3),
  R2 = c(
    permanova_bray_complex["Model", "R2"],
    permanova_bray_protease["Model", "R2"],
    permanova_bray_interaction["Model", "R2"],
    permanova_jaccard_complex["Model", "R2"],
    permanova_jaccard_protease["Model", "R2"],
    permanova_jaccard_interaction["Model", "R2"],
    permanova_aitchison_complex["Model", "R2"],
    permanova_aitchison_protease["Model", "R2"],
    permanova_aitchison_interaction["Model", "R2"]
  ),
  p_value = c(
    permanova_bray_complex["Model", "Pr(>F)"],
    permanova_bray_protease["Model", "Pr(>F)"],
    permanova_bray_interaction["Model", "Pr(>F)"],
    permanova_jaccard_complex["Model", "Pr(>F)"],
    permanova_jaccard_protease["Model", "Pr(>F)"],
    permanova_jaccard_interaction["Model", "Pr(>F)"],
    permanova_aitchison_complex["Model", "Pr(>F)"],
    permanova_aitchison_protease["Model", "Pr(>F)"],
    permanova_aitchison_interaction["Model", "Pr(>F)"]
  )
)

permanova_summary$significance <- ifelse(permanova_summary$p_value < 0.001, "***",
                                  ifelse(permanova_summary$p_value < 0.01, "**",
                                  ifelse(permanova_summary$p_value < 0.05, "*", "ns")))

kable(permanova_summary, digits = 4, caption = "PERMANOVA Summary: All Distance Metrics")

PERMANOVA Summary: All Distance Metrics

Distance	Factor	R2	p_value	significance
Bray-Curtis	Complex	0.0520	0.752	ns
Bray-Curtis	Protease	0.0377	0.338	ns
Bray-Curtis	Complex:Protease	0.1936	0.315	ns
Jaccard	Complex	0.0844	0.186	ns
Jaccard	Protease	0.0307	0.618	ns
Jaccard	Complex:Protease	0.2089	0.094	ns
Aitchison	Complex	0.0740	0.325	ns
Aitchison	Protease	0.0308	0.678	ns
Aitchison	Complex:Protease	0.1997	0.110	ns

Differential Abundance Analysis

Prepare data for differential abundance:

# ALDEx2 and ANCOM-BC need taxa as rows and samples as columns
# species_counts is already in this format

# Filter low-prevalence taxa (present in at least 10% of samples)
prevalence <- rowSums(species_counts > 0) / ncol(species_counts)
species_counts_filtered <- species_counts[prevalence >= 0.10, ]


# Check dimensions
dim(species_counts_filtered)

[1] 1245   29

# Verify sample order matches metadata
all(colnames(species_counts_filtered) == rownames(meta_tab))

[1] TRUE

ALDEx2 Analysis

ALDEx2 for Complex factor:

# ALDEx2 requires character or factor for conditions
# For 3-level factor, use aldex.kw (Kruskal-Wallis)
meta_tab$complex <- as.character(meta_tab$complex)
set.seed(123)
aldex_complex <- aldex.clr(species_counts_filtered, 
                            meta_tab$complex, 
                            mc.samples = 128, 
                            denom = "all",
                            verbose = FALSE)

# Kruskal-Wallis test for 3 groups
aldex_complex_kw <- aldex.kw(aldex_complex)

# Add taxon names
aldex_complex_kw$taxon <- rownames(aldex_complex_kw)

# Filter significant results (using glm.eBH for FDR-corrected p-values)
aldex_complex_sig <- aldex_complex_kw[aldex_complex_kw$kw.eBH < 0.05, ]

# Sort by p-value
aldex_complex_sig <- aldex_complex_sig[order(aldex_complex_sig$kw.eBH), ]

# Display results
nrow(aldex_complex_sig)

[1] 0

kable(head(aldex_complex_sig, 20), digits = 4, 
      caption = "ALDEx2: Significant taxa by Complex (KW test, BH adjusted p < 0.05)")

ALDEx2: Significant taxa by Complex (KW test, BH adjusted p < 0.05)

kw.ep	kw.eBH	glm.ep	glm.eBH	taxon

ALDEx2 for Protease factor:

# For 2-level factor, use aldex.ttest (Welch's t-test and Wilcoxon)
meta_tab$protease <- as.character(meta_tab$protease)
set.seed(123)
aldex_protease <- aldex.clr(species_counts_filtered, 
                             meta_tab$protease, 
                             mc.samples = 128, 
                             denom = "all",
                             verbose = FALSE)

# t-test and Wilcoxon test
aldex_protease_tt <- aldex.ttest(aldex_protease)

# Effect size
aldex_protease_effect <- aldex.effect(aldex_protease)

# Combine results
aldex_protease_all <- data.frame(aldex_protease_tt, aldex_protease_effect)
aldex_protease_all$taxon <- rownames(aldex_protease_all)

# Filter significant results (Wilcoxon BH-adjusted)
aldex_protease_sig <- aldex_protease_all[aldex_protease_all$wi.eBH < 0.05, ]

# Sort by effect size
aldex_protease_sig <- aldex_protease_sig[order(abs(aldex_protease_sig$effect), decreasing = TRUE), ]

nrow(aldex_protease_sig)

[1] 0

kable(head(aldex_protease_sig[, c("taxon", "wi.eBH", "effect", "overlap")], 20), digits = 4,
      caption = "ALDEx2: Significant taxa by Protease (Wilcoxon, BH adjusted p < 0.05)")

ALDEx2: Significant taxa by Protease (Wilcoxon, BH adjusted p < 0.05)

taxon	wi.eBH	effect	overlap

ALDEx2 Effect Size Plot - Protease:

# Prepare data for plotting
aldex_protease_all$significant <- ifelse(aldex_protease_all$wi.eBH < 0.05, "Significant", "Not Significant")
aldex_protease_all$direction <- ifelse(aldex_protease_all$effect > 0, "Higher in prot", "Higher in cont")

# MA plot (Bland-Altman)
p1 <- ggplot(aldex_protease_all, aes(x = rab.all, y = diff.btw, color = significant)) +
  geom_point(alpha = 0.5, size = 2) +
  scale_color_manual(values = c("Significant" = "#D55E00", "Not Significant" = "grey70")) +
  geom_hline(yintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Mean CLR abundance",
    y = "Difference between groups",
    color = "",
    title = "MA Plot: Protease Effect"
  ) +
  theme_publication

# Effect size plot
p2 <- ggplot(aldex_protease_all, aes(x = diff.btw, y = -log10(wi.eBH), color = significant)) +
  geom_point(alpha = 0.5, size = 2) +
  scale_color_manual(values = c("Significant" = "#D55E00", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Difference between groups (CLR)",
    y = "-log10(BH adjusted p-value)",
    color = "",
    title = "Volcano Plot: Protease Effect"
  ) +
  theme_publication

p1 + p2 +
  plot_annotation(title = "ALDEx2: Protease Differential Abundance",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

ALDEx2 for Interaction (using glm):

Os resultados abaixo mostra a mesma coisa, não foi segnificativo para quando ajusta para FDR mas tem varios taxons que foi significativo. Isso é um conceito importante pq mudar o seu resultado completamente. Da uma lida nesse documento https://totallab.com/resources/p-values-fdr-q-values/

# Create model matrix for interaction
meta_tab$complex <- factor(meta_tab$complex, levels = c("low", "medium", "high"))
meta_tab$protease <- factor(meta_tab$protease, levels = c("cont", "prot"))

mm <- model.matrix(~ complex * protease, data = meta_tab)

set.seed(123)
aldex_interaction <- aldex.clr(species_counts_filtered, 
                                mm, 
                                mc.samples = 128, 
                                denom = "all",
                                verbose = FALSE)

# GLM test
aldex_interaction_glm <- aldex.glm(aldex_interaction, mm)

|------------(25%)----------(50%)----------(75%)----------|

# Extract interaction term results
interaction_cols <- grep("complex.*protease", colnames(aldex_interaction_glm), value = TRUE)

# Get p-values for interaction terms
aldex_interaction_results <- aldex_interaction_glm[, c(interaction_cols)]
aldex_interaction_results$taxon <- rownames(aldex_interaction_results)

# Find significant interactions (any interaction term)
pval_cols <- grep("pval.eBH", interaction_cols, value = TRUE)

if (length(pval_cols) > 0) {
  aldex_interaction_results$min_pval <- apply(aldex_interaction_results[, pval_cols, drop = FALSE], 1, min, na.rm = TRUE)
  aldex_interaction_sig <- aldex_interaction_results[aldex_interaction_results$min_pval < 0.05, ]
  aldex_interaction_sig <- aldex_interaction_sig[order(aldex_interaction_sig$min_pval), ]
  
  nrow(aldex_interaction_sig)
  kable(head(aldex_interaction_sig, 20), digits = 4,
        caption = "ALDEx2: Significant taxa with Complex × Protease interaction (BH adjusted p < 0.05)")
}

ANCOM-BC Analysis

Aqui eu usei outro metodo para achar diferença entre as especies. Tambem não achou nada significativo ajustando para FDR. Entretanto, o ultimo heat map eu coloquei para fazer coloca ros que deu siginificativo na interação. Tem bastante coisa legal, vc precisa namorar um pouco para ver qual é do seu interesse.

Create phyloseq object for ANCOM-BC:

Remove zero-variance taxa before ANCOM-BC:

# Create interaction group
meta_tab$interaction_group <- interaction(meta_tab$complex, meta_tab$protease, sep = "_")

# Check how many samples per interaction group
table(meta_tab$interaction_group)

   low_cont medium_cont   high_cont    low_prot medium_prot   high_prot 
          4           5           5           5           5           5 

# Function to identify problematic taxa
find_zero_variance_taxa <- function(counts_mat, group_var) {
  problem_taxa <- c()
  
  for (taxon in rownames(counts_mat)) {
    counts <- as.numeric(counts_mat[taxon, ])
    
    for (grp in unique(group_var)) {
      grp_counts <- counts[group_var == grp]
      
      # Check if all values are the same (zero variance)
      if (length(unique(grp_counts)) == 1) {
        problem_taxa <- c(problem_taxa, taxon)
        break
      }
    }
  }
  
  return(unique(problem_taxa))
}

# Find problematic taxa for interaction groups
problem_taxa <- find_zero_variance_taxa(species_counts_filtered, meta_tab$interaction_group)

length(problem_taxa)

[1] 589

# Remove problematic taxa
species_counts_interaction <- species_counts_filtered[!rownames(species_counts_filtered) %in% problem_taxa, ]

dim(species_counts_interaction)

[1] 656  29

#| label: filter-min-counts-per-group

# For each taxon, require at least 2 non-zero values in each interaction group
keep_taxa <- apply(species_counts_interaction, 1, function(x) {
  counts <- as.numeric(x)
  
  all_groups_ok <- TRUE
  for (grp in unique(meta_tab$interaction_group)) {
    grp_counts <- counts[meta_tab$interaction_group == grp]
    
    # Require at least 2 non-zero values AND variance > 0
    n_nonzero <- sum(grp_counts > 0)
    has_variance <- var(grp_counts) > 0
    
    if (n_nonzero < 2 | !has_variance) {
      all_groups_ok <- FALSE
      break
    }
  }
  
  return(all_groups_ok)
})

species_counts_interaction <- species_counts_interaction[keep_taxa, ]

dim(species_counts_interaction)

[1] 508  29

#| label: create-ps-interaction

# Create phyloseq object with filtered data
otu_interaction <- otu_table(species_counts_interaction, taxa_are_rows = TRUE)
sample_interaction <- sample_data(meta_tab)

ps <- phyloseq(otu_interaction, sample_interaction)

ps

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 508 taxa and 29 samples ]
sample_data() Sample Data:       [ 29 samples by 9 sample variables ]

ANCOM-BC for Complex factor

set.seed(123)
ancom_complex <- ancombc2(
  data = ps,
  fix_formula = "complex",
  p_adj_method = "BH",
  prv_cut = 0.10,
  lib_cut = 1000,
  group = "complex",
  struc_zero = FALSE,
  neg_lb = FALSE,
  alpha = 0.05,
  global = TRUE,
  pairwise = TRUE,
  dunnet = FALSE,
  trend = FALSE,
  verbose = FALSE
)

# Extract results
ancom_complex_res <- ancom_complex$res

# Filter significant (q < 0.05 for any comparison)
ancom_complex_sig <- ancom_complex_res %>%
  filter(q_complexmedium < 0.05 | q_complexhigh < 0.05)

nrow(ancom_complex_sig)

[1] 0

kable(head(ancom_complex_sig[, c("taxon", "lfc_complexmedium", "lfc_complexhigh", 
                                  "q_complexmedium", "q_complexhigh")], 20), 
      digits = 4,
      caption = "ANCOM-BC: Significant taxa by Complex (BH adjusted q < 0.05)")

ANCOM-BC: Significant taxa by Complex (BH adjusted q < 0.05)

taxon	lfc_complexmedium	lfc_complexhigh	q_complexmedium	q_complexhigh

ANCOM-BC for Protease factor:

set.seed(123)
ancom_protease <- ancombc2(
  data = ps,
  fix_formula = "protease",
  p_adj_method = "BH",
  prv_cut = 0.10,
  lib_cut = 1000,
  group = NULL,
  struc_zero = FALSE,
  neg_lb = FALSE,
  alpha = 0.05,
  global = FALSE,
  pairwise = FALSE,
  dunnet = FALSE,
  trend = FALSE,
  verbose = FALSE
)

# Extract results
ancom_protease_res <- ancom_protease$res

# Filter significant
ancom_protease_sig <- ancom_protease_res %>%
  filter(q_proteaseprot < 0.05)

# Sort by log fold change
ancom_protease_sig <- ancom_protease_sig[order(abs(ancom_protease_sig$lfc_proteaseprot), decreasing = TRUE), ]

nrow(ancom_protease_sig)

[1] 0

kable(head(ancom_protease_sig[, c("taxon", "lfc_proteaseprot", "se_proteaseprot", 
                                   "q_proteaseprot")], 20), 
      digits = 4,
      caption = "ANCOM-BC: Significant taxa by Protease (BH adjusted q < 0.05)")

ANCOM-BC: Significant taxa by Protease (BH adjusted q < 0.05)

taxon	lfc_proteaseprot	se_proteaseprot	q_proteaseprot

ANCOM-BC for Interaction:

set.seed(123)
ancom_interaction <- ancombc2(
  data = ps,
  fix_formula = "complex * protease",
  p_adj_method = "BH",
  prv_cut = 0.10,
  lib_cut = 1000,
  group = NULL,
  struc_zero = FALSE,
  neg_lb = FALSE,
  alpha = 0.05,
  global = FALSE,
  pairwise = FALSE,
  dunnet = FALSE,
  trend = FALSE,
  verbose = FALSE
)

# Extract results
ancom_interaction_res <- ancom_interaction$res

# Check column names for interaction terms
colnames(ancom_interaction_res)

 [1] "taxon"                               
 [2] "lfc_(Intercept)"                     
 [3] "lfc_complexmedium"                   
 [4] "lfc_complexhigh"                     
 [5] "lfc_proteaseprot"                    
 [6] "lfc_complexmedium:proteaseprot"      
 [7] "lfc_complexhigh:proteaseprot"        
 [8] "se_(Intercept)"                      
 [9] "se_complexmedium"                    
[10] "se_complexhigh"                      
[11] "se_proteaseprot"                     
[12] "se_complexmedium:proteaseprot"       
[13] "se_complexhigh:proteaseprot"         
[14] "W_(Intercept)"                       
[15] "W_complexmedium"                     
[16] "W_complexhigh"                       
[17] "W_proteaseprot"                      
[18] "W_complexmedium:proteaseprot"        
[19] "W_complexhigh:proteaseprot"          
[20] "p_(Intercept)"                       
[21] "p_complexmedium"                     
[22] "p_complexhigh"                       
[23] "p_proteaseprot"                      
[24] "p_complexmedium:proteaseprot"        
[25] "p_complexhigh:proteaseprot"          
[26] "q_(Intercept)"                       
[27] "q_complexmedium"                     
[28] "q_complexhigh"                       
[29] "q_proteaseprot"                      
[30] "q_complexmedium:proteaseprot"        
[31] "q_complexhigh:proteaseprot"          
[32] "diff_(Intercept)"                    
[33] "diff_complexmedium"                  
[34] "diff_complexhigh"                    
[35] "diff_proteaseprot"                   
[36] "diff_complexmedium:proteaseprot"     
[37] "diff_complexhigh:proteaseprot"       
[38] "passed_ss_(Intercept)"               
[39] "passed_ss_complexmedium"             
[40] "passed_ss_complexhigh"               
[41] "passed_ss_proteaseprot"              
[42] "passed_ss_complexmedium:proteaseprot"
[43] "passed_ss_complexhigh:proteaseprot"  

# Filter for significant interaction terms
ancom_interaction_sig <- ancom_interaction_res %>%
  filter(`p_complexmedium:proteaseprot` < 0.05 | `p_complexhigh:proteaseprot` < 0.10)

nrow(ancom_interaction_sig)

[1] 50

# Display significant interactions
kable(ancom_interaction_sig[, c("taxon", 
                                 "lfc_complexmedium:proteaseprot", 
                                 "lfc_complexhigh:proteaseprot",
                                 "q_complexmedium:proteaseprot", 
                                 "q_complexhigh:proteaseprot",
                                 "passed_ss_complexmedium:proteaseprot",
                                 "passed_ss_complexhigh:proteaseprot")], 
      digits = 4,
      caption = "ANCOM-BC: Significant Complex × Protease interactions (q < 0.05)")

ANCOM-BC: Significant Complex × Protease interactions (q < 0.05)

taxon	lfc_complexmedium:proteaseprot	lfc_complexhigh:proteaseprot	q_complexmedium:proteaseprot	q_complexhigh:proteaseprot	passed_ss_complexmedium:proteaseprot	passed_ss_complexhigh:proteaseprot
Dialister hominis	-0.2997	1.8939	0.9875	0.9858	TRUE	TRUE
Dialister massiliensis	-1.8853	-0.7889	0.8837	0.9858	FALSE	TRUE
Butyrivibrio fibrisolvens	-2.2807	-0.3276	0.9438	0.9858	TRUE	TRUE
Butyrivibrio hungatei	-1.6746	-0.2148	0.9438	0.9858	TRUE	TRUE
Butyrivibrio proteoclasticus	-1.6137	0.1608	0.8837	0.9883	FALSE	TRUE
Blautia producta	-1.2478	0.3677	0.9438	0.9858	TRUE	TRUE
Chordicoccus furentiruminis	-1.7094	0.1858	0.9438	0.9883	TRUE	TRUE
Lachnoclostridium phocaeense	-1.4706	-0.3161	0.9490	0.9858	TRUE	TRUE
[Clostridium] hylemonae	-1.8329	0.0568	0.8837	0.9968	FALSE	TRUE
Lachnoanaerobaculum gingivalis	-1.7353	-0.1363	0.8837	0.9883	FALSE	TRUE
Coprococcus sp. ART55/1	-2.7026	2.1685	0.8837	0.8566	FALSE	FALSE
Syntrophobotulus glycolicus	-1.8977	-1.5623	0.9490	0.9858	FALSE	TRUE
Eubacterium maltosivorans	0.0280	1.2893	0.9890	0.9858	TRUE	FALSE
Eubacterium limosum	-1.6327	1.1582	0.9438	0.9858	FALSE	TRUE
Intestinibaculum porci	-1.7437	0.0265	0.8837	0.9968	FALSE	TRUE
Parafannyhessea umbonata	-3.6662	0.4485	0.8837	0.9858	TRUE	TRUE
Olsenella timonensis	0.1869	1.9007	0.9875	0.9858	TRUE	TRUE
Olsenella sp. oral taxon 807	-0.5603	1.8409	0.9490	0.9858	TRUE	FALSE
Thermophilibacter immobilis	1.2507	1.7037	0.9490	0.9858	TRUE	TRUE
Prevotella sp. oral taxon 475	-2.3336	0.2448	0.9490	0.9883	TRUE	TRUE
Prevotella sp. oral taxon 299	0.0341	2.1389	0.9894	0.9858	TRUE	TRUE
Prevotella corporis	-0.8378	1.2119	0.9490	0.9858	TRUE	TRUE
Prevotella scopos	-3.3055	-0.6671	0.8837	0.9858	TRUE	TRUE
Prevotella communis	-0.5191	1.3718	0.9789	0.9858	TRUE	TRUE
Pseudoprevotella muciniphila	0.2981	2.3216	0.9875	0.8232	TRUE	TRUE
Paraprevotella clara	-0.1737	1.6501	0.9875	0.9072	TRUE	TRUE
Bacteroides fragilis	-0.2294	1.6157	0.9875	0.9858	TRUE	TRUE
Alistipes finegoldii	-0.5558	1.6241	0.9741	0.9858	TRUE	TRUE
Parabacteroides chongii	0.3716	2.0749	0.9875	0.8566	TRUE	FALSE
Porphyromonas sp. oral taxon 275	-1.3825	1.8534	0.9490	0.9858	TRUE	TRUE
Tenuifilum thalassicum	-2.2412	0.6578	0.8837	0.9858	TRUE	TRUE
Cruoricaptor ignavus	-1.5444	0.9985	0.9490	0.9858	FALSE	TRUE
Sutterella faecalis	-1.6208	-1.0991	0.9490	0.9858	FALSE	TRUE
Sutterella wadsworthensis	-1.9140	-0.7402	0.8837	0.9858	FALSE	TRUE
Desulfovibrio piger	-0.4109	1.9870	0.9875	0.9858	TRUE	TRUE
Desulfovibrio fairfieldensis	-0.3773	1.9044	0.9875	0.9858	TRUE	TRUE
Ligilactobacillus agilis	1.2201	2.8991	0.9490	0.8232	FALSE	FALSE
Lentibacillus sp. CBA3610	-1.2422	-1.5174	0.9490	0.9858	TRUE	FALSE
[Ruminococcus] torques	-0.8666	1.5405	0.9490	0.9858	TRUE	FALSE
Claveliimonas bilis	-0.9488	1.6320	0.9490	0.9858	TRUE	FALSE
Clostridium manihotivorum	-0.9495	-1.5812	0.9490	0.9858	TRUE	TRUE
Eubacterium ventriosum	-1.7350	-0.3582	0.9490	0.9858	FALSE	TRUE
Corynebacterium diphtheriae	-0.8743	-1.4359	0.9490	0.9858	TRUE	TRUE
Lacrimispora sphenoides	-1.6198	0.7624	0.8837	0.9858	FALSE	TRUE
Clostridium sp. BJN0001	-1.9262	-2.2659	0.8837	0.8566	FALSE	FALSE
Geosporobacter ferrireducens	-0.0040	1.7323	0.9980	0.9858	TRUE	TRUE
Alkalibacter rhizosphaerae	-0.6093	2.2027	0.9490	0.8566	TRUE	FALSE
Denitrobacterium detoxificans	0.2146	1.2516	0.9875	0.9858	TRUE	TRUE
Calothrix sp. PCC 7507	0.9130	1.2676	0.9490	0.9858	FALSE	TRUE
Longitalea sp. SCSIO 12813	-0.5377	2.1102	0.9670	0.8566	TRUE	FALSE

Volcano plot for interaction terms:

# Medium:Protease interaction
ancom_interaction_res$sig_med_int <- ifelse(
  ancom_interaction_res$`p_complexmedium:proteaseprot` < 0.05, 
  "Significant", "Not Significant"
)

p1 <- ggplot(ancom_interaction_res, 
             aes(x = `lfc_complexmedium:proteaseprot`, 
                 y = -log10(`p_complexmedium:proteaseprot`), 
                 color = sig_med_int)) +
  geom_point(alpha = 0.6, size = 2) +
  scale_color_manual(values = c("Significant" = "#D55E00", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Log Fold Change",
    y = "-log10(p-value)",
    color = "",
    title = "Medium × Protease Interaction"
  ) +
  theme_publication +
  theme(legend.position = "bottom")

# High:Protease interaction
ancom_interaction_res$sig_high_int <- ifelse(
  ancom_interaction_res$`p_complexhigh:proteaseprot` < 0.05, 
  "Significant", "Not Significant"
)

p2 <- ggplot(ancom_interaction_res, 
             aes(x = `lfc_complexhigh:proteaseprot`, 
                 y = -log10(`p_complexhigh:proteaseprot`), 
                 color = sig_high_int)) +
  geom_point(alpha = 0.6, size = 2) +
  scale_color_manual(values = c("Significant" = "#009E73", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Log Fold Change",
    y = "-log10(p-value)",
    color = "",
    title = "High × Protease Interaction"
  ) +
  theme_publication +
  theme(legend.position = "bottom")

p1 + p2 +
  plot_annotation(title = "ANCOM-BC: Complex × Protease Interaction Effects",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Heatmap of significant interaction taxa:

# Get taxa with significant interactions
interaction_taxa <- ancom_interaction_res %>%
  filter(`p_complexmedium:proteaseprot` < 0.05 | `p_complexhigh:proteaseprot` < 0.05) %>%
  pull(taxon)

if (length(interaction_taxa) > 0) {
  
  # Get CLR-transformed abundances
  species_pseudo <- species_counts_filtered[interaction_taxa, , drop = FALSE] + 1
  species_clr <- log(species_pseudo) - rowMeans(log(species_pseudo))
  
  # Order samples by Complex (and then by Protease within Complex)
  sample_order <- rownames(meta_tab)[order(meta_tab$complex, meta_tab$protease)]
  
  # Reorder the CLR matrix columns
  species_clr_ordered <- species_clr[, sample_order]
  
  # Create annotation with ordered samples
  annotation_col <- data.frame(
    Complex = meta_tab[sample_order, "complex"],
    Protease = meta_tab[sample_order, "protease"],
    row.names = sample_order
  )
  
  annotation_colors <- list(
    Complex = complex_colors,
    Protease = protease_colors
  )
  
  # Add gaps between Complex groups
  # Find positions where Complex changes
  complex_ordered <- meta_tab[sample_order, "complex"]
  gaps_col <- which(complex_ordered[-1] != complex_ordered[-length(complex_ordered)])
  
  # Plot heatmap
  pheatmap(
    species_clr_ordered,
    scale = "row",
    cluster_rows = TRUE,
    cluster_cols = FALSE,
    clustering_distance_rows = "euclidean",
    clustering_method = "ward.D2",
    annotation_col = annotation_col,
    annotation_colors = annotation_colors,
    show_colnames = FALSE,
    gaps_col = gaps_col,
    color = colorRampPalette(c("#0072B2", "white", "#D55E00"))(100),
    fontsize_row = 8,
    fontsize_col = 8,
    main = "Taxa with Significant Complex × Protease Interaction"
  )
} else {
  print("No taxa with significant interaction effects")
}

ANCOM-BC Volcano Plot - Protease:

# Prepare data
ancom_protease_res$significant <- ifelse(ancom_protease_res$diff_proteaseprot == TRUE, 
                                          "Significant", "Not Significant")
ancom_protease_res$direction <- ifelse(ancom_protease_res$lfc_proteaseprot > 0, 
                                        "Higher in prot", "Higher in cont")

# Volcano plot
p_volcano <- ggplot(ancom_protease_res, aes(x = lfc_proteaseprot, y = -log10(q_proteaseprot), 
                                             color = significant)) +
  geom_point(alpha = 0.6, size = 2) +
  scale_color_manual(values = c("Significant" = "#D55E00", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Log Fold Change (prot vs cont)",
    y = "-log10(q-value)",
    color = "",
    title = "ANCOM-BC: Protease Effect"
  ) +
  theme_publication

# Add labels for top significant taxa
if (nrow(ancom_protease_sig) > 0) {
  top_taxa <- head(ancom_protease_sig, 10)
  p_volcano <- p_volcano +
    geom_text_repel(data = ancom_protease_res[ancom_protease_res$taxon %in% top_taxa$taxon, ],
                    aes(label = taxon),
                    size = 3, max.overlaps = 15,
                    box.padding = 0.5)
}

p_volcano

ANCOM-BC Volcano Plot-Complex

# Medium vs Low
ancom_complex_res$sig_medium <- ifelse(ancom_complex_res$q_complexmedium < 0.05, 
                                        "Significant", "Not Significant")

p1 <- ggplot(ancom_complex_res, aes(x = lfc_complexmedium, y = -log10(q_complexmedium), 
                                     color = sig_medium)) +
  geom_point(alpha = 0.6, size = 2) +
  scale_color_manual(values = c("Significant" = "#E69F00", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Log Fold Change (medium vs low)",
    y = "-log10(q-value)",
    color = "",
    title = "Medium vs Low"
  ) +
  theme_publication +
  theme(legend.position = "none")

# High vs Low
ancom_complex_res$sig_high <- ifelse(ancom_complex_res$q_complexhigh < 0.05, 
                                      "Significant", "Not Significant")

p2 <- ggplot(ancom_complex_res, aes(x = lfc_complexhigh, y = -log10(q_complexhigh), 
                                     color = sig_high)) +
  geom_point(alpha = 0.6, size = 2) +
  scale_color_manual(values = c("Significant" = "#009E73", "Not Significant" = "grey70")) +
  geom_hline(yintercept = -log10(0.05), linetype = "dashed", color = "red") +
  geom_vline(xintercept = 0, linetype = "dashed", color = "black") +
  labs(
    x = "Log Fold Change (high vs low)",
    y = "-log10(q-value)",
    color = "",
    title = "High vs Low"
  ) +
  theme_publication +
  theme(legend.position = "none")

p1 + p2 +
  plot_annotation(title = "ANCOM-BC: Complex Effect",
                  theme = theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 16)))

Consensus Approach (ALDEX2 + ANCOM-BC)

Aqui os taxas que tiveram p value menor que 0.05 nos dois metodos.

# Find taxa significant in BOTH methods for Protease
aldex_sig_taxa <- aldex_protease_all$taxon[aldex_protease_all$wi.ep < 0.05]
ancom_sig_taxa <- ancom_protease_res$taxon[ancom_protease_res$p_proteaseprot < 0.05]

consensus_protease <- intersect(aldex_sig_taxa, ancom_sig_taxa)

# Create consensus table
if (length(consensus_protease) > 0) {
  consensus_protease_df <- data.frame(
    taxon = consensus_protease,
    aldex_effect = aldex_protease_all$effect[match(consensus_protease, aldex_protease_all$taxon)],
    aldex_pval = aldex_protease_all$wi.ep[match(consensus_protease, aldex_protease_all$taxon)],
    ancom_lfc = ancom_protease_res$lfc_proteaseprot[match(consensus_protease, ancom_protease_res$taxon)],
    ancom_pval = ancom_protease_res$p_proteaseprot[match(consensus_protease, ancom_protease_res$taxon)]
  )
  
  consensus_protease_df$direction <- ifelse(consensus_protease_df$aldex_effect > 0, 
                                             "Higher in prot", "Higher in cont")
  
  consensus_protease_df <- consensus_protease_df[order(abs(consensus_protease_df$aldex_effect), 
                                                        decreasing = TRUE), ]
  
  kable(consensus_protease_df, digits = 4,
        caption = paste0("Consensus: Taxa significant in both ALDEx2 and ANCOM-BC for Protease (n = ", 
                         length(consensus_protease), ")"))
} else {
  print("No taxa significant in both methods for Protease")
}

Consensus: Taxa significant in both ALDEx2 and ANCOM-BC for Protease (n = 1)

taxon	aldex_effect	aldex_pval	ancom_lfc	ancom_pval	direction
Salmonella enterica	0.4534	0.0212	1.1229	0.0182	Higher in prot

Consensus Venn Diagram:

# Create data for Venn-like visualization
venn_data <- data.frame(
  Method = c("ALDEx2 only", "ANCOM-BC only", "Both"),
  Count = c(
    length(setdiff(aldex_sig_taxa, ancom_sig_taxa)),
    length(setdiff(ancom_sig_taxa, aldex_sig_taxa)),
    length(consensus_protease)
  )
)

p_venn <- ggplot(venn_data, aes(x = Method, y = Count, fill = Method)) +
  geom_bar(stat = "identity", alpha = 0.8) +
  geom_text(aes(label = Count), vjust = -0.5, size = 5, fontface = "bold") +
  scale_fill_manual(values = c("ALDEx2 only" = "#56B4E9", 
                                "ANCOM-BC only" = "#E69F00", 
                                "Both" = "#009E73")) +
  labs(
    x = "",
    y = "Number of significant taxa",
    title = "Consensus: Protease Effect"
  ) +
  theme_publication +
  theme(legend.position = "none")

p_venn

Plot selected taxa boxplots:

Bruno, aqui caso vc queira fazer alguns plots so de alguns taxas. Que vc achar interessante. Ai so mudar o nome e pedir para rodar. Esse codigo é para os fatores separadamento. Para vc descobrir o nome do taxa é só colocar esse código.

# ============================================
# SEARCH FOR ALL TAXA 
# ============================================
row.names(species_frac)

   [1] "Selenomonas ruminantium"                                
   [2] "Selenomonas sputigena"                                  
   [3] "Selenomonas sp. oral taxon 920"                         
   [4] "Selenomonas sp. oral taxon 126"                         
   [5] "Selenomonas sp. oral taxon 478"                         
   [6] "Selenomonas sp. oral taxon 136"                         
   [7] "Selenomonas timonae"                                    
   [8] "Selenomonas dianae"                                     
   [9] "Megamonas hypermegale"                                  
  [10] "Megamonas funiformis"                                   
  [11] "Pectinatus frisingensis"                                
  [12] "Selenobaculum gbiensis"                                 
  [13] "uncultured Sporomusa sp."                               
  [14] "Sporomusa termitida"                                    
  [15] "Pelosinus sp. UFO1"                                     
  [16] "Methylomusa anaerophila"                                
  [17] "Megasphaera elsdenii"                                   
  [18] "Megasphaera hexanoica"                                  
  [19] "Megasphaera massiliensis"                               
  [20] "Megasphaera stantonii"                                  
  [21] "Dialister succinatiphilus"                              
  [22] "Dialister pneumosintes"                                 
  [23] "Dialister hominis"                                      
  [24] "Dialister massiliensis"                                 
  [25] "Veillonella rodentium"                                  
  [26] "Veillonella rogosae"                                    
  [27] "Acidaminococcus fermentans"                             
  [28] "Acidaminococcus intestini"                              
  [29] "Phascolarctobacterium succinatutens"                    
  [30] "Phascolarctobacterium sp. Marseille-Q4147"              
  [31] "Phascolarctobacterium faecium"                          
  [32] "Lactobacillus amylovorus"                               
  [33] "Lactobacillus johnsonii"                                
  [34] "Lactobacillus delbrueckii"                              
  [35] "Lactobacillus acidophilus"                              
  [36] "Lactobacillus crispatus"                                
  [37] "Lactobacillus iners"                                    
  [38] "Lactobacillus sp. ESL0785"                              
  [39] "Lactobacillus helveticus"                               
  [40] "Lactobacillus gasseri"                                  
  [41] "Lactobacillus intestinalis"                             
  [42] "Lactobacillus kefiranofaciens"                          
  [43] "Lactobacillus taiwanensis"                              
  [44] "Lactobacillus acetotolerans"                            
  [45] "Lactobacillus amylolyticus"                             
  [46] "Limosilactobacillus mucosae"                            
  [47] "Limosilactobacillus reuteri"                            
  [48] "Limosilactobacillus fermentum"                          
  [49] "Ligilactobacillus ruminis"                              
  [50] "Ligilactobacillus salivarius"                           
  [51] "Lactiplantibacillus plantarum"                          
  [52] "Lacticaseibacillus pantheris"                           
  [53] "Lacticaseibacillus paracasei"                           
  [54] "Lacticaseibacillus zeae"                                
  [55] "Amylolactobacillus amylophilus"                         
  [56] "Streptococcus suis"                                     
  [57] "Streptococcus thermophilus"                             
  [58] "Streptococcus agalactiae"                               
  [59] "Streptococcus sanguinis"                                
  [60] "Enterococcus faecalis"                                  
  [61] "Enterococcus faecium"                                   
  [62] "Paenibacillus sp. B01"                                  
  [63] "Paenibacillus sp. sptzw28"                              
  [64] "Paenibacillus sp. RUD330"                               
  [65] "Paenibacillus sp. FSL R7-0331"                          
  [66] "Paenibacillus sp. R14(2021)"                            
  [67] "Paenibacillus sp. 32O-W"                                
  [68] "Paenibacillus sp. PHS-Z3"                               
  [69] "Paenibacillus sp. HWE-109"                              
  [70] "Paenibacillus sp. FSL H7-0357"                          
  [71] "Paenibacillus albicereus"                               
  [72] "Paenibacillus mucilaginosus"                            
  [73] "Paenibacillus polymyxa"                                 
  [74] "Paenibacillus beijingensis"                             
  [75] "Paenibacillus rhizovicinus"                             
  [76] "Paenibacillus lycopersici"                              
  [77] "Paenibacillus dendritiformis"                           
  [78] "Paenibacillus macerans"                                 
  [79] "Paenibacillus thiaminolyticus"                          
  [80] "Paenibacillus stellifer"                                
  [81] "Paenibacillus ihbetae"                                  
  [82] "Paenibacillus durus"                                    
  [83] "Paenibacillus montanisoli"                              
  [84] "Paenibacillus tritici"                                  
  [85] "Paenibacillus cellulosilyticus"                         
  [86] "Paenibacillus odorifer"                                 
  [87] "Paenibacillus donghaensis"                              
  [88] "Brevibacillus sp. WF146"                                
  [89] "Brevibacillus brevis"                                   
  [90] "Brevibacillus marinus"                                  
  [91] "Brevibacillus composti"                                 
  [92] "Cohnella candidum"                                      
  [93] "Cohnella herbarum"                                      
  [94] "Thermobacillus composti"                                
  [95] "Saccharibacillus brassicae"                             
  [96] "Bacillus velezensis"                                    
  [97] "Bacillus amyloliquefaciens"                             
  [98] "Bacillus subtilis"                                      
  [99] "Bacillus anthracis"                                     
 [100] "Bacillus cereus"                                        
 [101] "Bacillus thuringiensis"                                 
 [102] "Bacillus sp. ZHX3"                                      
 [103] "Bacillus sp. ZY-1-1"                                    
 [104] "Bacillus altitudinis"                                   
 [105] "Heyndrickxia coagulans"                                 
 [106] "Priestia megaterium"                                    
 [107] "Mesobacillus foraminis"                                 
 [108] "Rossellomorea marisflavi"                               
 [109] "Staphylococcus aureus"                                  
 [110] "Staphylococcus epidermidis"                             
 [111] "Staphylococcus condimenti"                              
 [112] "Staphylococcus pseudintermedius"                        
 [113] "Staphylococcus capitis"                                 
 [114] "Alicyclobacillus acidocaldarius"                        
 [115] "Alicyclobacillus sp. TC"                                
 [116] "Alicyclobacillus mengziensis"                           
 [117] "Alicyclobacillus fastidiosus"                           
 [118] "Tumebacillus avium"                                     
 [119] "Effusibacillus dendaii"                                 
 [120] "Planococcus lenghuensis"                                
 [121] "Sporosarcina sp. 0.2-SM1T-5"                            
 [122] "Hydrogenibacillus sp. N12"                              
 [123] "Agathobacter rectalis"                                  
 [124] "Roseburia hominis"                                      
 [125] "Roseburia rectibacter"                                  
 [126] "Roseburia intestinalis"                                 
 [127] "Butyrivibrio fibrisolvens"                              
 [128] "Butyrivibrio crossotus"                                 
 [129] "Butyrivibrio hungatei"                                  
 [130] "Butyrivibrio proteoclasticus"                           
 [131] "Anaerostipes hadrus"                                    
 [132] "Anaerostipes caccae"                                    
 [133] "Blautia obeum"                                          
 [134] "Blautia liquoris"                                       
 [135] "Blautia producta"                                       
 [136] "Blautia sp. SC05B48"                                    
 [137] "Blautia sp. NBRC 113351"                                
 [138] "Blautia hansenii"                                       
 [139] "Blautia wexlerae"                                       
 [140] "Blautia pseudococcoides"                                
 [141] "Enterocloster bolteae"                                  
 [142] "Enterocloster clostridioformis"                         
 [143] "Enterocloster asparagiformis"                           
 [144] "Chordicoccus furentiruminis"                            
 [145] "Dorea longicatena"                                      
 [146] "Dorea formicigenerans"                                  
 [147] "Marvinbryantia formatexigens"                           
 [148] "Pseudobutyrivibrio xylanivorans"                        
 [149] "Novisyntrophococcus fermenticellae"                     
 [150] "Lachnoclostridium phytofermentans"                      
 [151] "[Clostridium] scindens"                                 
 [152] "Lachnoclostridium phocaeense"                           
 [153] "[Clostridium] hylemonae"                                
 [154] "Lachnoanaerobaculum umeaense"                           
 [155] "Lachnoanaerobaculum gingivalis"                         
 [156] "Coprococcus comes"                                      
 [157] "Coprococcus catus"                                      
 [158] "Coprococcus eutactus"                                   
 [159] "Coprococcus sp. ART55/1"                                
 [160] "Anaerobutyricum hallii"                                 
 [161] "Lachnospira eligens"                                    
 [162] "Anaerocolumna cellulosilytica"                          
 [163] "Wansuia hejianensis"                                    
 [164] "Lacrimispora saccharolytica"                            
 [165] "Lacrimispora xylanolytica"                              
 [166] "Stomatobaculum sp. F0698"                               
 [167] "Simiaoa sunii"                                          
 [168] "Wujia chipingensis"                                     
 [169] "[Ruminococcus] gnavus"                                  
 [170] "[Ruminococcus] lactaris"                                
 [171] "Herbinix luporum"                                       
 [172] "Epulopiscium sp. 'N.t. morphotype B'"                   
 [173] "Qiania dongpingensis"                                   
 [174] "Faecalibacterium prausnitzii"                           
 [175] "Faecalibacterium sp. I3-3-33"                           
 [176] "Faecalibacterium sp. HTF-F"                             
 [177] "Faecalibacterium sp. I4-1-79"                           
 [178] "Faecalibacterium sp. IP-3-29"                           
 [179] "Faecalibacterium sp. I2-3-92"                           
 [180] "Faecalibacterium sp. I3-3-89"                           
 [181] "Faecalibacterium sp. I4-3-84"                           
 [182] "Faecalibacterium sp. IP-1-18"                           
 [183] "Faecalibacterium duncaniae"                             
 [184] "Subdoligranulum variabile"                              
 [185] "Ruminococcus albus"                                     
 [186] "Ruminococcus champanellensis"                           
 [187] "Ruminococcus gauvreauii"                                
 [188] "Ruminococcus bicirculans (ex Wegman et al. 2014)"       
 [189] "Ruminococcus bovis"                                     
 [190] "Oscillibacter hominis"                                  
 [191] "Ruthenibacterium lactatiformans"                        
 [192] "Dysosmobacter welbionis"                                
 [193] "Lawsonibacter asaccharolyticus"                         
 [194] "Flavonifractor plautii"                                 
 [195] "Anaerotruncus colihominis"                              
 [196] "Pusillibacter faecalis"                                 
 [197] "Solibaculum mannosilyticum"                             
 [198] "Vescimonas coprocola"                                   
 [199] "Vescimonas fastidiosa"                                  
 [200] "Ethanoligenens harbinense"                              
 [201] "Caproicibacterium lactatifermentans"                    
 [202] "Caproicibacterium amylolyticum"                         
 [203] "Acutalibacter muris"                                    
 [204] "Caproicibacter fermentans"                              
 [205] "Acetivibrio thermocellus"                               
 [206] "Caproiciproducens sp. NJN-50"                           
 [207] "Thermocaproicibacter melissae"                          
 [208] "Clostridium sp. MB40-C1"                                
 [209] "Clostridium sp. SY8519"                                 
 [210] "Clostridium sp. 16K-1-R1"                               
 [211] "Clostridium sp. MD294"                                  
 [212] "Clostridium botulinum"                                  
 [213] "Clostridium formicaceticum"                             
 [214] "Clostridium perfringens"                                
 [215] "Clostridium beijerinckii"                               
 [216] "Candidatus Arthromitus sp. SFB-rat-Yit"                 
 [217] "Hungatella hathewayi"                                   
 [218] "Proteiniclasticum sp. QWL-01"                           
 [219] "Serpentinicella alkaliphila"                            
 [220] "Syntrophobotulus glycolicus"                            
 [221] "Desulfitobacterium dehalogenans"                        
 [222] "Symbiobacterium thermophilum"                           
 [223] "Caldinitratiruptor microaerophilus"                     
 [224] "Emergencia timonensis"                                  
 [225] "Aminipila luticellarii"                                 
 [226] "Flintibacter sp. KGMB00164"                             
 [227] "Intestinimonas butyriciproducens"                       
 [228] "Massilistercora timonensis"                             
 [229] "Clostridioides difficile"                               
 [230] "Eubacterium maltosivorans"                              
 [231] "Eubacterium limosum"                                    
 [232] "Acetobacterium wieringae"                               
 [233] "Maliibacterium massiliense"                             
 [234] "Dehalobacterium formicoaceticum"                        
 [235] "Acididesulfobacillus acetoxydans"                       
 [236] "Aristaeella lactis"                                     
 [237] "Aristaeella hokkaidonensis"                             
 [238] "Christensenella minuta"                                 
 [239] "Vallitalea guaymasensis"                                
 [240] "Thermincola potens"                                     
 [241] "Gelria sp. Kuro-4"                                      
 [242] "Halobacteroides halobius"                               
 [243] "Acetohalobium arabaticum"                               
 [244] "Intestinibaculum porci"                                 
 [245] "Allobaculum mucilyticum"                                
 [246] "Allobaculum sp. Allo2"                                  
 [247] "Bulleidia sp. zg-1006"                                  
 [248] "Faecalibaculum rodentium"                               
 [249] "Amedibacterium intestinale"                             
 [250] "Catenibacterium mitsuokai"                              
 [251] "[Clostridium] innocuum"                                 
 [252] "Murdochiella vaginalis"                                 
 [253] "Sedimentibacter sp. zth1"                               
 [254] "Ndongobacter massiliensis"                              
 [255] "Microbacterium sp. JZ31"                                
 [256] "Microbacterium oleivorans"                              
 [257] "Microbacterium testaceum"                               
 [258] "Microbacterium luteolum"                                
 [259] "Microbacterium oxydans"                                 
 [260] "Agromyces soli"                                         
 [261] "Leucobacter rhizosphaerae"                              
 [262] "Agreia sp. COWG"                                        
 [263] "Micrococcus luteus"                                     
 [264] "Cellulomonas fimi"                                      
 [265] "Paraoerskovia marina"                                   
 [266] "Brachybacterium avium"                                  
 [267] "Cellulosimicrobium cellulans"                           
 [268] "Intrasporangium calvum"                                 
 [269] "Sanguibacter sp. HDW7"                                  
 [270] "Streptomyces sp. WMMC500"                               
 [271] "Streptomyces sp. SN-593"                                
 [272] "Streptomyces sp. T12"                                   
 [273] "Streptomyces sp. AM 2-1-1"                              
 [274] "Streptomyces sp. Alt1"                                  
 [275] "Streptomyces sp. LX-29"                                 
 [276] "Streptomyces tirandamycinicus"                          
 [277] "Mycolicibacterium aubagnense"                           
 [278] "Corynebacterium simulans"                               
 [279] "Corynebacterium marinum"                                
 [280] "Corynebacterium halotolerans"                           
 [281] "Nocardia brasiliensis"                                  
 [282] "Nocardia nova"                                          
 [283] "Nocardia asteroides"                                    
 [284] "Prescottella equi"                                      
 [285] "Bifidobacterium longum"                                 
 [286] "Bifidobacterium adolescentis"                           
 [287] "Bifidobacterium breve"                                  
 [288] "Bifidobacterium angulatum"                              
 [289] "Bifidobacterium choerinum"                              
 [290] "Bifidobacterium pseudocatenulatum"                      
 [291] "Bifidobacterium thermophilum"                           
 [292] "Nocardioides sp. S-1144"                                
 [293] "Nocardioides ochotonae"                                 
 [294] "Nocardioides faecalis"                                  
 [295] "Pimelobacter simplex"                                   
 [296] "Propionibacterium freudenreichii"                       
 [297] "Propionibacterium acidifaciens"                         
 [298] "Cutibacterium acnes"                                    
 [299] "Amycolatopsis sp. FDAARGOS 1241"                        
 [300] "Lentzea sp. HUAS12"                                     
 [301] "Actinomyces radicidentis"                               
 [302] "Trueperella pyogenes"                                   
 [303] "Trueperella abortisuis"                                 
 [304] "Varibaculum prostatecancerukia"                         
 [305] "Micromonospora sp. WMMD882"                             
 [306] "Catellatospora sp. IY07-71"                             
 [307] "Nonomuraea gerenzanensis"                               
 [308] "Actinomadura sp. NAK00032"                              
 [309] "Actinomadura madurae"                                   
 [310] "Frankia sp. QA3"                                        
 [311] "Epidermidibacterium keratini"                           
 [312] "Parafannyhessea umbonata"                               
 [313] "Olsenella uli"                                          
 [314] "Olsenella timonensis"                                   
 [315] "Olsenella sp. oral taxon 807"                           
 [316] "Parolsenella massiliensis"                              
 [317] "Parolsenella catena"                                    
 [318] "Thermophilibacter immobilis"                            
 [319] "Atopobium sp. oral taxon 416"                           
 [320] "Collinsella aerofaciens"                                
 [321] "Collinsella stercoris"                                  
 [322] "Eggerthella lenta"                                      
 [323] "Eggerthella guodeyinii"                                 
 [324] "Berryella intestinalis"                                 
 [325] "Slackia heliotrinireducens"                             
 [326] "Arabiibacter massiliensis"                              
 [327] "Xiamenia xianingshaonis"                                
 [328] "Conexibacter woesei"                                    
 [329] "Paraconexibacter antarcticus"                           
 [330] "Miltoncostaea marina"                                   
 [331] "Miltoncostaea oceani"                                   
 [332] "Rubrobacter xylanophilus"                               
 [333] "Baekduia alba"                                          
 [334] "Baekduia soli"                                          
 [335] "Actinomarinicola tropica"                               
 [336] "Dermatobacter hominis"                                  
 [337] "Cyanobacterium aponinum"                                
 [338] "Roseiflexus castenholzii"                               
 [339] "Tepidiforma flava"                                      
 [340] "Dehalococcoides mccartyi"                               
 [341] "Caldilinea aerophila"                                   
 [342] "Prevotella sp. oral taxon 475"                          
 [343] "Prevotella sp. Rep29"                                   
 [344] "Prevotella sp. E9-3"                                    
 [345] "Prevotella sp. E13-17"                                  
 [346] "Prevotella sp. oral taxon 299"                          
 [347] "Prevotella sp. E15-22"                                  
 [348] "Prevotella sp. E2-28"                                   
 [349] "Prevotella veroralis"                                   
 [350] "Prevotella dentalis"                                    
 [351] "Prevotella multiformis"                                 
 [352] "Prevotella herbatica"                                   
 [353] "Prevotella bryantii"                                    
 [354] "Prevotella ruminicola"                                  
 [355] "Prevotella denticola"                                   
 [356] "Prevotella corporis"                                    
 [357] "Prevotella oris"                                        
 [358] "Prevotella nigrescens"                                  
 [359] "Prevotella scopos"                                      
 [360] "Prevotella communis"                                    
 [361] "Prevotella histicola"                                   
 [362] "Prevotella intermedia"                                  
 [363] "Prevotella fusca"                                       
 [364] "Prevotella bivia"                                       
 [365] "Prevotella melaninogenica"                              
 [366] "Prevotella jejuni"                                      
 [367] "Segatella copri"                                        
 [368] "Hoylesella buccalis"                                    
 [369] "Hoylesella enoeca"                                      
 [370] "Pseudoprevotella muciniphila"                           
 [371] "Paraprevotella clara"                                   
 [372] "Paraprevotella xylaniphila"                             
 [373] "Bacteroides fragilis"                                   
 [374] "Bacteroides thetaiotaomicron"                           
 [375] "Bacteroides xylanisolvens"                              
 [376] "Bacteroides zhangwenhongii"                             
 [377] "Bacteroides stercoris"                                  
 [378] "Bacteroides salyersiae"                                 
 [379] "Bacteroides uniformis"                                  
 [380] "Bacteroides sp. DH3716P"                                
 [381] "Bacteroides ovatus"                                     
 [382] "Bacteroides helcogenes"                                 
 [383] "Bacteroides faecium"                                    
 [384] "Bacteroides nordii"                                     
 [385] "Bacteroides zoogleoformans"                             
 [386] "Bacteroides coprosuis"                                  
 [387] "Bacteroides eggerthii"                                  
 [388] "Bacteroides intestinalis"                               
 [389] "Bacteroides cellulosilyticus"                           
 [390] "Bacteroides caccae"                                     
 [391] "Bacteroides faecis"                                     
 [392] "Bacteroides caecimuris"                                 
 [393] "Bacteroides heparinolyticus"                            
 [394] "Phocaeicola vulgatus"                                   
 [395] "Phocaeicola salanitronis"                               
 [396] "Phocaeicola coprophilus"                                
 [397] "Phocaeicola dorei"                                      
 [398] "Sodaliphilus pleomorphus"                               
 [399] "Duncaniella dubosii"                                    
 [400] "Muribaculum gordoncarteri"                              
 [401] "Muribaculum intestinale"                                
 [402] "Paramuribaculum intestinale"                            
 [403] "Alistipes finegoldii"                                   
 [404] "Alistipes megaguti"                                     
 [405] "uncultured Alistipes sp."                               
 [406] "Alistipes communis"                                     
 [407] "Alistipes dispar"                                       
 [408] "Alistipes ihumii"                                       
 [409] "Alistipes sp. dk3624"                                   
 [410] "Alistipes onderdonkii"                                  
 [411] "Alistipes senegalensis"                                 
 [412] "Parabacteroides chongii"                                
 [413] "Parabacteroides merdae"                                 
 [414] "Parabacteroides distasonis"                             
 [415] "Parabacteroides goldsteinii"                            
 [416] "Parabacteroides johnsonii"                              
 [417] "Tannerella serpentiformis"                              
 [418] "Tannerella forsythia"                                   
 [419] "Petrimonas mucosa"                                      
 [420] "Porphyromonas sp. oral taxon 275"                       
 [421] "Porphyromonas gingivalis"                               
 [422] "Porphyromonas cangingivalis"                            
 [423] "Tenuifilum thalassicum"                                 
 [424] "Barnesiella viscericola"                                
 [425] "Butyricimonas faecalis"                                 
 [426] "Salinivirga cyanobacteriivorans"                        
 [427] "Paludibacter propionicigenes"                           
 [428] "Draconibacterium orientale"                             
 [429] "Lutibacter sp. A64"                                     
 [430] "Capnocytophaga gingivalis"                              
 [431] "Polaribacter reichenbachii"                             
 [432] "Cruoricaptor ignavus"                                   
 [433] "Olivibacter sp. LS-1"                                   
 [434] "Chlorobaculum sp. MV4-Y"                                
 [435] "Rhodothermus marinus"                                   
 [436] "Salinibacter ruber"                                     
 [437] "Cyclonatronum proteinivorum"                            
 [438] "Gemmatirosa kalamazoonensis"                            
 [439] "Escherichia coli"                                       
 [440] "Escherichia albertii"                                   
 [441] "Escherichia sp. E4742"                                  
 [442] "Salmonella enterica"                                    
 [443] "Candidatus Annandia adelgestsuga"                       
 [444] "Candidatus Westeberhardia cardiocondylae"               
 [445] "Klebsiella pneumoniae"                                  
 [446] "Klebsiella variicola"                                   
 [447] "Enterobacter hormaechei"                                
 [448] "Enterobacter roggenkampii"                              
 [449] "Enterobacter ludwigii"                                  
 [450] "Enterobacter cloacae"                                   
 [451] "Enterobacter asburiae"                                  
 [452] "Citrobacter freundii"                                   
 [453] "Shigella flexneri"                                      
 [454] "Cronobacter sakazakii"                                  
 [455] "Pluralibacter gergoviae"                                
 [456] "Morganella morganii"                                    
 [457] "Buchnera aphidicola"                                    
 [458] "Serratia symbiotica"                                    
 [459] "Serratia marcescens"                                    
 [460] "Pectobacterium quasiaquaticum"                          
 [461] "Pseudomonas aeruginosa"                                 
 [462] "Pseudomonas putida"                                     
 [463] "Pseudomonas fluorescens"                                
 [464] "Pseudomonas kurunegalensis"                             
 [465] "uncultured Pseudomonas sp."                             
 [466] "Stutzerimonas stutzeri"                                 
 [467] "Stutzerimonas balearica"                                
 [468] "Succinivibrio dextrinosolvens"                          
 [469] "Aeromonas salmonicida"                                  
 [470] "Aeromonas veronii"                                      
 [471] "Frischella perrara"                                     
 [472] "Lysobacter sp. KIS68-7"                                 
 [473] "Lysobacter solisilvae"                                  
 [474] "Stenotrophomonas maltophilia"                           
 [475] "Dyella sp. BiH032"                                      
 [476] "Tahibacter amnicola"                                    
 [477] "Vibrio cholerae"                                        
 [478] "Coxiella endosymbiont of Amblyomma nuttalli"            
 [479] "Acinetobacter baumannii"                                
 [480] "Glaesserella parasuis"                                  
 [481] "Wenzhouxiangella marina"                                
 [482] "Cardiobacterium hominis"                                
 [483] "Cardiobacterium sp. Marseille-Q4385"                    
 [484] "Salinisphaera sp. LB1"                                  
 [485] "Rhizobium leguminosarum"                                
 [486] "Agrobacterium tumefaciens"                              
 [487] "Pararhizobium sp. YC-54"                                
 [488] "Sinorhizobium fredii"                                   
 [489] "Ensifer adhaerens"                                      
 [490] "Ciceribacter thiooxidans"                               
 [491] "Bradyrhizobium sp. WD16"                                
 [492] "Bradyrhizobium diazoefficiens"                          
 [493] "Rhodopseudomonas palustris"                             
 [494] "Variibacter gotjawalensis"                              
 [495] "Chelativorans sp. AA-79"                                
 [496] "Methylorubrum extorquens"                               
 [497] "Pelagibacterium sp. YIM 151497"                         
 [498] "Stappia indica"                                         
 [499] "Bosea vaviloviae"                                       
 [500] "Beijerinckia indica"                                    
 [501] "Sphingomonas insulae"                                   
 [502] "Rhodobacter capsulatus"                                 
 [503] "Cereibacter azotoformans"                               
 [504] "Thioclava nitratireducens"                              
 [505] "Alloyangia pacifica"                                    
 [506] "Roseomonas sp. OT10"                                    
 [507] "Azospirillum brasilense"                                
 [508] "Azospirillum sp. B510"                                  
 [509] "Hypericibacter adhaerens"                               
 [510] "Brevundimonas sp. AJA228-03"                            
 [511] "Caulobacter segnis"                                     
 [512] "Phenylobacterium sp. LH3H17"                            
 [513] "Burkholderia multivorans"                               
 [514] "Burkholderia oklahomensis"                              
 [515] "Paraburkholderia sabiae"                                
 [516] "Paraburkholderia bryophila"                             
 [517] "Cupriavidus pauculus"                                   
 [518] "Cupriavidus campinensis"                                
 [519] "Ephemeroptericola cinctiostellae"                       
 [520] "Duodenibacillus massiliensis"                           
 [521] "Sutterella faecalis"                                    
 [522] "Sutterella wadsworthensis"                              
 [523] "Sutterella megalosphaeroides"                           
 [524] "Variovorax paradoxus"                                   
 [525] "Ramlibacter tataouinensis"                              
 [526] "Telluria mixta"                                         
 [527] "Achromobacter xylosoxidans"                             
 [528] "Pigmentiphaga sp. H8"                                   
 [529] "Rubrivivax gelatinosus"                                 
 [530] "Rhizobacter sp. AJA081-3"                               
 [531] "Crenobacter cavernae"                                   
 [532] "Azoarcus olearius"                                      
 [533] "Parazoarcus communis"                                   
 [534] "Azospira restricta"                                     
 [535] "Niveibacterium microcysteis"                            
 [536] "Ferribacterium limneticum"                              
 [537] "Casimicrobium huifangae"                                
 [538] "Desulfovibrio piger"                                    
 [539] "Desulfovibrio fairfieldensis"                           
 [540] "Candidatus Desulfovibrio trichonymphae"                 
 [541] "Desulfovibrio desulfuricans"                            
 [542] "Desulfovibrio vulgaris"                                 
 [543] "Maridesulfovibrio hydrothermalis"                       
 [544] "Oleidesulfovibrio alaskensis"                           
 [545] "Salidesulfovibrio onnuriiensis"                         
 [546] "Thermodesulfomicrobium sp. WS"                          
 [547] "Geomonas sp. RF6"                                       
 [548] "Geotalea uraniireducens"                                
 [549] "Desulfosarcina alkanivorans"                            
 [550] "Desulfosarcina ovata"                                   
 [551] "Desulfobulbus propionicus"                              
 [552] "Chlamydia suis"                                         
 [553] "Luteolibacter ambystomatis"                             
 [554] "Akkermansia glycaniphila"                               
 [555] "Lacunisphaera limnophila"                               
 [556] "Ereboglobus luteus"                                     
 [557] "Tichowtungia aerotolerans"                              
 [558] "Archangium violaceum"                                   
 [559] "Anaeromyxobacter paludicola"                            
 [560] "Anaeromyxobacter sp. Fw109-5"                           
 [561] "Sorangium cellulosum"                                   
 [562] "Polyangium aurulentum"                                  
 [563] "Labilithrix luteola"                                    
 [564] "Haliangium ochraceum"                                   
 [565] "Nannocystis poenicansa"                                 
 [566] "Granulicella sp. 5B5"                                   
 [567] "Terriglobus roseus"                                     
 [568] "Geothrix sp. PMB-07"                                    
 [569] "Chloracidobacterium aggregatum"                         
 [570] "Cloacibacillus porcorum"                                
 [571] "Fretibacterium fastidiosum"                             
 [572] "Pyramidobacter piscolens"                               
 [573] "Treponema denticola"                                    
 [574] "Nitrospira japonica"                                    
 [575] "Persicimonas caeni"                                     
 [576] "Porcine astrovirus 4"                                   
 [577] "Astrovirus wild boar/WBAstV-1/2011/HUN"                 
 [578] "Teschovirus A"                                          
 [579] "Burzaovirus coli"                                       
 [580] "Lactobacillus sp. ESL0680"                              
 [581] "Lactobacillus sp. IBH004"                               
 [582] "Lactobacillus sp. PV034"                                
 [583] "Lactobacillus sp. AMBV1719"                             
 [584] "Lactobacillus sp. ESL0681"                              
 [585] "Lactobacillus sp. ESL0677"                              
 [586] "Lactobacillus sp. 3B(2020)"                             
 [587] "Lactobacillus ultunensis"                               
 [588] "Lactobacillus jensenii"                                 
 [589] "Lactobacillus kullabergensis"                           
 [590] "Lactobacillus panisapium"                               
 [591] "Lactobacillus apis"                                     
 [592] "Lactobacillus paragasseri"                              
 [593] "Lactobacillus terrae"                                   
 [594] "Limosilactobacillus vaginalis"                          
 [595] "Limosilactobacillus portuensis"                         
 [596] "Limosilactobacillus oris"                               
 [597] "Ligilactobacillus agilis"                               
 [598] "Ligilactobacillus murinus"                              
 [599] "Lactiplantibacillus paraplantarum"                      
 [600] "Lactiplantibacillus pentosus"                           
 [601] "Lacticaseibacillus rhamnosus"                           
 [602] "Lacticaseibacillus manihotivorans"                      
 [603] "Lacticaseibacillus sp. KACC 23028"                      
 [604] "Leuconostoc mesenteroides"                              
 [605] "Leuconostoc kimchii"                                    
 [606] "Leuconostoc sp. LN180020"                               
 [607] "Leuconostoc citreum"                                    
 [608] "Latilactobacillus curvatus"                             
 [609] "Latilactobacillus sakei"                                
 [610] "Pediococcus acidilactici"                               
 [611] "Pediococcus claussenii"                                 
 [612] "Lentilactobacillus buchneri"                            
 [613] "Lentilactobacillus laojiaonis"                          
 [614] "Lentilactobacillus curieae"                             
 [615] "Weissella cibaria"                                      
 [616] "Weissella confusa"                                      
 [617] "Bombilactobacillus bombi"                               
 [618] "Bombilactobacillus folatiphilus"                        
 [619] "Bombilactobacillus thymidiniphilus"                     
 [620] "Schleiferilactobacillus harbinensis"                    
 [621] "Fructilactobacillus lindneri"                           
 [622] "Acetilactobacillus jinshanensis"                        
 [623] "Periweissella cryptocerci"                              
 [624] "Carnobacterium maltaromaticum"                          
 [625] "Dolosigranulum pigrum"                                  
 [626] "Streptococcus alactolyticus"                            
 [627] "Streptococcus pyogenes"                                 
 [628] "Streptococcus infantis"                                 
 [629] "Streptococcus constellatus"                             
 [630] "Streptococcus dysgalactiae"                             
 [631] "Streptococcus pneumoniae"                               
 [632] "Streptococcus mutans"                                   
 [633] "Streptococcus equinus"                                  
 [634] "Streptococcus sobrinus"                                 
 [635] "Streptococcus mitis"                                    
 [636] "Lactococcus cremoris"                                   
 [637] "Lactococcus garvieae"                                   
 [638] "Enterococcus hirae"                                     
 [639] "Tetragenococcus halophilus"                             
 [640] "Tetragenococcus osmophilus"                             
 [641] "Aerococcus urinaehominis"                               
 [642] "Aerococcus christensenii"                               
 [643] "Aerococcus urinae"                                      
 [644] "Fundicoccus culcitae"                                   
 [645] "Ignavigranum ruoffiae"                                  
 [646] "Bacillus halotolerans"                                  
 [647] "Bacillus paranthracis"                                  
 [648] "Bacillus mycoides"                                      
 [649] "Bacillus wiedmannii"                                    
 [650] "Bacillus sp. Y1"                                        
 [651] "Bacillus sp. CMF21"                                     
 [652] "Bacillus sp. Lzh-5"                                     
 [653] "Bacillus carboniphilus"                                 
 [654] "Lysinibacillus sp. 2017"                                
 [655] "Lysinibacillus timonensis"                              
 [656] "Virgibacillus sp. MSP4-1"                               
 [657] "Virgibacillus halodenitrificans"                        
 [658] "Cytobacillus oceanisediminis"                           
 [659] "Peribacillus frigoritolerans"                           
 [660] "Geobacillus stearothermophilus"                         
 [661] "Lentibacillus sp. CBA3610"                              
 [662] "Staphylococcus roterodami"                              
 [663] "Staphylococcus simulans"                                
 [664] "Staphylococcus nepalensis"                              
 [665] "Staphylococcus sp. IVB6240"                             
 [666] "Staphylococcus argenteus"                               
 [667] "Jeotgalicoccus sp. ATCC 8456"                           
 [668] "Nosocomiicoccus ampullae"                               
 [669] "Paenibacillus physcomitrellae"                          
 [670] "Paenibacillus psychroresistens"                         
 [671] "Brevibacillus sp. NSP2.1"                               
 [672] "Brevibacillus sp. DP1.3A"                               
 [673] "Cohnella abietis"                                       
 [674] "Sporosarcina sp. Marseille-Q4943"                       
 [675] "Solibacillus silvestris"                                
 [676] "Solibacillus sp. R5-41"                                 
 [677] "Planococcus sp. MB-3u-03"                               
 [678] "Ureibacillus thermophilus"                              
 [679] "Listeria monocytogenes"                                 
 [680] "Listeria innocua"                                       
 [681] "Brochothrix thermosphacta"                              
 [682] "Kyrpidia spormannii"                                    
 [683] "Exiguobacterium sibiricum"                              
 [684] "Gemella sp. zg-570"                                     
 [685] "Blautia argi"                                           
 [686] "Blautia massiliensis (ex Durand et al. 2017)"           
 [687] "[Ruminococcus] torques"                                 
 [688] "Anaeropeptidivorans aminofermentans"                    
 [689] "Anaerotignum propionicum"                               
 [690] "Sellimonas intestinalis"                                
 [691] "Kineothrix sp. MB12-C1"                                 
 [692] "Claveliimonas bilis"                                    
 [693] "Ruminococcus sp. SR1/5"                                 
 [694] "Caproicibacterium sp. BJN0003"                          
 [695] "Petroclostridium sp. X23"                               
 [696] "Acetivibrio saccincola"                                 
 [697] "Paludicola sp. MB14-C6"                                 
 [698] "Fastidiosipila sanguinis"                               
 [699] "Monoglobus pectinilyticus"                              
 [700] "Clostridium sp. M62/1"                                  
 [701] "Clostridium bornimense"                                 
 [702] "Clostridium baratii"                                    
 [703] "Clostridium acetobutylicum"                             
 [704] "Clostridium manihotivorum"                              
 [705] "Clostridium isatidis"                                   
 [706] "Clostridium taeniosporum"                               
 [707] "Clostridium chauvoei"                                   
 [708] "Hungatella xylanolytica"                                
 [709] "Eubacterium ventriosum"                                 
 [710] "Eubacterium sp. MSJ-33"                                 
 [711] "Eubacterium hominis"                                    
 [712] "Romboutsia sp. 13368"                                   
 [713] "Desulforamulus ruminis"                                 
 [714] "Desulforamulus ferrireducens"                           
 [715] "Candidatus Formimonas warabiya"                         
 [716] "Petrocella atlantisensis"                               
 [717] "Heliorestis convoluta"                                  
 [718] "Desulfoscipio gibsoniae"                                
 [719] "Biomaibacter acetigenes"                                
 [720] "Catenibacterium sp. co_0103"                            
 [721] "Thomasclavelia ramosa"                                  
 [722] "Erysipelothrix larvae"                                  
 [723] "Erysipelothrix rhusiopathiae"                           
 [724] "Anaerococcus prevotii"                                  
 [725] "Peptoniphilus equinus"                                  
 [726] "Miniphocaeibacter halophilus"                           
 [727] "Finegoldia magna"                                       
 [728] "Schnuerera ultunensis"                                  
 [729] "Ezakiella coagulans"                                    
 [730] "Limnochorda pilosa"                                     
 [731] "Arthrobacter woluwensis"                                
 [732] "Corynebacterium maris"                                  
 [733] "Corynebacterium camporealensis"                         
 [734] "Corynebacterium diphtheriae"                            
 [735] "Mycobacterium sp. SMC-4"                                
 [736] "Mycobacterium tuberculosis"                             
 [737] "Streptomyces sp. HUAS CX7"                              
 [738] "Actinomyces sp. zg-332"                                 
 [739] "Thermomonospora curvata"                                
 [740] "Blastococcus saxobsidens"                               
 [741] "Egicoccus halophilus"                                   
 [742] "Euzebya pacifica"                                       
 [743] "Conexibacter sp. DBS9H8"                                
 [744] "Anaerolinea thermophila"                                
 [745] "Pelolinea submarina"                                    
 [746] "Phototrophicus methaneseepsis"                          
 [747] "Candidatus Promineofilum breve"                         
 [748] "Crinalium epipsammum"                                   
 [749] "[Phormidium] sp. ETS-05"                                
 [750] "Pseudanabaena galeata"                                  
 [751] "Mycoplasmopsis phocirhinis"                             
 [752] "Mycoplasmopsis felis"                                   
 [753] "Candidatus Mycoplasma mahonii"                          
 [754] "Mycoplasma sp. (ex Biomphalaria glabrata)"              
 [755] "Paulownia witches'-broom phytoplasma"                   
 [756] "Thermus caldilimi"                                      
 [757] "Oceanithermus profundus"                                
 [758] "Deinococcus proteolyticus"                              
 [759] "Truepera radiovictrix"                                  
 [760] "Fimbriimonas ginsengisoli"                              
 [761] "Capsulimonas corticalis"                                
 [762] "Actinobacillus porcitonsillarum"                        
 [763] "Moraxella osloensis"                                    
 [764] "Lidleunavirus Ldl1"                                     
 [765] "Lidleunavirus ViSo2018a"                                
 [766] "Lactobacillus phage phiAQ113"                           
 [767] "Cequinquevirus c5"                                      
 [768] "Mamastrovirus 2"                                        
 [769] "Limosilactobacillus pontis"                             
 [770] "Limosilactobacillus panis"                              
 [771] "Limosilactobacillus gastricus"                          
 [772] "Ligilactobacillus sp. BD7642"                           
 [773] "Leuconostoc lactis"                                     
 [774] "Fructilactobacillus sanfranciscensis"                   
 [775] "Companilactobacillus ginsenosidimutans"                 
 [776] "Liquorilactobacillus hordei"                            
 [777] "Loigolactobacillus bifermentans"                        
 [778] "Furfurilactobacillus rossiae"                           
 [779] "Streptococcus merionis"                                 
 [780] "Streptococcus pluranimalium"                            
 [781] "Streptococcus equi"                                     
 [782] "Streptococcus chenjunshii"                              
 [783] "Streptococcus ratti"                                    
 [784] "Streptococcus parasuis"                                 
 [785] "Streptococcus salivarius"                               
 [786] "Streptococcus parauberis"                               
 [787] "Streptococcus oriscaviae"                               
 [788] "Streptococcus pasteurianus"                             
 [789] "Enterococcus cecorum"                                   
 [790] "Globicatella sanguinis"                                 
 [791] "Bacillus licheniformis"                                 
 [792] "Bacillus vallismortis"                                  
 [793] "Geobacillus subterraneus"                               
 [794] "Mesobacillus jeotgali"                                  
 [795] "Fictibacillus phosphorivorans"                          
 [796] "Pontibacillus chungwhensis"                             
 [797] "Caldalkalibacillus thermarum"                           
 [798] "Paenibacillus sp. PK3_47"                               
 [799] "Paenibacillus sp. FSL R7-0273"                          
 [800] "Paenibacillus sp. C31"                                  
 [801] "Paenibacillus sp. BIHB 4019"                            
 [802] "Paenibacillus sp. IHB B 3084"                           
 [803] "Paenibacillus alvei"                                    
 [804] "Paenibacillus konkukensis"                              
 [805] "Paenibacillus swuensis"                                 
 [806] "Paenibacillus elgii"                                    
 [807] "Cohnella sp. LGH"                                       
 [808] "Aneurinibacillus soli"                                  
 [809] "Planococcus sp. 107-1"                                  
 [810] "Sporolactobacillus terrae"                              
 [811] "Pullulanibacillus sp. KACC 23026"                       
 [812] "Anaerostipes rhamnosivorans"                            
 [813] "Anaerocolumna sp. AGMB13025"                            
 [814] "Anaerocolumna sp. MB42-C2"                              
 [815] "Anaerocolumna chitinilytica"                            
 [816] "Anaerocolumna sedimenticola"                            
 [817] "Lacrimispora sphenoides"                                
 [818] "[Clostridium] colinum"                                  
 [819] "Anaeromicropila herbilytica"                            
 [820] "Acetivibrio clariflavus"                                
 [821] "Mageeibacillus indolicus"                               
 [822] "Pseudoclostridium thermosuccinogenes"                   
 [823] "Thermoclostridium stercorarium"                         
 [824] "Clostridium sp. 'deep sea'"                             
 [825] "Clostridium sp. BJN0001"                                
 [826] "Clostridium sp. BNL1100"                                
 [827] "Clostridium sp. DL-VIII"                                
 [828] "Clostridium kluyveri"                                   
 [829] "Clostridium cadaveris"                                  
 [830] "Clostridium pasteurianum"                               
 [831] "Clostridium cellulovorans"                              
 [832] "Clostridium diolis"                                     
 [833] "Clostridium estertheticum"                              
 [834] "Clostridium tyrobutyricum"                              
 [835] "Clostridium aceticum"                                   
 [836] "Clostridium felsineum"                                  
 [837] "Caloramator sp. Dgby_cultured_2"                        
 [838] "Geosporobacter ferrireducens"                           
 [839] "Oceanirhabdus sp. W0125-5"                              
 [840] "Aminipila butyrica"                                     
 [841] "Aminipila terrae"                                       
 [842] "Mogibacterium neglectum"                                
 [843] "Carboxydocella thermautotrophica"                       
 [844] "Eubacterium callanderi"                                 
 [845] "Acetobacterium woodii"                                  
 [846] "Alkalibacter rhizosphaerae"                             
 [847] "Terrisporobacter hibernicus"                            
 [848] "Terrisporobacter mayombei"                              
 [849] "Peptacetobacter hiranonis"                              
 [850] "Vallitalea pronyensis"                                  
 [851] "Cellulosilyticum sp. WCF-2"                             
 [852] "Heliomicrobium modesticaldum"                           
 [853] "Syntrophomonas wolfei"                                  
 [854] "Thermoanaerobacter italicus"                            
 [855] "Ammonifex degensii"                                     
 [856] "Anoxybacter fermentans"                                 
 [857] "Moorella thermoacetica"                                 
 [858] "Thomasclavelia spiroformis"                             
 [859] "Longicatena caecimuris"                                 
 [860] "Allocoprobacillus halotolerans"                         
 [861] "Faecalibacillus intestinalis"                           
 [862] "Peptoniphilus ivorii"                                   
 [863] "Gottschalkia acidurici"                                 
 [864] "Acidilutibacter cellobiosedens"                         
 [865] "endosymbiont 'TC1' of Trimyema compressum"              
 [866] "Arthrobacter sp. Y-9"                                   
 [867] "Microbacterium sediminis"                               
 [868] "Leucobacter triazinivorans"                             
 [869] "Agrococcus carbonis"                                    
 [870] "Microterricola viridarii"                               
 [871] "Gryllotalpicola protaetiae"                             
 [872] "Brachybacterium saurashtrense"                          
 [873] "Brachybacterium huguangmaarense"                        
 [874] "Serinicoccus chungangensis"                             
 [875] "Streptomyces sp. Tu 2975"                               
 [876] "Streptomyces sp. AM2-3-1"                               
 [877] "Streptomyces sp. BPTC-684"                              
 [878] "Streptomyces sp. MBT27"                                 
 [879] "Streptomyces sp. MA3_2.13"                              
 [880] "Streptomyces sp. C8S0"                                  
 [881] "Streptomyces venezuelae"                                
 [882] "Streptomyces tsukubensis"                               
 [883] "Streptomyces incarnatus"                                
 [884] "Mycobacterium sp. MS1601"                               
 [885] "Corynebacterium poyangense"                             
 [886] "Corynebacterium glutamicum"                             
 [887] "Corynebacterium guangdongense"                          
 [888] "Rhodococcus erythropolis"                               
 [889] "Rhodococcus opacus"                                     
 [890] "Nocardia sp. PE-7"                                      
 [891] "Bifidobacterium animalis"                               
 [892] "Bifidobacterium subtile"                                
 [893] "Bifidobacterium pseudolongum"                           
 [894] "Bifidobacterium asteroides"                             
 [895] "Bifidobacterium scardovii"                              
 [896] "Bifidobacterium bifidum"                                
 [897] "Parascardovia denticolens"                              
 [898] "Acidipropionibacterium acidipropionici"                 
 [899] "Amycolatopsis sp. 2-15"                                 
 [900] "Amycolatopsis sp. EV170708-02-1"                        
 [901] "Saccharopolyspora gloriosae"                            
 [902] "Saccharopolyspora erythraea"                            
 [903] "Kutzneria chonburiensis"                                
 [904] "Saccharothrix sp. 6-C"                                  
 [905] "Micromonospora maris"                                   
 [906] "Actinomyces israelii"                                   
 [907] "Trueperella pecoris"                                    
 [908] "Nocardiopsis akebiae"                                   
 [909] "Streptomonospora litoralis"                             
 [910] "Streptosporangium roseum"                               
 [911] "Stackebrandtia nassauensis"                             
 [912] "Lancefieldella sp. Marseille-Q7238"                     
 [913] "Lancefieldella parvula"                                 
 [914] "Leptogranulimonas caecicola"                            
 [915] "Collinsella sp. zg1085"                                 
 [916] "Coriobacterium glomerans"                               
 [917] "Adlercreutzia hattorii"                                 
 [918] "Adlercreutzia equolifaciens"                            
 [919] "Gordonibacter urolithinfaciens"                         
 [920] "Gordonibacter pamelaeae"                                
 [921] "Raoultibacter timonensis"                               
 [922] "Denitrobacterium detoxificans"                          
 [923] "Phoenicibacter congonensis"                             
 [924] "Rubrobacter tropicus"                                   
 [925] "Acidimicrobium ferrooxidans"                            
 [926] "Moorena producens"                                      
 [927] "Synechococcus sp. Minos11"                              
 [928] "Trichothermofontia sichuanensis"                        
 [929] "Calothrix sp. PCC 7507"                                 
 [930] "Anthocerotibacter panamensis"                           
 [931] "Ktedonosporobacter rubrisoli"                           
 [932] "Thermoflexus hugenholtzii"                              
 [933] "Ureaplasma diversum"                                    
 [934] "Spiroplasma ixodetis"                                   
 [935] "Alteracholeplasma palmae"                               
 [936] "Metamycoplasma hominis"                                 
 [937] "Mycoplasmoides fastidiosum"                             
 [938] "Deinococcus gobiensis"                                  
 [939] "Thermus thermophilus"                                   
 [940] "Thermus oshimai"                                        
 [941] "Allomeiothermus silvanus"                               
 [942] "Sphaerobacter thermophilus"                             
 [943] "Bacteroides sp. CACC 737"                               
 [944] "Bacteroides sp. M10"                                    
 [945] "Bacteroides sp. D2"                                     
 [946] "Alistipes shahii"                                       
 [947] "Alistipes indistinctus"                                 
 [948] "Parabacteroides faecis"                                 
 [949] "Porphyromonas asaccharolytica"                          
 [950] "Porphyromonas crevioricanis"                            
 [951] "Porphyromonas endodontalis"                             
 [952] "Butyricimonas virosa"                                   
 [953] "Odoribacter splanchnicus"                               
 [954] "Proteiniphilum propionicum"                             
 [955] "Proteiniphilum saccharofermentans"                      
 [956] "Coprobacter fastidiosus"                                
 [957] "Alkaliflexus sp. Ai-910"                                
 [958] "Alkalitalea saponilacus"                                
 [959] "Croceibacter atlanticus"                                
 [960] "Candidatus Ornithobacterium hominis"                    
 [961] "Candidatus Karelsulcia muelleri"                        
 [962] "Hymenobacter sp. YIM 151500-1"                          
 [963] "Hymenobacter sp. DG25B"                                 
 [964] "Hymenobacter sp. YIM 151858-1"                          
 [965] "Pontibacter sp. XAAS-72"                                
 [966] "Chondrinema litorale"                                   
 [967] "Anseongella ginsenosidimutans"                          
 [968] "Longitalea sp. SCSIO 12813"                             
 [969] "Rhodocaloribacter litoris"                              
 [970] "Fibrobacter succinogenes"                               
 [971] "secondary endosymbiont of Trabutina mannipara"          
 [972] "Klebsiella aerogenes"                                   
 [973] "Litorivicinus lipolyticus"                              
 [974] "Vibrio parahaemolyticus"                                
 [975] "Vibrio sp. THAF191c"                                    
 [976] "Photobacterium sp. TY1-4"                               
 [977] "Bibersteinia trehalosi"                                 
 [978] "Rhizobium gallicum"                                     
 [979] "Aquibium oceanicum"                                     
 [980] "Rhodoplanes sp. Z2-YC6860"                              
 [981] "Parvibaculum lavamentivorans"                           
 [982] "Porphyrobacter sp. YT40"                                
 [983] "Salipiger sp. CCB-MM3"                                  
 [984] "Asaia bogorensis"                                       
 [985] "Comamonas aquatica"                                     
 [986] "Oxalobacter aliiformigenes"                             
 [987] "Sterolibacterium denitrificans"                         
 [988] "Campylobacter lanienae"                                 
 [989] "Campylobacter jejuni"                                   
 [990] "Campylobacter sp. RM6137"                               
 [991] "Campylobacter coli"                                     
 [992] "Candidatus Campylobacter infans"                        
 [993] "Helicobacter canadensis"                                
 [994] "Helicobacter himalayensis"                              
 [995] "Helicobacter enhydrae"                                  
 [996] "Helicobacter cinaedi"                                   
 [997] "Helicobacter pylori"                                    
 [998] "Treponema peruense"                                     
 [999] "Treponema ruminis"                                      
[1000] "Treponema succinifaciens"                               
[1001] "Treponema parvum"                                       
[1002] "Treponema brennaborense"                                
[1003] "Treponema pedis"                                        
[1004] "Treponema phagedenis"                                   
[1005] "Sphaerochaeta pleomorpha"                               
[1006] "Sphaerochaeta associata"                                
[1007] "Parasphaerochaeta coccoides"                            
[1008] "Gracilinema caldarium"                                  
[1009] "Desulfovibrio sp. G11"                                  
[1010] "Geotalea daltonii"                                      
[1011] "Mariniblastus fucicola"                                 
[1012] "Planctomyces sp. SH-PL62"                               
[1013] "Akkermansia muciniphila"                                
[1014] "Luteolibacter sp. SL250"                                
[1015] "Fontisphaera persica"                                   
[1016] "Mucispirillum schaedleri"                               
[1017] "Sandaracinus amylolyticus"                              
[1018] "Microvenator marinus"                                   
[1019] "Methanobrevibacter sp. YE315"                           
[1020] "Methanosphaera stadtmanae"                              
[1021] "Candidatus Methanomethylophilus alvus"                  
[1022] "Candidatus Methanoplasma termitum"                      
[1023] "Oengusvirus oengus"                                     
[1024] "Cacepaovirus simiae"                                    
[1025] "Lentilactobacillus parabuchneri"                        
[1026] "Loigolactobacillus coryniformis"                        
[1027] "Lapidilactobacillus dextrinicus"                        
[1028] "Streptococcus anginosus"                                
[1029] "Streptococcus lutetiensis"                              
[1030] "Streptococcus gallolyticus"                             
[1031] "Streptococcus macedonicus"                              
[1032] "Streptococcus ruminicola"                               
[1033] "Streptococcus iniae"                                    
[1034] "Desemzia incerta"                                       
[1035] "Bacillus pseudomycoides"                                
[1036] "Bacillus badius"                                        
[1037] "Bacillus shivajii"                                      
[1038] "Bacillus pumilus"                                       
[1039] "Virgibacillus necropolis"                               
[1040] "Cytobacillus firmus"                                    
[1041] "Rossellomorea sp. KS-H15a"                              
[1042] "Parageobacillus caldoxylosilyticus"                     
[1043] "Fictibacillus enclensis"                                
[1044] "Psychrobacillus sp. AK 1817"                            
[1045] "Salisediminibacterium selenitireducens"                 
[1046] "Shouchella clausii"                                     
[1047] "Paenibacillus sp. 19GGS1-52"                            
[1048] "Paenibacillus sp. YPD9-1"                               
[1049] "Paenibacillus sp. JDR-2"                                
[1050] "Paenibacillus borealis"                                 
[1051] "Paenibacillus typhae"                                   
[1052] "Paenibacillus cellulositrophicus"                       
[1053] "Staphylococcus agnetis"                                 
[1054] "Staphylococcus cohnii"                                  
[1055] "Abyssicoccus albus"                                     
[1056] "Planococcus plakortidis"                                
[1057] "Ureibacillus thermosphaericus"                          
[1058] "Jeotgalibacillus malaysiensis"                          
[1059] "Ruminiclostridium herbifermentans"                      
[1060] "Anaerotignum sp. MB30-C6"                               
[1061] "Clostridium intestinale"                                
[1062] "Clostridium gasigenes"                                  
[1063] "Clostridium scatologenes"                               
[1064] "Clostridium sporogenes"                                 
[1065] "Thermaerobacter sp. FW80"                               
[1066] "Fenollaria sporofastidiosus"                            
[1067] "Clostridioides sp. ES-S-0054-01"                        
[1068] "Peptoclostridium acidaminophilum"                       
[1069] "Desulfitobacterium hafniense"                           
[1070] "Desulfosporosinus youngiae"                             
[1071] "Erysipelothrix piscisicarius"                           
[1072] "Tissierella sp. MB52-C2"                                
[1073] "Arthrobacter sp. StoSoilB20"                            
[1074] "Curtobacterium flaccumfaciens"                          
[1075] "Rathayibacter sp. VKM Ac-2804"                          
[1076] "Demequina sp. TMPB413"                                  
[1077] "Janibacter limosus"                                     
[1078] "Corynebacterium ulcerans"                               
[1079] "Corynebacterium confusum"                               
[1080] "Mycolicibacillus koreensis"                             
[1081] "Mycobacteroides immunogenum"                            
[1082] "Mycolicibacter hiberniae"                               
[1083] "Gordonia sp. NB41Y"                                     
[1084] "Gordonia jinghuaiqii"                                   
[1085] "Segniliparus rotundus"                                  
[1086] "Streptomyces sp. KMM 9044"                              
[1087] "Streptomyces sp. 71268"                                 
[1088] "Streptomyces sp. Caat 7-52"                             
[1089] "Streptomyces sp. CB01881"                               
[1090] "Streptomyces sp. WZ-12"                                 
[1091] "Streptomyces sp. QHH-9511"                              
[1092] "Streptomyces collinus"                                  
[1093] "Streptomyces dangxiongensis"                            
[1094] "Streptomyces vietnamensis"                              
[1095] "Streptomyces vilmorinianum"                             
[1096] "Yinghuangia sp. ASG 101"                                
[1097] "Bifidobacterium sp. ESL0775"                            
[1098] "Bifidobacterium lemurum"                                
[1099] "Bifidobacterium dentium"                                
[1100] "Gardnerella leopoldii"                                  
[1101] "Scardovia inopinata"                                    
[1102] "Tessaracoccus palaemonis"                               
[1103] "Tessaracoccus flavescens"                               
[1104] "Tessaracoccus defluvii"                                 
[1105] "Nocardioides sp. BP30"                                  
[1106] "Nocardioides dongkuii"                                  
[1107] "Kribbella sp. CA-293567"                                
[1108] "Micromonospora sp. WMMC415"                             
[1109] "Couchioplanes caeruleus"                                
[1110] "Streptomonospora nanhaiensis"                           
[1111] "Eggerthella sp. YY7918"                                 
[1112] "Berryella wangjianweii"                                 
[1113] "Rubrobacter radiotolerans"                              
[1114] "Rubrobacter marinus"                                    
[1115] "Aquihabitans sp. G128"                                  
[1116] "Chloroflexus aggregans"                                 
[1117] "Spiroplasma endosymbiont of 'Nebria riversi'"           
[1118] "Acholeplasma hippikon"                                  
[1119] "Limnospira indica"                                      
[1120] "Synechococcus sp. PCC 7336"                             
[1121] "Pleurocapsa sp. PCC 7327"                               
[1122] "Deinococcus ficus"                                      
[1123] "Ornithobacterium rhinotracheale"                        
[1124] "Pontibacter russatus"                                   
[1125] "Chryseolinea soli"                                      
[1126] "Providencia huaxiensis"                                 
[1127] "Rouxiella badensis"                                     
[1128] "Pseudomonas marincola"                                  
[1129] "Halomonas sp. I5-271120"                                
[1130] "Halomonas tianxiuensis"                                 
[1131] "Endozoicomonas sp. GU-1"                                
[1132] "Pleionea sp. HL-JVS1"                                   
[1133] "Methylomonas sp. EFPC3"                                 
[1134] "Methylomonas koyamae"                                   
[1135] "Methylococcus sp. EFPC2"                                
[1136] "Agrobacterium fabacearum"                               
[1137] "Shinella sumterensis"                                   
[1138] "Martelella endophytica"                                 
[1139] "Jiella sp. HL-NP1"                                      
[1140] "Rhodomicrobium lacus"                                   
[1141] "Bosea sp. F3-2"                                         
[1142] "Paracoccus sanguinis"                                   
[1143] "Paracoccus albus"                                       
[1144] "Neotabrizicola shimadae"                                
[1145] "Burkholderia ambifaria"                                 
[1146] "Paraburkholderia acidiphila"                            
[1147] "Paraburkholderia tropica"                               
[1148] "Mycoavidus cysteinexigens"                              
[1149] "Pseudoduganella armeniaca"                              
[1150] "Janthinobacterium agaricidamnosum"                      
[1151] "Achromobacter insolitus"                                
[1152] "Aquella oligotrophica"                                  
[1153] "Solidesulfovibrio carbinoliphilus"                      
[1154] "Pseudodesulfovibrio tunisiensis"                        
[1155] "Geobacter sp. DSM 9736"                                 
[1156] "Treponema sp. OMZ 787"                                  
[1157] "Adhaeretor mobilis"                                     
[1158] "Burzaovirus faecalis"                                   
[1159] "Burzaovirus intestinihominis"                           
[1160] "Lactobacillus sp. PV012"                                
[1161] "Limosilactobacillus frumenti"                           
[1162] "Leuconostoc sp. MTCC 10508"                             
[1163] "Pediococcus damnosus"                                   
[1164] "Oenococcus oeni"                                        
[1165] "Levilactobacillus brevis"                               
[1166] "Levilactobacillus suantsaii"                            
[1167] "Levilactobacillus zymae"                                
[1168] "Weissella ceti"                                         
[1169] "Loigolactobacillus backii"                              
[1170] "Companilactobacillus zhachilii"                         
[1171] "Secundilactobacillus malefermentans"                    
[1172] "Paucilactobacillus nenjiangensis"                       
[1173] "Streptococcus porcinus"                                 
[1174] "Streptococcus pseudoporcinus"                           
[1175] "Streptococcus oralis"                                   
[1176] "Lactococcus paracarnosus"                               
[1177] "Lactococcus lactis"                                     
[1178] "Lactococcus allomyrinae"                                
[1179] "Vagococcus fluvialis"                                   
[1180] "Granulicatella elegans"                                 
[1181] "Granulicatella adiacens"                                
[1182] "Jeotgalibaca porci"                                     
[1183] "Aerococcus sanguinicola"                                
[1184] "Suicoccus acidiformans"                                 
[1185] "Bacillus atrophaeus"                                    
[1186] "Bacillus inaquosorum"                                   
[1187] "Bacillus nitratireducens"                               
[1188] "Bacillus sp. KH172YL63"                                 
[1189] "Bacillus sp. FJAT-14266"                                
[1190] "Bacillus methanolicus"                                  
[1191] "Priestia flexa"                                         
[1192] "Priestia aryabhattai"                                   
[1193] "Priestia filamentosa"                                   
[1194] "Heyndrickxia oleronia"                                  
[1195] "Cytobacillus gottheilii"                                
[1196] "Lysinibacillus fusiformis"                              
[1197] "Lysinibacillus agricola"                                
[1198] "Virgibacillus sp. NKC19-16"                             
[1199] "Neobacillus sp. PS2-9"                                  
[1200] "Neobacillus sp. OS1-32"                                 
[1201] "Neobacillus sp. OS1-33"                                 
[1202] "Neobacillus sp. PS3-12"                                 
[1203] "Peribacillus simplex"                                   
[1204] "Peribacillus muralis"                                   
[1205] "Geobacillus sp. 46C-IIa"                                
[1206] "Fictibacillus sp. KU28468"                              
[1207] "Metabacillus sp. cB07"                                  
[1208] "Niallia sp. Man26"                                      
[1209] "Oceanobacillus oncorhynchi"                             
[1210] "Gracilibacillus salitolerans"                           
[1211] "Ectobacillus sp. JY-23"                                 
[1212] "Radiobacillus deserti"                                  
[1213] "Salisediminibacterium beveridgei"                       
[1214] "Siminovitchia fortis"                                   
[1215] "Fervidibacillus albus"                                  
[1216] "Gottfriedia acidiceleris"                               
[1217] "Staphylococcus delphini"                                
[1218] "Staphylococcus sp. NRL 22/194"                          
[1219] "Staphylococcus auricularis"                             
[1220] "Staphylococcus pettenkoferi"                            
[1221] "Staphylococcus hominis"                                 
[1222] "Staphylococcus lugdunensis"                             
[1223] "Staphylococcus haemolyticus"                            
[1224] "Mammaliicoccus sciuri"                                  
[1225] "Salinicoccus halodurans"                                
[1226] "Paenibacillus sp. G2S3"                                 
[1227] "Paenibacillus sp. JZ16"                                 
[1228] "Paenibacillus sp. SYP-B4298"                            
[1229] "Paenibacillus sp. H1-7"                                 
[1230] "Paenibacillus sp. D2_2"                                 
[1231] "Paenibacillus riograndensis"                            
[1232] "Paenibacillus guangzhouensis"                           
[1233] "Paenibacillus sabinae"                                  
[1234] "Paenibacillus albus"                                    
[1235] "Paenibacillus tianjinensis"                             
[1236] "Paenibacillus andongensis"                              
[1237] "Paenibacillus lautus"                                   
[1238] "Paenibacillus larvae"                                   
[1239] "Paenibacillus naphthalenovorans"                        
[1240] "Aneurinibacillus sp. B1"                                
[1241] "Aneurinibacillus sp. Ricciae_BoGa-3"                    
[1242] "Cohnella cholangitidis"                                 
[1243] "Alicyclobacillus sp. SO9"                               
[1244] "Alicyclobacillus sp. ALC3"                              
[1245] "Sporosarcina sp. Marseille-Q4063"                       
[1246] "Sporosarcina ureae"                                     
[1247] "Sporosarcina thermotolerans"                            
[1248] "Planococcus maritimus"                                  
[1249] "Planococcus halotolerans"                               
[1250] "Kurthia sp. YJT4"                                       
[1251] "Rummeliibacillus stabekisii"                            
[1252] "Kroppenstedtia eburnea"                                 
[1253] "Ruminiclostridium cellulolyticum"                       
[1254] "Ruminiclostridium papyrosolvens"                        
[1255] "Clostridium sp. C1"                                     
[1256] "Clostridium sp. OS1-26"                                 
[1257] "Clostridium sp. JN-1"                                   
[1258] "Clostridium butyricum"                                  
[1259] "Clostridium fermenticellae"                             
[1260] "Clostridium thermarum"                                  
[1261] "Clostridium argentinense"                               
[1262] "Clostridium saccharoperbutylacetonicum"                 
[1263] "Clostridium saccharobutylicum"                          
[1264] "Clostridium tagluense"                                  
[1265] "Clostridium drakei"                                     
[1266] "Crassaminicella thermophila"                            
[1267] "Crassaminicella indica"                                 
[1268] "Caloramator sp. E03"                                    
[1269] "Caloramator sp. mosi_1"                                 
[1270] "Alkaliphilus sp. B6464"                                 
[1271] "Caminicella sporogenes"                                 
[1272] "Mogibacterium diversum"                                 
[1273] "Mogibacterium pumilum"                                  
[1274] "Thermaerobacter marianensis"                            
[1275] "Acetobacterium sp. KB-1"                                
[1276] "Paeniclostridium sordellii"                             
[1277] "Filifactor alocis"                                      
[1278] "Acetoanaerobium sticklandii"                            
[1279] "Peptostreptococcus sp. CBA3647"                         
[1280] "Dehalobacter restrictus"                                
[1281] "Desulfofarcimen acetoxidans"                            
[1282] "Caldanaerobacter subterraneus"                          
[1283] "Thermoanaerobacterium sp. RBIITD"                       
[1284] "Thermoanaerobacterium xylanolyticum"                    
[1285] "Thermoanaerobacter kivui"                               
[1286] "Thermacetogenium phaeum"                                
[1287] "Carboxydothermus hydrogenoformans"                      
[1288] "Mahella australiensis"                                  
[1289] "Halanaerobium hydrogeniformans"                         
[1290] "Halothermothrix orenii"                                 
[1291] "Moorella sp. Hama-1"                                    
[1292] "Zhaonella formicivorans"                                
[1293] "Thermosediminibacter oceani"                            
[1294] "Koleobacter methoxysyntrophicus"                        
[1295] "Erysipelothrix sp. HDW6B"                               
[1296] "Tannockella kyphosi"                                    
[1297] "Anaerococcus mediterraneensis"                          
[1298] "Peptoniphilus sp. SAHP1"                                
[1299] "Parvimonas micra"                                       
[1300] "Gudongella oleilytica"                                  
[1301] "Sedimentibacter sp. MB35-C1"                            
[1302] "Arthrobacter sp. U41"                                   
[1303] "Arthrobacter sp. StoSoilB5"                             
[1304] "Kocuria rosea"                                          
[1305] "Kocuria turfanensis"                                    
[1306] "Microbacterium amylolyticum"                            
[1307] "Leucobacter muris"                                      
[1308] "Cryobacterium sp. SO2"                                  
[1309] "Cryobacterium soli"                                     
[1310] "Rathayibacter festucae"                                 
[1311] "Glaciibacter superstes"                                 
[1312] "Brevibacterium aurantiacum"                             
[1313] "Janibacter sp. CX7"                                     
[1314] "Mycobacterium sp. JS623"                                
[1315] "Mycobacterium avium"                                    
[1316] "Mycobacterium colombiense"                              
[1317] "Mycobacterium kubicae"                                  
[1318] "Mycobacterium lacus"                                    
[1319] "Mycolicibacterium sediminis"                            
[1320] "Mycobacteroides salmoniphilum"                          
[1321] "Corynebacterium zhongnanshanii"                         
[1322] "Corynebacterium ciconiae"                               
[1323] "Corynebacterium liangguodongii"                         
[1324] "Corynebacterium imitans"                                
[1325] "Corynebacterium vitaeruminis"                           
[1326] "Corynebacterium ammoniagenes"                           
[1327] "Corynebacterium jeikeium"                               
[1328] "Rhodococcus fascians"                                   
[1329] "Nocardia tengchongensis"                                
[1330] "Nocardia sputorum"                                      
[1331] "Dietzia kunjamensis"                                    
[1332] "Lawsonella clevelandensis"                              
[1333] "Streptomyces sp. AM 4-1-1"                              
[1334] "Streptomyces sp. ITFR-21"                               
[1335] "Streptomyces sp. P3"                                    
[1336] "Streptomyces phaeolivaceus"                             
[1337] "Streptomyces angustmyceticus"                           
[1338] "Streptomyces griseorubiginosus"                         
[1339] "Streptomyces buecherae"                                 
[1340] "Streptomyces luteoverticillatus"                        
[1341] "Streptomyces actuosus"                                  
[1342] "Streptomyces olivoreticuli"                             
[1343] "Streptomyces prasinus"                                  
[1344] "Streptomyces alboflavus"                                
[1345] "Streptomyces mobaraensis"                               
[1346] "Peterkaempfera bronchialis"                             
[1347] "Actinacidiphila bryophytorum"                           
[1348] "Cutibacterium sp. CBA3108"                              
[1349] "Propioniciclava sp. MC1595"                             
[1350] "Nocardioides sp. HDW12B"                                
[1351] "Friedmanniella luteola"                                 
[1352] "Actinopolymorpha singaporensis"                         
[1353] "Bifidobacterium pullorum"                               
[1354] "Bifidobacterium catenulatum"                            
[1355] "Actinomyces procaprae"                                  
[1356] "Schaalia sp. JY-X169"                                   
[1357] "Amycolatopsis sp. WQ 127309"                            
[1358] "Amycolatopsis acidiphila"                               
[1359] "Saccharopolyspora rosea"                                
[1360] "Kutzneria albida"                                       
[1361] "Kibdelosporangium phytohabitans"                        
[1362] "Allokutzneria albata"                                   
[1363] "Verrucosispora sp. WMMD1129"                            
[1364] "Actinoplanes sp. L3-i22"                                
[1365] "Actinoplanes sp. NRRL 3884"                             
[1366] "Dactylosporangium aurantiacum"                          
[1367] "Thermobispora bispora"                                  
[1368] "Nocardiopsis gilva"                                     
[1369] "Blastococcus sp. PRF04-17"                              
[1370] "Modestobacter marinus"                                  
[1371] "Geodermatophilus obscurus"                              
[1372] "Actinopolyspora erythraea"                              
[1373] "Mycoplasma capricolum"                                  
[1374] "Mycoplasma phocoenae"                                   
[1375] "Mycoplasmopsis bovis"                                   
[1376] "Mycoplasmopsis meleagridis"                             
[1377] "Candidatus Hepatoplasma crinochetorum"                  
[1378] "Spiroplasma platyhelix"                                 
[1379] "Mesoplasma syrphidae"                                   
[1380] "Haploplasma axanthum"                                   
[1381] "Hujiaoplasma nucleasis"                                 
[1382] "Nostoc flagelliforme"                                   
[1383] "Calothrix sp. NIES-3974"                                
[1384] "Sphaerospermopsis torques-reginae"                      
[1385] "Geminocystis herdmanii"                                 
[1386] "Leptolyngbya sp. 7M"                                    
[1387] "Leptolyngbya sp. BL0902"                                
[1388] "Leptolyngbya boryana"                                   
[1389] "Halomicronema hongdechloris"                            
[1390] "Synechococcus sp. CC9902"                               
[1391] "Synechococcus elongatus"                                
[1392] "Chroococcidiopsis sp. CCMEE 29"                         
[1393] "Thermobaculum terrenum"                                 
[1394] "Deinococcus sp. NW-56"                                  
[1395] "Deinococcus aetherius"                                  
[1396] "Chthonomonas calidirosea"                               
[1397] "Bacteroides luhongzhouii"                               
[1398] "Coprobacter secundus"                                   
[1399] "Porphyromonas somerae"                                  
[1400] "Candidatus Azobacteroides pseudotrichonymphae"          
[1401] "Maribellus comscasis"                                   
[1402] "Labilibaculum antarcticum"                              
[1403] "Flavobacterium sp. CC-SYL302"                           
[1404] "Flavobacterium limnophilum"                             
[1405] "Nonlabens marinus"                                      
[1406] "Nonlabens spongiae"                                     
[1407] "Allomuricauda lutaonensis"                              
[1408] "Allomuricauda aurantiaca"                               
[1409] "Muriicola soli"                                         
[1410] "Kordia antarctica"                                      
[1411] "Chryseobacterium sp. LJ668"                             
[1412] "Chryseobacterium indologenes"                           
[1413] "Chryseobacterium suipulveris"                           
[1414] "Riemerella anatipestifer"                               
[1415] "Hymenobacter nivis"                                     
[1416] "Hymenobacter yonginensis"                               
[1417] "Hymenobacter busanensis"                                
[1418] "Hymenobacter psoromatis"                                
[1419] "Hymenobacter aerilatus"                                 
[1420] "Hymenobacter tibetensis"                                
[1421] "Pontibacter sp. G13"                                    
[1422] "Algoriphagus sp. Y33"                                   
[1423] "Algoriphagus machipongonensis"                          
[1424] "Aquiflexum balticum"                                    
[1425] "Belliella baltica"                                      
[1426] "Spirosoma taeanense"                                    
[1427] "Spirosoma rigui"                                        
[1428] "Cytophaga hutchinsonii"                                 
[1429] "Rhodocytophaga rosea"                                   
[1430] "Tellurirhabdus rosea"                                   
[1431] "Leadbetterella byssophila"                              
[1432] "Fibrella sp. ES10-3-2-2"                                
[1433] "Sphingobacterium spiritivorum"                          
[1434] "Mucilaginibacter daejeonensis"                          
[1435] "Mucilaginibacter ginsenosidivorans"                     
[1436] "Chitinophaga sp. XS-30"                                 
[1437] "Chitinophaga oryzae"                                    
[1438] "Chitinophaga alhagiae"                                  
[1439] "Ferruginibacter lapsinanis"                             
[1440] "Flavisolibacter ginsenosidimutans"                      
[1441] "Lacibacter sp. S13-6-22"                                
[1442] "Haliscomenobacter hydrossis"                            
[1443] "Candidatus Sulfidibacterium hydrothermale"              
[1444] "Prosthecochloris aestuarii"                             
[1445] "Escherichia marmotae"                                   
[1446] "Escherichia fergusonii"                                 
[1447] "Klebsiella quasipneumoniae"                             
[1448] "Salmonella sp."                                         
[1449] "Enterobacter cancerogenus"                              
[1450] "Enterobacter bugandensis"                               
[1451] "Citrobacter portucalensis"                              
[1452] "Citrobacter sp. S171"                                   
[1453] "Shigella dysenteriae"                                   
[1454] "Shigella boydii"                                        
[1455] "Shigella sonnei"                                        
[1456] "Enterobacteriaceae endosymbiont of Donacia versicolorea"
[1457] "Leclercia adecarboxylata"                               
[1458] "Candidatus Riesia pediculicola"                         
[1459] "Pseudocitrobacter corydidari"                           
[1460] "Yersinia entomophaga"                                   
[1461] "Proteus mirabilis"                                      
[1462] "Pantoea sp. X85"                                        
[1463] "Pantoea dispersa"                                       
[1464] "Erwinia tracheiphila"                                   
[1465] "Pseudomonas sp. CIP-10"                                 
[1466] "Pseudomonas oryzihabitans"                              
[1467] "Pseudomonas chlororaphis"                               
[1468] "Pseudomonas oryzae"                                     
[1469] "Marinobacter sp. LPB0319"                               
[1470] "Xanthomonas campestris"                                 
[1471] "Aeromonas hydrophila"                                   
[1472] "Pseudoalteromonas sp. SCSIO 43201"                      
[1473] "Halomonas sp. JS92-SW72"                                
[1474] "Marinobacterium rhizophilum"                            
[1475] "Vibrio alginolyticus"                                   
[1476] "Photobacterium damselae"                                
[1477] "Acinetobacter indicus"                                  
[1478] "Guyparkeria halophila"                                  
[1479] "Woeseia oceani"                                         
[1480] "Hydrogenovibrio marinus"                                
[1481] "Piscirickettsia salmonis"                               
[1482] "Francisella tularensis"                                 
[1483] "Legionella pneumophila"                                 
[1484] "Shinella sp. HZN7"                                      
[1485] "Bradyrhizobium sp. CB1650"                              
[1486] "Methylobacterium currus"                                
[1487] "Methylobacterium indicum"                               
[1488] "Xanthobacter dioxanivorans"                             
[1489] "Labrenzia sp. PHM005"                                   
[1490] "Martelella lutilitoris"                                 
[1491] "Methylocapsa sp. D3K7"                                  
[1492] "Sinirhodobacter sp. HNIBRBA609"                         
[1493] "Erythrobacter litoralis"                                
[1494] "Altererythrobacter sp. TH136"                           
[1495] "Komagataeibacter nataicola"                             
[1496] "Acetobacter aceti"                                      
[1497] "Nitrospirillum amazonense"                              
[1498] "Candidatus Phycorickettsia trachydisci"                 
[1499] "Kordiimonas sp. SCSIO 12610"                            
[1500] "Neisseria yangbaofengii"                                
[1501] "Kingella potus"                                         
[1502] "Treponema pallidum"                                     
[1503] "Treponema socranskii"                                   
[1504] "Brucepastera parasyntrophica"                           
[1505] "Sphaerochaeta globosa"                                  
[1506] "Sediminispirochaeta smaragdinae"                        
[1507] "Spirochaeta africana"                                   
[1508] "Spirochaeta thermophila"                                
[1509] "Brachyspira intermedia"                                 
[1510] "Desulfovibrio ferrophilus"                              
[1511] "Desulforapulum autotrophicum"                           
[1512] "Lignipirellula cremea"                                  
[1513] "Aeoliella mucimassa"                                    
[1514] "Botrimarina mediterranea"                               
[1515] "Candidatus Velamenicoccus archaeovorus"                 
[1516] "Sebaldella termitidis"                                  
[1517] "Candidatus Koribacter versatilis"                       
[1518] "Luteitalea sp. TBR-22"                                  
[1519] "Fervidobacterium pennivorans"                           
[1520] "Methanobrevibacter smithii"                             
[1521] "Sapelovirus A"                                          
[1522] "Eponavirus epona"                                       
[1523] "Fenollaria massiliensis"                                
[1524] "Proteiniborus sp. MB09-C3"                              
[1525] "Clostridium sp. JN-9"                                   
[1526] "Clostridium gelidum"                                    
[1527] "Clostridium novyi"                                      
[1528] "Clostridium tetani"                                     
[1529] "Clostridium septicum"                                   
[1530] "Clostridium carboxidivorans"                            
[1531] "Alkaliphilus oremlandii"                                
[1532] "Sarcina sp. JB2"                                        
[1533] "Paraclostridium bifermentans"                           
[1534] "Hathewaya histolytica"                                  
[1535] "Romboutsia ilealis"                                     
[1536] "Cellulosilyticum lentocellum"                           
[1537] "Desulfosporosinus orientis"                             
[1538] "Desulfosporosinus acidiphilus"                          
[1539] "Desulfosporosinus meridiei"                             
[1540] "Desulfitobacterium dichloroeliminans"                   
[1541] "Desulfitobacterium metallireducens"                     
[1542] "Candidatus Contubernalis alkalaceticum"                 
[1543] "Desulfotomaculum nigrificans"                           
[1544] "Alkalicella caledoniensis"                              
[1545] "Thermoanaerobacterium thermosaccharolyticum"            
[1546] "Thermoanaerobacter sp. X514"                            
[1547] "Halanaerobium praevalens"                               
[1548] "Caldicellulosiruptor owensensis"                        
[1549] "Caldicellulosiruptor morganii"                          
[1550] "Caldicellulosiruptor kronotskyensis"                    
[1551] "Moorella glycerini"                                     
[1552] "Tepidanaerobacter acetatoxydans"                        
[1553] "Ligilactobacillus animalis"                             
[1554] "Lactiplantibacillus argentoratensis"                    
[1555] "Pediococcus pentosaceus"                                
[1556] "Weissella jogaejeotgali"                                
[1557] "Weissella soli"                                         
[1558] "Lentilactobacillus hilgardii"                           
[1559] "Companilactobacillus futsaii"                           
[1560] "Streptococcus sp. HN38"                                 
[1561] "Streptococcus cristatus"                                
[1562] "Streptococcus gordonii"                                 
[1563] "Streptococcus canis"                                    
[1564] "Streptococcus acidominimus"                             
[1565] "Carnobacterium inhibens"                                
[1566] "Enterococcus durans"                                    
[1567] "Enterococcus gilvus"                                    
[1568] "Enterococcus gallinarum"                                
[1569] "Enterococcus wangshanyuanii"                            
[1570] "Enterococcus mundtii"                                   
[1571] "Vagococcus penaei"                                      
[1572] "Bacillus cytotoxicus"                                   
[1573] "Bacillus sp. CMF12"                                     
[1574] "Bacillus sp. FJAT-18017"                                
[1575] "Bacillus sp. LJBS17"                                    
[1576] "Bacillus sp. 1NLA3E"                                    
[1577] "Bacillus glycinifermentans"                             
[1578] "Bacillus gobiensis"                                     
[1579] "Bacillus aquiflavi"                                     
[1580] "Bacillus safensis"                                      
[1581] "Bacillus swezeyi"                                       
[1582] "Lentibacillus amyloliquefaciens"                        
[1583] "Geobacillus proteiniphilus"                             
[1584] "Geobacillus thermodenitrificans"                        
[1585] "Neobacillus sp. PS3-34"                                 
[1586] "Neobacillus sp. 114"                                    
[1587] "Neobacillus sp. DY30"                                   
[1588] "Neobacillus cucumis"                                    
[1589] "Neobacillus novalis"                                    
[1590] "Neobacillus mesonae"                                    
[1591] "Cytobacillus kochii"                                    
[1592] "Lysinibacillus sphaericus"                              
[1593] "Virgibacillus sp. SK37"                                 
[1594] "Peribacillus asahii"                                    
[1595] "Mesobacillus sp. AQ2"                                   
[1596] "Salicibibacter cibi"                                    
[1597] "Pontibacillus sp. ALD_SL1"                              
[1598] "Halalkalibacterium halodurans"                          
[1599] "Fictibacillus arsenicus"                                
[1600] "Sutcliffiella horikoshii"                               
[1601] "Anoxybacillus flavithermus"                             
[1602] "Shouchella lehensis"                                    
[1603] "Halobacillus sp. SSHM10-5"                              
[1604] "Niallia circulans"                                      
[1605] "Oceanobacillus iheyensis"                               
[1606] "Amphibacillus xylanus"                                  
[1607] "Gracilibacillus sp. SSPM10-3"                           
[1608] "Pseudalkalibacillus hwajinpoensis"                      
[1609] "Pradoshia sp. D12"                                      
[1610] "Terribacillus goriensis"                                
[1611] "Caldibacillus thermoamylovorans"                        
[1612] "Alkalihalophilus pseudofirmus"                          
[1613] "Paenalkalicoccus suaedae"                               
[1614] "Paenibacillus sp. FSL P4-0081"                          
[1615] "Paenibacillus sp. URB8-2"                               
[1616] "Paenibacillus sp. RC67"                                 
[1617] "Paenibacillus sp. FSL R5-0912"                          
[1618] "Paenibacillus sp. FSL R5-0345"                          
[1619] "Paenibacillus sp. PK4536"                               
[1620] "Paenibacillus sp. DCT19"                                
[1621] "Paenibacillus sp. N3/727"                               
[1622] "Paenibacillus sp. YPG26"                                
[1623] "Paenibacillus baekrokdamisoli"                          
[1624] "Paenibacillus crassostreae"                             
[1625] "Paenibacillus urinalis"                                 
[1626] "Paenibacillus barcinonensis"                            
[1627] "Paenibacillus kribbensis"                               
[1628] "Paenibacillus woosongensis"                             
[1629] "Paenibacillus graminis"                                 
[1630] "Paenibacillus protaetiae"                               
[1631] "Paenibacillus pabuli"                                   
[1632] "Paenibacillus lentus"                                   
[1633] "Paenibacillus algicola"                                 
[1634] "Paenibacillus xylanexedens"                             
[1635] "Paenibacillus bovis"                                    
[1636] "Paenibacillus chitinolyticus"                           
[1637] "Paenibacillus peoriae"                                  
[1638] "Paenibacillus brasilensis"                              
[1639] "Paenibacillus azoreducens"                              
[1640] "Brevibacillus borstelensis"                             
[1641] "Brevibacillus laterosporus"                             
[1642] "Brevibacillus choshinensis"                             
[1643] "Staphylococcus chromogenes"                             
[1644] "Staphylococcus warneri"                                 
[1645] "Staphylococcus saccharolyticus"                         
[1646] "Macrococcus armenti"                                    
[1647] "Macrococcus equipercicus"                               
[1648] "Planococcus sp. PAMC 21323"                             
[1649] "Planococcus sp. N056"                                   
[1650] "Planococcus sp. N022"                                   
[1651] "Viridibacillus sp. JNUCC-6"                             
[1652] "Listeria newyorkensis"                                  
[1653] "Listeria weihenstephanensis"                            
[1654] "Alicyclobacillus cycloheptanicus"                       
[1655] "Exiguobacterium antarcticum"                            
[1656] "Gemella haemolysans"                                    
[1657] "Pelosinus fermentans"                                   
[1658] "Veillonella parvula"                                    
[1659] "Erysipelothrix sp. HDW6A"                               
[1660] "Erysipelothrix sp. A18Y020d"                            
[1661] "Erysipelothrix inopinata"                               
[1662] "Turicibacter sp. H121"                                  
[1663] "Turicibacter sanguinis"                                 
[1664] "Peptoniphilus sp. GNH"                                  
[1665] "Arthrobacter sp. NtRootA1"                              
[1666] "Arthrobacter sp. StoSoilB22"                            
[1667] "Arthrobacter sp. zg-Y815"                               
[1668] "Pseudarthrobacter sp. BIM B-2242"                       
[1669] "Pseudarthrobacter defluvii"                             
[1670] "Pseudarthrobacter psychrotolerans"                      
[1671] "Rothia mucilaginosa"                                    
[1672] "Kocuria sp. TGY1127_2"                                  
[1673] "Citricoccus sp. SGAir0253"                              
[1674] "Citricoccus sp. I39-566"                                
[1675] "Microbacterium sp. nov. GSS16"                          
[1676] "Microbacterium esteraromaticum"                         
[1677] "Microbacterium wangchenii"                              
[1678] "Agrococcus sp. SL85"                                    
[1679] "Leifsonia shinshuensis"                                 
[1680] "Rhodoluna lacicola"                                     
[1681] "Herbiconiux sp. L3-i23"                                 
[1682] "Mycetocola zhujimingii"                                 
[1683] "Cellulomonas sp. H30R-01"                               
[1684] "Cellulomonas sp. JZ18"                                  
[1685] "Cellulomonas sp. NS3"                                   
[1686] "Cellulomonas chengniuliangii"                           
[1687] "Xylanimonas allomyrinae"                                
[1688] "Corynebacterium heidelbergense"                         
[1689] "Corynebacterium sp. SCR221107"                          
[1690] "Corynebacterium sp. Z-1"                                
[1691] "Corynebacterium doosanense"                             
[1692] "Corynebacterium incognita"                              
[1693] "Corynebacterium choanae"                                
[1694] "Corynebacterium sphenisci"                              
[1695] "Corynebacterium urogenitale"                            
[1696] "Corynebacterium lactis"                                 
[1697] "Corynebacterium aquatimens"                             
[1698] "Corynebacterium mustelae"                               
[1699] "Corynebacterium tuberculostearicum"                     
[1700] "Mycobacterium sp. Aquia_213"                            
[1701] "Mycobacterium sp. EPa45"                                
[1702] "Mycobacterium xenopi"                                   
[1703] "Mycolicibacterium tokaiense"                            
[1704] "Rhodococcus sp. P1Y"                                    
[1705] "Nocardia farcinica"                                     
[1706] "Nocardia yunnanensis"                                   
[1707] "Gordonia sp. PP30"                                      
[1708] "Tomitella fengzijianii"                                 
[1709] "Streptomyces sp. Z423-1"                                
[1710] "Streptomyces sp. ST13-2-2"                              
[1711] "Streptomyces sp. VNUA24"                                
[1712] "Streptomyces sp. HL-66"                                 
[1713] "Streptomyces sp. W1SF4"                                 
[1714] "Streptomyces sp. MRC013"                                
[1715] "Streptomyces sp. JB150"                                 
[1716] "Streptomyces sp. VNUA116"                               
[1717] "Streptomyces sp. WA1-19"                                
[1718] "Streptomyces sp. GS7"                                   
[1719] "Streptomyces sp. FIT100"                                
[1720] "Streptomyces sp. BB1-1-1"                               
[1721] "Streptomyces vinaceus"                                  
[1722] "Streptomyces noursei"                                   
[1723] "Streptomyces griseochromogenes"                         
[1724] "Streptomyces seoulensis"                                
[1725] "Streptomyces albus"                                     
[1726] "Streptomyces nitrosporeus"                              
[1727] "Streptomyces coralus"                                   
[1728] "Streptomyces calvus"                                    
[1729] "Streptomyces clavuligerus"                              
[1730] "Streptomyces paludis"                                   
[1731] "Streptomyces niveus"                                    
[1732] "Streptomyces viridosporus"                              
[1733] "Streptomyces xanthii"                                   
[1734] "Streptomyces subrutilus"                                
[1735] "Streptomyces inhibens"                                  
[1736] "Cutibacterium modestum"                                 
[1737] "Cutibacterium avidum"                                   
[1738] "Tessaracoccus sp. MC1865"                               
[1739] "Microlunatus soli"                                      
[1740] "Nocardioides sp. LMS-CY"                                
[1741] "Nocardioides yefusunii"                                 
[1742] "Nocardioides panacisoli"                                
[1743] "Nocardioides ungokensis"                                
[1744] "Gardnerella vaginalis"                                  
[1745] "Micromonospora echinofusca"                             
[1746] "Actinoplanes sp. OR16"                                  
[1747] "Dactylosporangium fulvum"                               
[1748] "Solwaraspora sp. WMMD791"                               
[1749] "Polymorphospora rubra"                                  
[1750] "Salinispora tropica"                                    
[1751] "Amycolatopsis sp. 2-2"                                  
[1752] "Amycolatopsis sp. 4-36"                                 
[1753] "Amycolatopsis albispora"                                
[1754] "Amycolatopsis pretoriensis"                             
[1755] "Amycolatopsis methanolica"                              
[1756] "Amycolatopsis orientalis"                               
[1757] "Amycolatopsis thermalba"                                
[1758] "Pseudonocardia sp. DSM 110487"                          
[1759] "Saccharopolyspora gregorii"                             
[1760] "Kutzneria sp. CA-103260"                                
[1761] "Lentzea guizhouensis"                                   
[1762] "Actinomyces naeslundii"                                 
[1763] "Actinomyces qiguomingii"                                
[1764] "Schaalia odontolytica"                                  
[1765] "Schaalia turicensis"                                    
[1766] "Actinomadura sp. WMMA1423"                              
[1767] "Actinomadura graeca"                                    
[1768] "Nakamurella multipartita"                               
[1769] "Frankia casuarinae"                                     
[1770] "Cryptobacterium curtum"                                 
[1771] "Nostoc sp. 'Lobaria pulmonaria (5183) cyanobiont'"      
[1772] "Calothrix sp. 336/3"                                    
[1773] "Fischerella sp. NIES-3754"                              
[1774] "Planktothrix agardhii"                                  
[1775] "Oxynema aestuarii"                                      
[1776] "Oscillatoria acuminata"                                 
[1777] "Synechococcus sp. BMK-MC-1"                             
[1778] "Prochlorococcus marinus"                                
[1779] "Chamaesiphon minutus"                                   
[1780] "Mycoplasmopsis equigenitalium"                          
[1781] "Mycoplasmopsis cynos"                                   
[1782] "Mycoplasmopsis pulmonis"                                
[1783] "Spiroplasma tabanidicola"                               
[1784] "Mycoplasmoides gallisepticum"                           
[1785] "Chloroflexus aurantiacus"                               
[1786] "Deinococcus sp. QL22"                                   
[1787] "Deinococcus rubellus"                                   
[1788] "Deinococcus metallilatus"                               
[1789] "Deinococcus maricopensis"                               
[1790] "Bacteroides sp. A1C1"                                   
[1791] "Bacteroides sp. HF-162"                                 
[1792] "Bacteroides humanifaecis"                               
[1793] "Dysgonomonas sp. HDW5A"                                 
[1794] "Flavobacterium sp. GSB-24"                              
[1795] "Flavobacterium sp. N1719"                               
[1796] "Flavobacterium sp. N3904"                               
[1797] "Flavobacterium alkalisoli"                              
[1798] "Flavobacterium gilvum"                                  
[1799] "Flavobacterium kingsejongi"                             
[1800] "Flavobacterium psychrophilum"                           
[1801] "Flavobacterium album"                                   
[1802] "Capnocytophaga haemolytica"                             
[1803] "Capnocytophaga ochracea"                                
[1804] "Capnocytophaga sp. FDAARGOS_737"                        
[1805] "Capnocytophaga sputigena"                               
[1806] "Muricauda sp. SCSIO 65647"                              
[1807] "Allomuricauda oceani"                                   
[1808] "Maribacter sp. Hal144"                                  
[1809] "Maribacter sp. HTCC2170"                                
[1810] "Polaribacter sp. BM10"                                  
[1811] "Aquimarina sp. AD1"                                     
[1812] "Salegentibacter sp. T436"                               
[1813] "Robiginitalea biformata"                                
[1814] "Salinimicrobium tongyeongense"                          
[1815] "Chryseobacterium sp. SNU WT5"                           
[1816] "Chryseobacterium sp."                                   
[1817] "Chryseobacterium manosquense"                           
[1818] "Chryseobacterium taklimakanense"                        
[1819] "Chryseobacterium camelliae"                             
[1820] "Elizabethkingia ursingii"                               
[1821] "Elizabethkingia anophelis"                              
[1822] "Elizabethkingia bruuniana"                              
[1823] "Blattabacterium cuenoti"                                
[1824] "Hymenobacter sp. PAMC 26628"                            
[1825] "Hymenobacter sp. NBH84"                                 
[1826] "Hymenobacter sp. DG01"                                  
[1827] "Hymenobacter sp. 5317J-9"                               
[1828] "Hymenobacter sp. BRD128"                                
[1829] "Hymenobacter sp. HDW8"                                  
[1830] "Hymenobacter monticola"                                 
[1831] "Hymenobacter cellulosivorans"                           
[1832] "Hymenobacter baengnokdamensis"                          
[1833] "Hymenobacter sedentarius"                               
[1834] "Hymenobacter jejuensis"                                 
[1835] "Hymenobacter qilianensis"                               
[1836] "Hymenobacter oligotrophus"                              
[1837] "Hymenobacter cellulosilyticus"                          
[1838] "Pontibacter pudoricolor"                                
[1839] "Pontibacter actiniarum"                                 
[1840] "Pontibacter akesuensis"                                 
[1841] "Rufibacter radiotolerans"                               
[1842] "Rufibacter tibetensis"                                  
[1843] "Rufibacter sp. DG15C"                                   
[1844] "Spirosoma montaniterrae"                                
[1845] "Spirosoma oryzicola"                                    
[1846] "Spirosoma pollinicola"                                  
[1847] "Spirosoma rhododendri"                                  
[1848] "Spirosoma sp. KUDC1026"                                 
[1849] "Spirosoma endbachense"                                  
[1850] "Algoriphagus sp. NBT04N3"                               
[1851] "Mongoliitalea daihaiensis"                              
[1852] "Emticicia oligotrophica"                                
[1853] "Emticicia sp. 21SJ11W-3"                                
[1854] "Dyadobacter fermentans"                                 
[1855] "Dyadobacter sp. NIV53"                                  
[1856] "Dyadobacter pollutisoli"                                
[1857] "Runella rosea"                                          
[1858] "Runella sp. SP2"                                        
[1859] "Fibrella aestuarina"                                    
[1860] "Larkinella insperata"                                   
[1861] "Marinilongibacter aquaticus"                            
[1862] "Fulvivirga lutea"                                       
[1863] "Persicobacter sp. JZB09"                                
[1864] "Olivibacter sp. SDN3"                                   
[1865] "Mucilaginibacter mali"                                  
[1866] "Mucilaginibacter gotjawali"                             
[1867] "Mucilaginibacter ginsenosidivorax"                      
[1868] "Sphingobacterium thalpophilum"                          
[1869] "Chitinophaga filiformis"                                
[1870] "Flavihumibacter rivuli"                                 
[1871] "Filimonas lacunae"                                      
[1872] "Saprospira sp. CCB-QB6"                                 
[1873] "Melioribacter roseus"                                   
[1874] "Klebsiella michiganensis"                               
[1875] "Raoultella planticola"                                  
[1876] "Enterobacter sp. JUb54"                                 
[1877] "Salmonella bongori"                                     
[1878] "Kosakonia cowanii"                                      
[1879] "Plesiomonas shigelloides"                               
[1880] "Yersinia hibernica"                                     
[1881] "Ewingella americana"                                    
[1882] "Pantoea agglomerans"                                    
[1883] "Proteus terrae"                                         
[1884] "Limnobaculum parvum"                                    
[1885] "Pseudomonas sp. WJP1"                                   
[1886] "Pseudomonas sp. MM211"                                  
[1887] "Pseudomonas corrugata"                                  
[1888] "Pseudomonas syringae"                                   
[1889] "Pseudomonas fragi"                                      
[1890] "Pseudomonas silesiensis"                                
[1891] "Halopseudomonas phragmitis"                             
[1892] "Marinobacter sp. AN1"                                   
[1893] "Stenotrophomonas sp. A5588"                             
[1894] "Arenimonas daejeonensis"                                
[1895] "Rhodanobacter thiooxydans"                              
[1896] "Dyella telluris"                                        
[1897] "Frateuria edaphi"                                       
[1898] "Halomonas sp. DN3"                                      
[1899] "Halomonas sp. LR3S48"                                   
[1900] "Halotalea alkalilenta"                                  
[1901] "Marinomonas foliarum"                                   
[1902] "Aliamphritea hakodatensis"                              
[1903] "Oleiphilus messinensis"                                 
[1904] "Alloalcanivorax xenomutans"                             
[1905] "Vibrio mediterranei"                                    
[1906] "Vibrio vulnificus"                                      
[1907] "Vibrio penaeicida"                                      
[1908] "Vibrio mangrovi"                                        
[1909] "Vibrio plantisponsor"                                   
[1910] "Alteromonas sp. RKMC-009"                               
[1911] "Alteromonas macleodii"                                  
[1912] "Lacimicrobium alkaliphilum"                             
[1913] "Idiomarina sp."                                         
[1914] "Nitrosococcus halophilus"                               
[1915] "Thiocapsa bogorovii"                                    
[1916] "Acinetobacter sp. 10FS3-1"                              
[1917] "Moraxella bovoculi"                                     
[1918] "Moraxella nasovis"                                      
[1919] "Haemophilus haemolyticus"                               
[1920] "Haemophilus parainfluenzae"                             
[1921] "Actinobacillus sp. GY-402"                              
[1922] "Microbulbifer hydrolyticus"                             
[1923] "Halioglobus maricola"                                   
[1924] "Legionella longbeachae"                                 
[1925] "Methylomonas sp. UP202"                                 
[1926] "Methylococcus capsulatus"                               
[1927] "Gallaecimonas kandeliae"                                
[1928] "Candidatus Reidiella endopervernicosa"                  
[1929] "Steroidobacter denitrificans"                           
[1930] "Rhizobium sp. 11515TR"                                  
[1931] "Rhizobium sp. TH2"                                      
[1932] "Rhizobium sp. BT-175"                                   
[1933] "Rhizobium jaguaris"                                     
[1934] "Rhizobium phaseoli"                                     
[1935] "Pararhizobium sp. BT-229"                               
[1936] "Sinorhizobium meliloti"                                 
[1937] "Sinorhizobium alkalisoli"                               
[1938] "Bradyrhizobium elkanii"                                 
[1939] "Oricola thermophila"                                    
[1940] "Salaquimonas pukyongi"                                  
[1941] "Microvirga thermotolerans"                              
[1942] "Microvirga ossetica"                                    
[1943] "Bosea sp. RAC05"                                        
[1944] "Phreatobacter stygius"                                  
[1945] "Frigidibacter mobilis"                                  
[1946] "Qingshengfaniella alkalisoli"                           
[1947] "Haematobacter massiliensis"                             
[1948] "Pseudorhodobacter turbinis"                             
[1949] "Sulfitobacter albidus"                                  
[1950] "Ruegeria conchae"                                       
[1951] "Jannaschia sp. W003"                                    
[1952] "Jannaschia sp. GRR-S6-38"                               
[1953] "Leisingera caerulea"                                    
[1954] "Ketogulonicigenium vulgare"                             
[1955] "Roseivivax sp. THAF30"                                  
[1956] "Sphingomonas aliaeris"                                  
[1957] "Novosphingobium sp. 9"                                  
[1958] "Sphingorhabdus sp. M41"                                 
[1959] "Tardibacter chloracetimidivorans"                       
[1960] "Erythrobacter sp. HKB08"                                
[1961] "Erythrobacter mangrovi"                                 
[1962] "Altererythrobacter epoxidivorans"                       
[1963] "Croceicoccus marinus"                                   
[1964] "Roseomonas marmotae"                                    
[1965] "Acidiphilium multivorum"                                
[1966] "Commensalibacter melissae"                              
[1967] "Roseococcus microcysteis"                               
[1968] "Granulibacter bethesdensis"                             
[1969] "Azospirillum thermophilum"                              
[1970] "Magnetospirillum magneticum"                            
[1971] "Candidatus Endolissoclinum faulkneri"                   
[1972] "Brevundimonas sp. NIBR11"                               
[1973] "Caulobacter vibrioides"                                 
[1974] "Luteithermobacter gelatinilyticus"                      
[1975] "Burkholderia sp. DHOD12"                                
[1976] "Burkholderia mayonis"                                   
[1977] "Paraburkholderia caledonica"                            
[1978] "Paraburkholderia ginsengisoli"                          
[1979] "Paraburkholderia fungorum"                              
[1980] "Cupriavidus taiwanensis"                                
[1981] "Polynucleobacter wuianus"                               
[1982] "Pandoraea fibrosis"                                     
[1983] "Ralstonia solanacearum"                                 
[1984] "Caballeronia zhejiangensis"                             
[1985] "Lautropia mirabilis"                                    
[1986] "Turicimonas muris"                                      
[1987] "Hydrogenophaga sp. PBC"                                 
[1988] "Comamonas sp. Y33R10-2"                                 
[1989] "Acidovorax sp. KKS102"                                  
[1990] "Polaromonas sp. JS666"                                  
[1991] "Castellaniella defragrans"                              
[1992] "Massilia sp. PAMC28688"                                 
[1993] "Sphaerotilus sulfidivorans"                             
[1994] "Aquincola tertiaricarbonis"                             
[1995] "Aquabacterium olei"                                     
[1996] "Neisseria bacilliformis"                                
[1997] "Eikenella corrodens"                                    
[1998] "Eikenella exigua"                                       
[1999] "Snodgrassella alvi"                                     
[2000] "Paludibacterium paludis"                                
[2001] "Chitinimonas arctica"                                   
[2002] "Nitrosomonas sp."                                       
[2003] "Nitrosospira lacus"                                     
[2004] "Thiobacillus denitrificans"                             
[2005] "Thauera sp. GDN1"                                       
[2006] "Treponema primitia"                                     
[2007] "Salinispira pacifica"                                   
[2008] "Leadbettera azotonutricia"                              
[2009] "Leptospira kmetyi"                                      
[2010] "Turneriella parva"                                      
[2011] "Bremerella volcania"                                    
[2012] "Polystyrenella longa"                                   
[2013] "Rubinisphaera brasiliensis"                             
[2014] "Planctopirus ephydatiae"                                
[2015] "Stratiformator vulcanicus"                              
[2016] "Fuerstiella marisgermanici"                             
[2017] "Frigoriglobus tundricola"                               
[2018] "Urbifossiella limnaea"                                  
[2019] "Opitutus terrae"                                        
[2020] "Ruficoccus sp. ZRK36"                                   
[2021] "Desulfovibrio subterraneus"                             
[2022] "Desulfovibrio mangrovi"                                 
[2023] "Pseudodesulfovibrio sp. MCM B-1480"                     
[2024] "Pseudodesulfovibrio indicus"                            
[2025] "Pseudodesulfovibrio cashew"                             
[2026] "Desulfomicrobium sp. ZS1"                               
[2027] "Desulfohalobium retbaense"                              
[2028] "Geobacter sulfurreducens"                               
[2029] "Desulfuromonas sp. DDH964"                              
[2030] "Geoalkalibacter halelectricus"                          
[2031] "Desulfosarcina widdelii"                                
[2032] "Desulfoluna limicola"                                   
[2033] "uncultured Desulfatiglans sp."                          
[2034] "Desulfosediminicola ganghwensis"                        
[2035] "Desulfobacca acetoxidans"                               
[2036] "Candidatus Sulfurimonas baltica"                        
[2037] "Sulfurovum indicum"                                     
[2038] "Myxococcus stipitatus"                                  
[2039] "Myxococcus xanthus"                                     
[2040] "Pyxidicoccus parkwaysis"                                
[2041] "Acidisarcina polymorpha"                                
[2042] "Geothrix sp. 21YS21S-4"                                 
[2043] "Geothrix sp."                                           
[2044] "Sulfidibacter corallicola"                              
[2045] "Fusobacterium vincentii"                                
[2046] "Leptospirillum ferrooxidans"                            
[2047] "Sulfurihydrogenibium azorense"                          
[2048] "Denitrovibrio acetiphilus"                              
[2049] "Dissulfurimicrobium hydrothermale"                      
[2050] "Natronobacterium gregoryi"                              
[2051] "Lughvirus lugh"                                         
[2052] "Porcine astrovirus 2"                                   
[2053] "Porcine mastadenovirus A"                               
[2054] "Lactobacillus sp. JM1"                                  
[2055] "Fructobacillus americanaquae"                           
[2056] "Floricoccus penangensis"                                
[2057] "Aerococcus urinaeequi"                                  
[2058] "Neobacillus sp. PS3-40"                                 
[2059] "Neobacillus sp. Marseille-Q6967"                        
[2060] "Metabacillus endolithicus"                              
[2061] "Butyricicoccus sp. GAM44"                               
[2062] "Dietzia lutea"                                          
[2063] "Streptomyces coeruleorubidus"                           
[2064] "Streptosporangium sp. 'caverna'"                        
[2065] "Spiroplasma gladiatoris"                                
[2066] "Roseiflexus sp. RS-1"                                   
[2067] "Aureimonas sp. SA4125"                                  
[2068] "Caulobacter sp. FWC26"                                  
[2069] "Tuwongella immobilis"                                   
[2070] "Jonquetella anthropi"                                   
[2071] "Kahnovirus oralis"                                      
[2072] "Pamirivirus faecium"                                    
[2073] "Clostridium autoethanogenum"                            
[2074] "Staphylococcus edaphicus"                               
[2075] "Paenibacillus sp. 481"                                  
[2076] "Alicyclobacillus dauci"                                 
[2077] "Helcococcus kunzii"                                     
[2078] "Arthrobacter sp. Helios"                                
[2079] "Arthrobacter crystallopoietes"                          
[2080] "Arthrobacter alpinus"                                   
[2081] "Rothia kristinae"                                       
[2082] "Microbacterium oryzae"                                  
[2083] "Leifsonia sp. ZF2019"                                   
[2084] "Leifsonia xyli"                                         
[2085] "Agrococcus sp. Marseille-Q4369"                         
[2086] "Cryobacterium breve"                                    
[2087] "Mycetocola spongiae"                                    
[2088] "Corynebacterium urealyticum"                            
[2089] "Corynebacterium kroppenstedtii"                         
[2090] "Corynebacterium falsenii"                               
[2091] "Mycobacterium simiae"                                   
[2092] "Mycolicibacterium crocinum"                             
[2093] "Gordonia sp. KTR9"                                      
[2094] "Streptomyces sp. ITFR-16"                               
[2095] "Streptomyces ficellus"                                  
[2096] "Streptomyces lydicus"                                   
[2097] "Streptomyces avermitilis"                               
[2098] "Changpingibacter yushuensis"                            
[2099] "Saccharopolyspora pogona"                               
[2100] "Saccharothrix espanaensis"                              
[2101] "Saccharomonospora cyanea"                               
[2102] "Micromonospora sp. LH3U1"                               
[2103] "Micromonospora endophytica"                             
[2104] "Micromonospora ferruginea"                              
[2105] "Actinoplanes sp. N902-109"                              
[2106] "Natronoglycomyces albus"                                
[2107] "Jiangella alkaliphila"                                  
[2108] "Conexibacter sp. SYSU D00693"                           
[2109] "Mycoplasma sp. Pen4"                                    
[2110] "Williamsoniiplasma somnilux"                            
[2111] "Thermomicrobium roseum"                                 
[2112] "Flavobacterium sp. CJ74"                                
[2113] "Euzebyella marina"                                      
[2114] "Galbibacter sp. BG1"                                    
[2115] "Chryseobacterium paludis"                               
[2116] "Owenweeksia hongkongensis"                              
[2117] "Hymenobacter canadensis"                                
[2118] "Hymenobacter volaticus"                                 
[2119] "Pontibacter sp. SGAir0037"                              
[2120] "Nibribacter ruber"                                      
[2121] "Spirosoma aerolatum"                                    
[2122] "Dyadobacter sandarakinus"                               
[2123] "Marivirga sp. BDSF4-3"                                  
[2124] "Mucilaginibacter sp. KACC 22063"                        
[2125] "Mucilaginibacter rubeus"                                
[2126] "Mucilaginibacter paludis"                               
[2127] "Sphingobacterium sp. ML3W"                              
[2128] "Sphingobacterium daejeonense"                           
[2129] "Pedobacter sp. HDW13"                                   
[2130] "Pedobacter cryoconitis"                                 
[2131] "Pedobacter endophyticus"                                
[2132] "Chitinophaga sp. HK235"                                 
[2133] "Niastella koreensis"                                    
[2134] "Saprospira grandis"                                     
[2135] "Kluyvera intermedia"                                    
[2136] "Nissabacter sp. SGAir0207"                              
[2137] "Pseudomonas sp. 15A4"                                   
[2138] "Pseudomonas sp. Q1-7"                                   
[2139] "Pseudomonas hamedanensis"                               
[2140] "Halopseudomonas litoralis"                              
[2141] "Actinobacillus indolicus"                               
[2142] "Glaesserella sp. 15-184"                                
[2143] "Rodentibacter heylii"                                   
[2144] "Haemophilus influenzae"                                 
[2145] "Bisgaardia hudsonensis"                                 
[2146] "Mergibacter septicus"                                   
[2147] "Aggregatibacter actinomycetemcomitans"                  
[2148] "Xanthomonas hortorum"                                   
[2149] "Xanthomonas oryzae"                                     
[2150] "Xanthomonas citri"                                      
[2151] "Stenotrophomonas sp. ESTM1D_MKCIP4_1"                   
[2152] "Vibrio tapetis"                                         
[2153] "Vibrio gallicus"                                        
[2154] "Halomonas sp. CKK8"                                     
[2155] "Salinimonas sediminis"                                  
[2156] "Catenovulum sediminis"                                  
[2157] "Rheinheimera mangrovi"                                  
[2158] "Candidatus Nitrosacidococcus sp. I8"                    
[2159] "Psychrobacter sp. KCTC 72983"                           
[2160] "Microbulbifer sp. A4B17"                                
[2161] "Microbulbifer celer"                                    
[2162] "Thiomicrospira microaerophila"                          
[2163] "Rhizobium sp. ACO-34A"                                  
[2164] "Agrobacterium larrymoorei"                              
[2165] "Pseudorhizobium banfieldiae"                            
[2166] "Bradyrhizobium canariense"                              
[2167] "Bradyrhizobium xenonodulans"                            
[2168] "Mesorhizobium sp. M2A.F.Ca.ET.046.03.2.1"               
[2169] "Microvirga sp. VF16"                                    
[2170] "Methylocystis sp. SC2"                                  
[2171] "Methylocystis parvus"                                   
[2172] "Aureimonas mangrovi"                                    
[2173] "Hyphomicrobium denitrificans"                           
[2174] "Phreatobacter cathodiphilus"                            
[2175] "uncultured Pleomorphomonas sp."                         
[2176] "Novosphingobium resinovorum"                            
[2177] "Sphingopyxis sp. YF1"                                   
[2178] "Sphingosinithalassobacter sp. CS137"                    
[2179] "Leisingera sp. S132"                                    
[2180] "Leisingera methylohalidivorans"                         
[2181] "Sulfitobacter mediterraneus"                            
[2182] "Phaeobacter inhibens"                                   
[2183] "Ponticoccus alexandrii"                                 
[2184] "Asticcacaulis sp. SL142"                                
[2185] "Neorickettsia helminthoeca"                             
[2186] "Burkholderia sp. NRF60-BP8"                             
[2187] "Burkholderia pseudomallei"                              
[2188] "Burkholderia gladioli"                                  
[2189] "Candidatus Vallotia tarda"                              
[2190] "Comamonas serinivorans"                                 
[2191] "Massilia putida"                                        
[2192] "Vogesella sp. XCS3"                                     
[2193] "Syntrophotalea carbinolica"                             
[2194] "Syntrophotalea acetylenivorans"                         
[2195] "Pelobacter propionicus"                                 
[2196] "Geobacter pickeringii"                                  
[2197] "Desulfobacter hydrogenophilus"                          
[2198] "Gemmata massiliana"                                     
[2199] "Humisphaera borealis"                                   
[2200] "Nibricoccus aquaticus"                                  
[2201] "Opitutus sp. GAS368"                                    
[2202] "Cystobacter fuscus"                                     
[2203] "Chondromyces crocatus"                                  
[2204] "Sulfuricurvum kujiense"                                 
[2205] "Terriglobus saanensis"                                  
[2206] "Sneathia vaginalis"                                     
[2207] "unidentified bacterial endosymbiont"                    
[2208] "Methanobrevibacter sp. AbM4"                            
[2209] "Aalivirus A"                                            
[2210] "Taranisvirus taranis"                                   
[2211] "Apilactobacillus kunkeei"                               
[2212] "Metabacillus litoralis"                                 
[2213] "Kahnovirus copri"                                       
[2214] "Dehalobacter sp. CF"                                    
[2215] "Natranaerobius thermophilus"                            
[2216] "Apilactobacillus apisilvae"                             
[2217] "Streptococcus sp. FDAARGOS_522"                         
[2218] "Streptococcus sp. zg-86"                                
[2219] "Allobacillus halotolerans"                              
[2220] "Paenibacillus sp. FSL H7-0737"                          
[2221] "Peptoniphilus harei"                                    
[2222] "Corynebacterium matruchotii"                            
[2223] "Streptomyces sp. CdTB01"                                
[2224] "Propionibacterium australiense"                         
[2225] "Actinomadura sp. WMMB 499"                              
[2226] "Xianfuyuplasma coldseepsis"                             
[2227] "Brevefilum fermentans"                                  
[2228] "Pseudomonas tructae"                                    
[2229] "Neorhizobium petrolearium"                              
[2230] "Candidatus Saccharimonas aalborgensis"                  
[2231] "Streptococcus infantarius"                              
[2232] "Paenibacillus jilunlii"                                 
[2233] "Microbacterium protaetiae"                              
[2234] "Nocardia seriolae"                                      
[2235] "Nonomuraea sp. ATCC 55076"                              
[2236] "Helicobacter hepaticus"                                 
[2237] "Enterovirus G"                                          
[2238] "Lactobacillus sp. ESL0684"                              
[2239] "Lactobacillus sp. ESL0731"                              
[2240] "Lactobacillus sp. ESL0700"                              
[2241] "Fructilactobacillus hinvesii"                           
[2242] "Weissella paramesenteroides"                            
[2243] "Streptococcus ferus"                                    
[2244] "Bacillus paralicheniformis"                             
[2245] "Bacillus tequilensis"                                   
[2246] "Bacillus stercoris"                                     
[2247] "Bacillus spizizenii"                                    
[2248] "Bacillus sp. 7D3"                                       
[2249] "Geobacillus thermoleovorans"                            
[2250] "Salicibibacter kimchii"                                 
[2251] "Shouchella miscanthi"                                   
[2252] "Mesobacillus subterraneus"                              
[2253] "Psychrobacillus glaciei"                                
[2254] "Halobacillus litoralis"                                 
[2255] "Staphylococcus sp. IVB6227"                             
[2256] "Staphylococcus sp. T93"                                 
[2257] "Staphylococcus succinus"                                
[2258] "Staphylococcus felis"                                   
[2259] "Macrococcus canis"                                      
[2260] "Paenibacillus sp. DR312"                                
[2261] "Paenisporosarcina cavernae"                             
[2262] "Paenisporosarcina antarctica"                           
[2263] "Alicyclobacillus acidoterrestris"                       
[2264] "Laceyella sacchari"                                     
[2265] "Crassaminicella profunda"                               
[2266] "Desulforamulus reducens"                                
[2267] "Turicibacter bilis"                                     
[2268] "Xylanimonas cellulosilytica"                            
[2269] "Ornithinimicrobium sp. HY006"                           
[2270] "Mycobacteroides abscessus"                              
[2271] "Rhodococcus aetherivorans"                              
[2272] "Streptomyces sp. NHF165"                                
[2273] "Streptomyces lunaelactis"                               
[2274] "Streptomyces xinghaiensis"                              
[2275] "Streptomyces nodosus"                                   
[2276] "Streptacidiphilus sp. PB12-B1b"                         
[2277] "Nocardioides sp. JQ2195"                                
[2278] "Actinoalloteichus sp. GBA129-24"                        
[2279] "Saccharothrix syringae"                                 
[2280] "Micromonospora craniellae"                              
[2281] "Actinomadura verrucosospora"                            
[2282] "Iamia sp. SCSIO 61187"                                  
[2283] "Phormidium yuhuli"                                      
[2284] "Microcystis sp. MC19"                                   
[2285] "Mycoplasma feriruminatoris"                             
[2286] "Mesomycoplasma neurolyticum"                            
[2287] "Candidatus Phytoplasma australiense"                    
[2288] "Acholeplasma laidlawii"                                 
[2289] "Malacoplasma penetrans"                                 
[2290] "Deinococcus sp. AJ005"                                  
[2291] "Fluviicola taffensis"                                   
[2292] "Chlamydia trachomatis"                                  
[2293] "Companilactobacillus allii"                             
[2294] "Microbacterium sp. 10M-3C3"                             
[2295] "Dermacoccus nishinomiyaensis"                           
[2296] "Mycolicibacterium goodii"                               
[2297] "Streptomyces sp. 769"                                   
[2298] "Sphingobacterium sp. BN32"                              
[2299] "Pseudomonas furukawaii"                                 
[2300] "Acinetobacter haemolyticus"                             
[2301] "Granulosicoccus antarcticus"                            
[2302] "Bradyrhizobium amphicarpaeae"                           
[2303] "Makelovirus prm1"                                       
[2304] "Lactobacillus sp. PV037"                                
[2305] "Streptococcus pantholopis"                              
[2306] "Jeotgalibaca sp. MA1X17-3"                              
[2307] "Enterococcus casseliflavus"                             
[2308] "Enterococcus raffinosus"                                
[2309] "Aerococcus viridans"                                    
[2310] "Bacillus sp. FJAT-42376"                                
[2311] "Bacillus infantis"                                      
[2312] "Cytobacillus spongiae"                                  
[2313] "Neobacillus sp. OS1-2"                                  
[2314] "Virgibacillus phasianinus"                              
[2315] "Niallia sp. RD1"                                        
[2316] "Anoxybacillus caldiproteolyticus"                       
[2317] "Paraliobacillus zengyii"                                
[2318] "Paenibacillus sp. JNUCC-31"                             
[2319] "Paenibacillus sp. BR1-192"                              
[2320] "Paenibacillus sp. CAA11"                                
[2321] "Paenibacillus amylolyticus"                             
[2322] "Paenibacillus antarcticus"                              
[2323] "Staphylococcus gallinarum"                              
[2324] "Jeotgalicoccus sp. WY2"                                 
[2325] "Macrococcus brunensis"                                  
[2326] "Tumebacillus algifaecis"                                
[2327] "Alkaliphilus metalliredigens"                           
[2328] "Thermanaerosceptrum fracticalcis"                       
[2329] "Thermoanaerobacterium sp. CMT5567-10"                   
[2330] "Veillonella atypica"                                    
[2331] "Caloranaerobacter azorensis"                            
[2332] "Arthrobacter sp. YC-RL1"                                
[2333] "Arthrobacter citreus"                                   
[2334] "Rothia dentocariosa"                                    
[2335] "Microbacterium foliorum"                                
[2336] "Humibacter ginsenosidimutans"                           
[2337] "Pontimonas salivibrio"                                  
[2338] "Arsenicicoccus sp. oral taxon 190"                      
[2339] "Georgenia faecalis"                                     
[2340] "Corynebacterium sp. LM112"                              
[2341] "Corynebacterium stationis"                              
[2342] "Corynebacterium pseudotuberculosis"                     
[2343] "Corynebacterium jeddahense"                             
[2344] "Mycolicibacterium sp. MU0053"                           
[2345] "[Mycobacterium] stephanolepidis"                        
[2346] "Nocardia huaxiensis"                                    
[2347] "Streptomyces sp. XD-27"                                 
[2348] "Streptomyces sp. CGMCC 4.7035"                          
[2349] "Streptomyces sp. NEAU-sy36"                             
[2350] "Streptomyces aurantiacus"                               
[2351] "Streptomyces xanthophaeus"                              
[2352] "Streptomyces deccanensis"                               
[2353] "Streptomyces griseoviridis"                             
[2354] "Kitasatospora sp. NA04385"                              
[2355] "Brooklawnia sp. SH051"                                  
[2356] "Nocardioides sp. WS12"                                  
[2357] "Bifidobacterium sp. ESL0790"                            
[2358] "Amycolatopsis sp. Hca4"                                 
[2359] "Amycolatopsis sp. YIM 10"                               
[2360] "Saccharomonospora viridis"                              
[2361] "Actinomyces massiliensis"                               
[2362] "Fannyhessea vaginae"                                    
[2363] "Actinobaculum sp. 313"                                  
[2364] "Micromonospora sp. WMMD812"                             
[2365] "Nocardiopsis exhalans"                                  
[2366] "Nocardiopsis alba"                                      
[2367] "Iamia majanohamensis"                                   
[2368] "Kovacikia minuta"                                       
[2369] "Leptolyngbya sp. O-77"                                  
[2370] "Deinococcus actinosclerus"                              
[2371] "Dysgonomonas sp. HDW5B"                                 
[2372] "Flavobacterium sp. IMCC34852"                           
[2373] "Flavobacterium commune"                                 
[2374] "Flavobacterium pectinovorum"                            
[2375] "Flavobacterium sangjuense"                              
[2376] "Flavobacterium magnum"                                  
[2377] "Flavobacterium johnsoniae"                              
[2378] "Flavobacterium anhuiense"                               
[2379] "Capnocytophaga canimorsus"                              
[2380] "Nonlabens sp. Hel1_33_55"                               
[2381] "Nonlabens ponticola"                                    
[2382] "Formosa sp. Hel1_31_208"                                
[2383] "Cellulophaga algicola"                                  
[2384] "Lacinutrix neustonica"                                  
[2385] "Chryseobacterium gallinarum"                            
[2386] "Chryseobacterium oryzae"                                
[2387] "Chryseobacterium joostei"                               
[2388] "Weeksella virosa"                                       
[2389] "Hymenobacter sp. APR13"                                 
[2390] "Hymenobacter sp. BT18"                                  
[2391] "Hymenobacter sediminicola"                              
[2392] "Pontibacter korlensis"                                  
[2393] "Dyadobacter chenhuakuii"                                
[2394] "Dyadobacter chenwenxiniae"                              
[2395] "Dyadobacter fanqingshengii"                             
[2396] "Larkinella sp. IE-0392"                                 
[2397] "Catalinimonas niigatensis"                              
[2398] "Porifericola rhodea"                                    
[2399] "Mucilaginibacter sp. 14171R-50"                         
[2400] "Mucilaginibacter robiniae"                              
[2401] "Pedobacter sp."                                         
[2402] "Pedobacter sp. D749"                                    
[2403] "Pedobacter sp. SL55"                                    
[2404] "Pedobacter riviphilus"                                  
[2405] "Pedobacter steynii"                                     
[2406] "Chitinophaga pinensis"                                  
[2407] "Chitinophaga agri"                                      
[2408] "Flavisolibacter tropicus"                               
[2409] "Pseudobacter ginsenosidimutans"                         
[2410] "Chlorobium limicola"                                    
[2411] "Citrobacter sp. CRE-46"                                 
[2412] "Citrobacter sp. RHB25-C09"                              
[2413] "Pantoea phytobeneficialis"                              
[2414] "Pseudomonas sp. St316"                                  
[2415] "Pseudomonas otitidis"                                   
[2416] "Xanthomonas sacchari"                                   
[2417] "Luteibacter anthropi"                                   
[2418] "Halomonas huangheensis"                                 
[2419] "Colwellia sp. PAMC 20917"                               
[2420] "Idiomarina loihiensis"                                  
[2421] "Ectothiorhodospira haloalkaliphila"                     
[2422] "Pasteurella dagmatis"                                   
[2423] "Mannheimia varigena"                                    
[2424] "Gallibacterium anatis"                                  
[2425] "Thiomicrorhabdus aquaedulcis"                           
[2426] "Bradyrhizobium erythrophlei"                            
[2427] "Pseudolabrys sp. FHR47"                                 
[2428] "Methylovirgula ligni"                                   
[2429] "Porphyrobacter sp. ULC335"                              
[2430] "Aliiroseovarius sp. M344"                               
[2431] "Yoonia vestfoldensis"                                   
[2432] "Sulfitobacter pontiacus"                                
[2433] "Roseovarius sp. THAF9"                                  
[2434] "Acetobacter pasteurianus"                               
[2435] "Lichenicola cladoniae"                                  
[2436] "Brevundimonas sp."                                      
[2437] "Burkholderia cepacia"                                   
[2438] "Rhodoferax sp. TBRC 17307"                              
[2439] "Rhodoferax antarcticus"                                 
[2440] "Pseudoduganella flava"                                  
[2441] "Alcaligenes faecalis"                                   
[2442] "Neisseria animaloris"                                   
[2443] "Nitrosomonas ureae"                                     
[2444] "Treponema vincentii"                                    
[2445] "Borreliella garinii"                                    
[2446] "Pseudodesulfovibrio sediminis"                          
[2447] "Maridesulfovibrio salexigens"                           
[2448] "Megalodesulfovibrio gigas"                              
[2449] "Geomonas subterranea"                                   
[2450] "Desulfuromonas versatilis"                              
[2451] "Desulfosediminicola flagellatus"                        
[2452] "Alienimonas californiensis"                             
[2453] "Tautonia plasticadhaerens"                              
[2454] "Ilyobacter polytropus"                                  
[2455] "Leptotrichia sp. HMT-225"                               
[2456] "Sulfurovum lithotrophicum"                              
[2457] "Paludibaculum fermentans"                               
[2458] "Geothrix sp. 21YS21S-2"                                 
[2459] "Candidatus Nanosynbacter sp. HMT-352"                   
[2460] "Candidatus Mycosynbacter amalyticus"                    
[2461] "Elusimicrobium minutum"                                 
[2462] "Tepidibacter sp. 8C15b"                                 
[2463] "Evansella cellulosilytica"                              
[2464] "Rothia nasimurium"                                      
[2465] "Streptomyces sp. 891-h"                                 
[2466] "Actinomyces sp. oral taxon 169"                         
[2467] "Klebsiella sp. PL-2018"                                 
[2468] "Yersinia pestis"                                        
[2469] "Frederiksenia canicola"                                 
[2470] "Bradyrhizobium sp. SK17"                                
[2471] "Streptomyces chromofuscus"                              
[2472] "Nocardioides humi"                                      
[2473] "Brevibacillus agri"                                     
[2474] "Candidatus Phytoplasma mali"                            
[2475] "Metamycoplasma orale"                                   
[2476] "Thermus scotoductus"                                    
[2477] "Dromedary astrovirus"                                   
[2478] "Candidatus Desulforudis audaxviator"                    
[2479] "Candidatus Syntrophocurvum alkaliphilum"                
[2480] "Mycobacterium sp. SMC-2"                                
[2481] "Kitasatospora sp. CM 4170"                              
[2482] "Candidatus Nardonella dryophthoridicola"                
[2483] "Helicobacter canis"                                     
[2484] "Helicobacter mustelae"                                  
[2485] "Pseudodesulfovibrio aespoeensis"                        
[2486] "Vulgatibacter incomptus"                                
[2487] "Methanosphaera sp. BMS"                                 
[2488] "Sichuan takin astrovirus"                               
[2489] "Picornavirales Tottori-HG1"                             
[2490] "Sporosarcina sp. P37"                                   
[2491] "Deinococcus sp. KNUC1210"                               
[2492] "Empedobacter falsenii"                                  
[2493] "Pasteurella multocida"                                  
[2494] "Candidatus Paraluminiphilus aquimaris"                  
[2495] "Ottowia sp. oral taxon 894"                             
[2496] "Lawsonia intracellularis"                               
[2497] "Oenococcus kitaharae"                                   
[2498] "Weissella koreensis"                                    
[2499] "Liquorilactobacillus mali"                              
[2500] "Bacillus siamensis"                                     
[2501] "Bacillus sp. NSP9.1"                                    
[2502] "Peribacillus sp. R9-11"                                 
[2503] "Shouchella hunanensis"                                  
[2504] "Staphylococcus saprophyticus"                           
[2505] "Planococcus donghaensis"                                
[2506] "Listeria grayi"                                         
[2507] "Kyrpidia tusciae"                                       
[2508] "Aceticella autotrophica"                                
[2509] "Natranaerofaba carboxydovora"                           
[2510] "Ezakiella massiliensis"                                 
[2511] "Kocuria rhizophila"                                     
[2512] "Sinomonas atrocyanea"                                   
[2513] "Clavibacter michiganensis"                              
[2514] "Ornithinimicrobium flavum"                              
[2515] "Streptomyces sp. FZ201"                                 
[2516] "Streptomyces sp. SYP-A7193"                             
[2517] "Streptomyces sp. HSG2"                                  
[2518] "Streptomyces sp. TLI_053"                               
[2519] "Kitasatospora sp. HUAS 3-15"                            
[2520] "Bifidobacterium sp. ESL0728"                            
[2521] "Pseudonocardia sp. EC080625-04"                         
[2522] "Phytohabitans suffuscus"                                
[2523] "Dehalogenimonas formicexedens"                          
[2524] "Mycoplasma sp. SG1"                                     
[2525] "Mycoplasma crocodyli"                                   
[2526] "[Mycoplasma] mobile"                                    
[2527] "Sphaerospermopsis kisseleviana"                         
[2528] "Gloeobacter kilaueensis"                                
[2529] "Acinetobacter nosocomialis"                             
[2530] "Mamastrovirus 3"                                        
[2531] "Secundilactobacillus paracollinoides"                   
[2532] "Melissococcus plutonius"                                
[2533] "Heyndrickxia vini"                                      
[2534] "Cytobacillus solani"                                    
[2535] "Alkalihalobacillus sp. AL-G"                            
[2536] "Brevibacillus sp. BB3-R1"                               
[2537] "Novibacillus thermophilus"                              
[2538] "Arthrobacter sp. MMS18-M83"                             
[2539] "Arthrobacter sp. zg-Y820"                               
[2540] "Arthrobacter gengyunqii"                                
[2541] "Microbacterium sp. zg-B96"                              
[2542] "Microbacterium sp. A18JL241"                            
[2543] "Microbacterium sp. SL75"                                
[2544] "Microbacterium endophyticum"                            
[2545] "Microbacterium terricola"                               
[2546] "Agromyces protaetiae"                                   
[2547] "Rathayibacter toxicus"                                  
[2548] "Leucobacter allii"                                      
[2549] "Protaetiibacter sp. SSC-01"                             
[2550] "Cellulomonas sp. Y8"                                    
[2551] "Cellulomonas xiejunii"                                  
[2552] "Brachybacterium faecium"                                
[2553] "Brevibacterium luteolum"                                
[2554] "Cellulosimicrobium protaetiae"                          
[2555] "Ruania suaedae"                                         
[2556] "Beutenbergia cavernae"                                  
[2557] "Mycobacterium sp. IDR2000157661"                        
[2558] "Mycolicibacterium sp. TUM20985"                         
[2559] "Mycolicibacterium moriokaense"                          
[2560] "Mycolicibacterium madagascariense"                      
[2561] "Nocardia terpenica"                                     
[2562] "Gordonia polyisoprenivorans"                            
[2563] "Streptomyces sp. MST-110588"                            
[2564] "Streptomyces sp. RPA4-2"                                
[2565] "Streptomyces sp. HM190"                                 
[2566] "Streptomyces sp. SCUT-3"                                
[2567] "Streptomyces sp. WAC 01438"                             
[2568] "Streptomyces sp. YIM 121038"                            
[2569] "Streptomyces sp. M92"                                   
[2570] "Streptomyces sp. FXJ1.172"                              
[2571] "Streptomyces kanamyceticus"                             
[2572] "Streptomyces alfalfae"                                  
[2573] "Streptomyces roseochromogenus"                          
[2574] "Streptomyces liliifuscus"                               
[2575] "Streptomyces murinus"                                   
[2576] "Streptomyces lienomycini"                               
[2577] "Streptomyces leeuwenhoekii"                             
[2578] "Streptomyces griseocarneus"                             
[2579] "Streptomyces chartreusis"                               
[2580] "Tessaracoccus aquimaris"                                
[2581] "Microlunatus elymi"                                     
[2582] "Propioniciclava coleopterorum"                          
[2583] "Acidipropionibacterium virtanenii"                      
[2584] "Raineyella fluvialis"                                   
[2585] "Nocardioides sp. S5"                                    
[2586] "Nocardioides sp. W7"                                    
[2587] "Micromonospora auratinigra"                             
[2588] "Micromonospora zamorensis"                              
[2589] "Actinoplanes derwentensis"                              
[2590] "Actinoplanes friuliensis"                               
[2591] "Plantactinospora sp. KBS50"                             
[2592] "Natronosporangium hydrolyticum"                         
[2593] "Amycolatopsis sp. BJA-103"                              
[2594] "Amycolatopsis sp. DG1A-15b"                             
[2595] "Amycolatopsis aidingensis"                              
[2596] "Pseudonocardia sp. HH130630-07"                         
[2597] "Actinosynnema pretiosum"                                
[2598] "Flaviflexus salsibiostraticola"                         
[2599] "Spiractinospora alimapuensis"                           
[2600] "Nonomuraea phyllanthi"                                  
[2601] "Nonomuraea coxensis"                                    
[2602] "Catenulispora acidiphila"                               
[2603] "Capillimicrobium parvum"                                
[2604] "Thermoleophilum album"                                  
[2605] "Spiroplasma clarkii"                                    
[2606] "Gloeocapsa sp. PCC 7428"                                
[2607] "Synechococcus sp. NB0720_010"                           
[2608] "Deinococcus geothermalis"                               
[2609] "Deinococcus aquaticus"                                  
[2610] "Deinococcus irradiatisoli"                              
[2611] "Stenotrophomonas pavanii"                               
[2612] "Pararhodospirillum photometricum"                       
[2613] "Oceanidesulfovibrio marinus"                            
[2614] "Rabbit astrovirus TN/2208/2010"                         
[2615] "Bovine astrovirus B76-2/HK"                             
[2616] "Arthrobacter sp. PAMC25564"                             
[2617] "Mumia sp. ZJ1417"                                       
[2618] "Micropruina glycogenica"                                
[2619] "Meiothermus taiwanensis"                                
[2620] "Pantoea eucrina"                                        
[2621] "Pseudomonas mendocina"                                  
[2622] "Pseudomonas sp. PSE14"                                  
[2623] "Histophilus somni"                                      
[2624] "Ancylobacter polymorphus"                               
[2625] "Pannonibacter phragmitetus"                             
[2626] "Fructilactobacillus cliffordii"                         
[2627] "Paucilactobacillus oligofermentans"                     
[2628] "Geobacillus genomosp. 3"                                
[2629] "Planococcus massiliensis"                               
[2630] "Micromonospora sp. L5"                                  
[2631] "Klebsiella oxytoca"                                     
[2632] "Raoultella ornithinolytica"                             
[2633] "Enterobacter oligotrophicus"                            
[2634] "Citrobacter braakii"                                    
[2635] "Arsenophonus nasoniae"                                  
[2636] "Serratia plymuthica"                                    
[2637] "Nitrosomonas eutropha"                                  
[2638] "Enterovirus goat/JL14"                                  
[2639] "Sichuan takin enterovirus"                              
[2640] "Microcella flavibacter"                                 
[2641] "Saccharopolyspora spinosa"                              
[2642] "Citrobacter freundii complex sp. CFNIH2"                
[2643] "Mycobacterium noviomagense"                             
[2644] "Streptomyces sp. WAC 01529"                             
[2645] "Cutibacterium granulosum"                               
[2646] "Pseudonocardia broussonetiae"                           
[2647] "Acidothermus cellulolyticus"                            
[2648] "Solitalea lacus"                                        
[2649] "Chelatococcus sp. CO-6"                                 
[2650] "Gardnerella swidsinskii"                                
[2651] "Algibacter luteus"                                      
[2652] "Pasivirus A"                                            
[2653] "Streptomyces sp. ICC4"                                  
[2654] "Gleimia hominis"                                        
[2655] "Nostoc sp. CENA543"                                     
[2656] "Staphylococcus arlettae"                                
[2657] "Thermoactinomyces vulgaris"                             
[2658] "Microbacterium elymi"                                   
[2659] "Parageobacillus thermoglucosidasius"                    
[2660] "Curtobacterium sp. MCLR17_036"                          
[2661] "Occultella kanbiaonis"                                  
[2662] "Mycolicibacterium mageritense"                          
[2663] "Tsukamurella paurometabola"                             
[2664] "Streptomyces sp. PCS3-D2"                               
[2665] "Streptomyces rectiverticillatus"                        
[2666] "Actinomyces howellii"                                   
[2667] "Mobiluncus curtisii"                                    
[2668] "Amycolatopsis keratiniphila"                            
[2669] "Dactylosporangium roseum"                               
[2670] "Burkholderia stabilis"                                  
[2671] "Chromobacterium sp. IIBBL 290-4"                        

# ============================================


# ============================================
# SEARCH FOR TAXA CONTAINING A KEYWORD
# ============================================
search_term <- "Lactobacillus"
# ============================================

matching_taxa <- rownames(species_frac)[grep(search_term, rownames(species_frac), ignore.case = TRUE)]

cat("Taxa matching '", search_term, "':\n", sep = "")

Taxa matching 'Lactobacillus':

print(matching_taxa)

 [1] "Lactobacillus amylovorus"              
 [2] "Lactobacillus johnsonii"               
 [3] "Lactobacillus delbrueckii"             
 [4] "Lactobacillus acidophilus"             
 [5] "Lactobacillus crispatus"               
 [6] "Lactobacillus iners"                   
 [7] "Lactobacillus sp. ESL0785"             
 [8] "Lactobacillus helveticus"              
 [9] "Lactobacillus gasseri"                 
[10] "Lactobacillus intestinalis"            
[11] "Lactobacillus kefiranofaciens"         
[12] "Lactobacillus taiwanensis"             
[13] "Lactobacillus acetotolerans"           
[14] "Lactobacillus amylolyticus"            
[15] "Limosilactobacillus mucosae"           
[16] "Limosilactobacillus reuteri"           
[17] "Limosilactobacillus fermentum"         
[18] "Ligilactobacillus ruminis"             
[19] "Ligilactobacillus salivarius"          
[20] "Amylolactobacillus amylophilus"        
[21] "Lactobacillus sp. ESL0680"             
[22] "Lactobacillus sp. IBH004"              
[23] "Lactobacillus sp. PV034"               
[24] "Lactobacillus sp. AMBV1719"            
[25] "Lactobacillus sp. ESL0681"             
[26] "Lactobacillus sp. ESL0677"             
[27] "Lactobacillus sp. 3B(2020)"            
[28] "Lactobacillus ultunensis"              
[29] "Lactobacillus jensenii"                
[30] "Lactobacillus kullabergensis"          
[31] "Lactobacillus panisapium"              
[32] "Lactobacillus apis"                    
[33] "Lactobacillus paragasseri"             
[34] "Lactobacillus terrae"                  
[35] "Limosilactobacillus vaginalis"         
[36] "Limosilactobacillus portuensis"        
[37] "Limosilactobacillus oris"              
[38] "Ligilactobacillus agilis"              
[39] "Ligilactobacillus murinus"             
[40] "Latilactobacillus curvatus"            
[41] "Latilactobacillus sakei"               
[42] "Lentilactobacillus buchneri"           
[43] "Lentilactobacillus laojiaonis"         
[44] "Lentilactobacillus curieae"            
[45] "Bombilactobacillus bombi"              
[46] "Bombilactobacillus folatiphilus"       
[47] "Bombilactobacillus thymidiniphilus"    
[48] "Schleiferilactobacillus harbinensis"   
[49] "Fructilactobacillus lindneri"          
[50] "Acetilactobacillus jinshanensis"       
[51] "Lactobacillus phage phiAQ113"          
[52] "Limosilactobacillus pontis"            
[53] "Limosilactobacillus panis"             
[54] "Limosilactobacillus gastricus"         
[55] "Ligilactobacillus sp. BD7642"          
[56] "Fructilactobacillus sanfranciscensis"  
[57] "Companilactobacillus ginsenosidimutans"
[58] "Liquorilactobacillus hordei"           
[59] "Loigolactobacillus bifermentans"       
[60] "Furfurilactobacillus rossiae"          
[61] "Sporolactobacillus terrae"             
[62] "Lentilactobacillus parabuchneri"       
[63] "Loigolactobacillus coryniformis"       
[64] "Lapidilactobacillus dextrinicus"       
[65] "Lactobacillus sp. PV012"               
[66] "Limosilactobacillus frumenti"          
[67] "Levilactobacillus brevis"              
[68] "Levilactobacillus suantsaii"           
[69] "Levilactobacillus zymae"               
[70] "Loigolactobacillus backii"             
[71] "Companilactobacillus zhachilii"        
[72] "Secundilactobacillus malefermentans"   
[73] "Paucilactobacillus nenjiangensis"      
[74] "Ligilactobacillus animalis"            
[75] "Lentilactobacillus hilgardii"          
[76] "Companilactobacillus futsaii"          
[77] "Lactobacillus sp. JM1"                 
[78] "Apilactobacillus kunkeei"              
[79] "Apilactobacillus apisilvae"            
[80] "Lactobacillus sp. ESL0684"             
[81] "Lactobacillus sp. ESL0731"             
[82] "Lactobacillus sp. ESL0700"             
[83] "Fructilactobacillus hinvesii"          
[84] "Companilactobacillus allii"            
[85] "Lactobacillus sp. PV037"               
[86] "Liquorilactobacillus mali"             
[87] "Secundilactobacillus paracollinoides"  
[88] "Fructilactobacillus cliffordii"        
[89] "Paucilactobacillus oligofermentans"    

# ============================================
# CHANGE THESE TAXA NAMES AS NEEDED
# ============================================
selected_taxa <- c(
  "Selenomonas ruminantium",
  "Lactobacillus amylovorus",
  "Prevotella copri",
  "Megasphaera elsdenii"
)
# ============================================

# Check which taxa exist in the data
available_taxa <- selected_taxa[selected_taxa %in% rownames(species_frac)]
missing_taxa <- selected_taxa[!selected_taxa %in% rownames(species_frac)]

if (length(missing_taxa) > 0) {
  message("Taxa not found in data: ", paste(missing_taxa, collapse = ", "))
}

if (length(available_taxa) > 0) {
  
  # Extract data for selected taxa
  plot_data <- data.frame(
    sample = colnames(species_frac),
    t(species_frac[available_taxa, , drop = FALSE])
  )
  
  # Reshape to long format
  plot_data_long <- plot_data %>%
    pivot_longer(
      cols = -sample,
      names_to = "taxon",
      values_to = "abundance"
    )
  
  # Merge with metadata
  plot_data_long <- merge(plot_data_long, meta_tab, by.x = "sample", by.y = "row.names")
  
  # Convert abundance to percentage
  plot_data_long$abundance_pct <- plot_data_long$abundance * 100
  
  # Plot by Complex
  p1 <- ggplot(plot_data_long, aes(x = complex, y = abundance_pct, fill = complex)) +
    geom_boxplot(outlier.shape = NA, alpha = 0.7) +
    geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
    facet_wrap(~ taxon, scales = "free_y", ncol = 2) +
    scale_fill_manual(values = complex_colors) +
    stat_compare_means(method = "kruskal.test", label = "p.format", 
                       label.x = 1.5, label.y.npc = 0.95, size = 3.5) +
    labs(
      x = "Diet Complexity",
      y = "Relative Abundance (%)",
      fill = "Complex",
      title = "Selected Taxa by Diet Complexity"
    ) +
    theme_publication +
    theme(
      legend.position = "none",
      strip.text = element_text(face = "bold.italic", size = 10)
    )
  
  # Plot by Protease
  p2 <- ggplot(plot_data_long, aes(x = protease, y = abundance_pct, fill = protease)) +
    geom_boxplot(outlier.shape = NA, alpha = 0.7) +
    geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
    facet_wrap(~ taxon, scales = "free_y", ncol = 2) +
    scale_fill_manual(values = protease_colors) +
    stat_compare_means(method = "wilcox.test", label = "p.format", 
                       label.x = 1.3, label.y.npc = 0.95, size = 3.5) +
    labs(
      x = "Protease Treatment",
      y = "Relative Abundance (%)",
      fill = "Protease",
      title = "Selected Taxa by Protease Treatment"
    ) +
    theme_publication +
    theme(
      legend.position = "none",
      strip.text = element_text(face = "bold.italic", size = 10)
    )
  
  print(p1)
  print(p2)
  
} else {
  print("No selected taxa found in the data")
}

Plot selected taxa with interaction (Complex × Protease):

Bruno, aqui caso vc queira fazer alguns plots so de alguns taxas. Que vc achar interessante. Ai so mudar o nome e pedir para rodar. Esse codigo é para interacão.

# ============================================
# CHANGE THESE TAXA NAMES AS NEEDED
# ============================================
selected_taxa <- c(
  "Selenomonas ruminantium",
  "Lactobacillus amylovorus",
  "Prevotella copri",
  "Megasphaera elsdenii"
)
# ============================================

# Check which taxa exist in the data
available_taxa <- selected_taxa[selected_taxa %in% rownames(species_frac)]

if (length(available_taxa) > 0) {
  
  # Extract data for selected taxa
  plot_data <- data.frame(
    sample = colnames(species_frac),
    t(species_frac[available_taxa, , drop = FALSE])
  )
  
  # Reshape to long format
  plot_data_long <- plot_data %>%
    pivot_longer(
      cols = -sample,
      names_to = "taxon",
      values_to = "abundance"
    )
  
  # Merge with metadata
  plot_data_long <- merge(plot_data_long, meta_tab, by.x = "sample", by.y = "row.names")
  
  # Convert abundance to percentage
  plot_data_long$abundance_pct <- plot_data_long$abundance * 100
  
  # Plot interaction
  p_interaction <- ggplot(plot_data_long, aes(x = complex, y = abundance_pct, fill = protease)) +
    geom_boxplot(outlier.shape = NA, alpha = 0.7) +
    geom_point(position = position_jitterdodge(jitter.width = 0.2), size = 2, alpha = 0.6) +
    facet_wrap(~ taxon, scales = "free_y", ncol = 2) +
    scale_fill_manual(values = protease_colors) +
    labs(
      x = "Diet Complexity",
      y = "Relative Abundance (%)",
      fill = "Protease",
      title = "Selected Taxa: Complex × Protease Interaction"
    ) +
    theme_publication +
    theme(
      legend.position = "bottom",
      strip.text = element_text(face = "bold.italic", size = 10)
    )
  
  print(p_interaction)
  
} else {
  print("No selected taxa found in the data")
}

Single taxon detailed plot:

# ============================================
# CHANGE THIS TAXON NAME AS NEEDED
# ============================================
single_taxon <- "Selenomonas ruminantium"
# ============================================

if (single_taxon %in% rownames(species_frac)) {
  
  # Extract data
  taxon_data <- data.frame(
    sample = colnames(species_frac),
    abundance = as.numeric(species_frac[single_taxon, ])
  )
  
  # Merge with metadata
  taxon_data <- merge(taxon_data, meta_tab, by.x = "sample", by.y = "row.names")
  taxon_data$abundance_pct <- taxon_data$abundance * 100
  
  # Pairwise comparisons for complex
  comparisons_complex <- list(c("low", "medium"), c("low", "high"), c("medium", "high"))
  
  # Plot
  p_single <- ggplot(taxon_data, aes(x = complex, y = abundance_pct, fill = protease)) +
    geom_boxplot(outlier.shape = NA, alpha = 0.7, position = position_dodge(0.8)) +
    geom_point(position = position_jitterdodge(jitter.width = 0.2, dodge.width = 0.8), 
               size = 3, alpha = 0.7) +
    scale_fill_manual(values = protease_colors) +
    labs(
      x = "Diet Complexity",
      y = "Relative Abundance (%)",
      fill = "Protease",
      title = bquote(italic(.(single_taxon)))
    ) +
    theme_publication +
    theme(
      legend.position = "right",
      plot.title = element_text(face = "bold.italic", size = 14)
    )
  
  print(p_single)
  
} else {
  print(paste("Taxon not found:", single_taxon))
}

Plot using CLR-transformed data (for statistical comparisons):

# ============================================
# CHANGE THESE TAXA NAMES AS NEEDED
# ============================================
selected_taxa <- c(
  "Selenomonas ruminantium",
  "Lactobacillus amylovorus",
  "Prevotella copri",
  "Megasphaera elsdenii"
)
# ============================================

# Check which taxa exist in the data
available_taxa <- selected_taxa[selected_taxa %in% rownames(species_counts_filtered)]

if (length(available_taxa) > 0) {
  
  # CLR transform
  species_pseudo <- species_counts_filtered + 1
  species_clr <- log(species_pseudo) - rowMeans(log(species_pseudo))
  
  # Extract data for selected taxa
  plot_data <- data.frame(
    sample = colnames(species_clr),
    t(species_clr[available_taxa, , drop = FALSE])
  )
  
  # Reshape to long format
  plot_data_long <- plot_data %>%
    pivot_longer(
      cols = -sample,
      names_to = "taxon",
      values_to = "clr_abundance"
    )
  
  # Merge with metadata
  plot_data_long <- merge(plot_data_long, meta_tab, by.x = "sample", by.y = "row.names")
  
  # Plot by Complex
  p_clr <- ggplot(plot_data_long, aes(x = complex, y = clr_abundance, fill = complex)) +
    geom_boxplot(outlier.shape = NA, alpha = 0.7) +
    geom_jitter(width = 0.2, size = 2, alpha = 0.6) +
    facet_wrap(~ taxon, scales = "free_y", ncol = 2) +
    scale_fill_manual(values = complex_colors) +
    stat_compare_means(method = "kruskal.test", label = "p.format", 
                       label.x = 1.5, label.y.npc = 0.95, size = 3.5) +
    labs(
      x = "Diet Complexity",
      y = "CLR Abundance",
      fill = "Complex",
      title = "Selected Taxa (CLR-transformed)"
    ) +
    theme_publication +
    theme(
      legend.position = "none",
      strip.text = element_text(face = "bold.italic", size = 10)
    )
  
  print(p_clr)
  
} else {
  print("No selected taxa found in the data")
}

Taxonomic Barplots - All Levels

Top taxa barplot - Phylum level:

# ============================================
# SETTINGS
# ============================================
n_top_taxa <- 10  # Number of top taxa to show
# ============================================

# Calculate mean abundance per taxon
phylum_mean <- rowMeans(phylum_frac)

# Get top taxa
top_phyla <- names(sort(phylum_mean, decreasing = TRUE))[1:n_top_taxa]

# Prepare data
phylum_plot <- as.data.frame(t(phylum_frac))
phylum_plot$sample <- rownames(phylum_plot)

# Merge with metadata
phylum_plot <- merge(phylum_plot, meta_tab, by.x = "sample", by.y = "row.names")

# Reshape to long format
phylum_long <- phylum_plot %>%
  pivot_longer(
    cols = all_of(rownames(phylum_frac)),
    names_to = "phylum",
    values_to = "abundance"
  )

# Group low-abundance taxa as "Other"
phylum_long$phylum_grouped <- ifelse(phylum_long$phylum %in% top_phyla, 
                                      phylum_long$phylum, "Other")

# Aggregate
phylum_agg <- phylum_long %>%
  group_by(sample, complex, protease, phylum_grouped) %>%
  summarise(abundance = sum(abundance), .groups = "drop")

# Set factor order (top taxa + Other at end)
phylum_agg$phylum_grouped <- factor(phylum_agg$phylum_grouped, 
                                     levels = c(top_phyla, "Other"))

# Order samples by complex and protease
phylum_agg$sample <- factor(phylum_agg$sample, 
                             levels = rownames(meta_tab)[order(meta_tab$complex, meta_tab$protease)])

# Extended color palette for taxa
taxa_colors <- c(cb_palette, "#666666", "#333333", "#AAAAAA")

# Plot
ggplot(phylum_agg, aes(x = sample, y = abundance * 100, fill = phylum_grouped)) +
  geom_bar(stat = "identity", position = "stack") +
  scale_fill_manual(values = taxa_colors) +
  facet_grid(~ complex, scales = "free_x", space = "free_x") +
  labs(
    x = "",
    y = "Relative Abundance (%)",
    fill = "Phylum",
    title = "Phylum-level Composition by Diet Complexity"
  ) +
  theme_publication +
  theme(
    axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, size = 8),
    legend.position = "right",
    strip.text = element_text(face = "bold", size = 12)
  )

Top taxa barplot - Genus level:

# ============================================
# SETTINGS
# ============================================
n_top_taxa <- 15  # Number of top taxa to show
# ============================================

# Calculate mean abundance per taxon
genus_mean <- rowMeans(genus_frac)

# Get top taxa
top_genera <- names(sort(genus_mean, decreasing = TRUE))[1:n_top_taxa]

# Prepare data
genus_plot <- as.data.frame(t(genus_frac))
genus_plot$sample <- rownames(genus_plot)

# Merge with metadata
genus_plot <- merge(genus_plot, meta_tab, by.x = "sample", by.y = "row.names")

# Reshape to long format
genus_long <- genus_plot %>%
  pivot_longer(
    cols = all_of(rownames(genus_frac)),
    names_to = "genus",
    values_to = "abundance"
  )

# Group low-abundance taxa as "Other"
genus_long$genus_grouped <- ifelse(genus_long$genus %in% top_genera, 
                                    genus_long$genus, "Other")

# Aggregate
genus_agg <- genus_long %>%
  group_by(sample, complex, protease, genus_grouped) %>%
  summarise(abundance = sum(abundance), .groups = "drop")

# Set factor order
genus_agg$genus_grouped <- factor(genus_agg$genus_grouped, 
                                   levels = c(top_genera, "Other"))

# Order samples
genus_agg$sample <- factor(genus_agg$sample, 
                            levels = rownames(meta_tab)[order(meta_tab$complex, meta_tab$protease)])

# Extended color palette
taxa_colors_ext <- colorRampPalette(cb_palette)(n_top_taxa + 1)

# Plot
ggplot(genus_agg, aes(x = sample, y = abundance * 100, fill = genus_grouped)) +
  geom_bar(stat = "identity", position = "stack") +
  scale_fill_manual(values = taxa_colors_ext) +
  facet_grid(~ complex, scales = "free_x", space = "free_x") +
  labs(
    x = "",
    y = "Relative Abundance (%)",
    fill = "Genus",
    title = "Genus-level Composition by Diet Complexity"
  ) +
  theme_publication +
  theme(
    axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, size = 8),
    legend.position = "right",
    legend.text = element_text(face = "italic"),
    strip.text = element_text(face = "bold", size = 12)
  )

Top taxa barplot - Species level:

# ============================================
# SETTINGS
# ============================================
n_top_taxa <- 15  # Number of top taxa to show
# ============================================

# Calculate mean abundance per taxon
species_mean <- rowMeans(species_frac)

# Get top taxa
top_species <- names(sort(species_mean, decreasing = TRUE))[1:n_top_taxa]

# Prepare data
species_plot <- as.data.frame(t(species_frac))
species_plot$sample <- rownames(species_plot)

# Merge with metadata
species_plot <- merge(species_plot, meta_tab, by.x = "sample", by.y = "row.names")

# Reshape to long format
species_long <- species_plot %>%
  pivot_longer(
    cols = all_of(rownames(species_frac)),
    names_to = "species",
    values_to = "abundance"
  )

# Group low-abundance taxa as "Other"
species_long$species_grouped <- ifelse(species_long$species %in% top_species, 
                                        species_long$species, "Other")

# Aggregate
species_agg <- species_long %>%
  group_by(sample, complex, protease, species_grouped) %>%
  summarise(abundance = sum(abundance), .groups = "drop")

# Set factor order
species_agg$species_grouped <- factor(species_agg$species_grouped, 
                                       levels = c(top_species, "Other"))

# Order samples
species_agg$sample <- factor(species_agg$sample, 
                              levels = rownames(meta_tab)[order(meta_tab$complex, meta_tab$protease)])

# Extended color palette
taxa_colors_ext <- colorRampPalette(cb_palette)(n_top_taxa + 1)

# Plot
ggplot(species_agg, aes(x = sample, y = abundance * 100, fill = species_grouped)) +
  geom_bar(stat = "identity", position = "stack") +
  scale_fill_manual(values = taxa_colors_ext) +
  facet_grid(~ complex, scales = "free_x", space = "free_x") +
  labs(
    x = "",
    y = "Relative Abundance (%)",
    fill = "Species",
    title = "Species-level Composition by Diet Complexity"
  ) +
  theme_publication +
  theme(
    axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, size = 8),
    legend.position = "right",
    legend.text = element_text(face = "italic"),
    strip.text = element_text(face = "bold", size = 12)
  )

capabilities()

       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE       FALSE        TRUE       FALSE        TRUE 
        NLS       Rprof     profmem       cairo         ICU long.double 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
    libcurl 
       TRUE