2.6 | Microbial composition analysis
Alpha diversity of the gut microbiome was calculated using the Shannon
index based on the genus and KO profiles by “vegan” packsge in R
(Dixon, 2003). The overall differences in the bacterial community
structures were evaluated by principal coordinate analysis (PCoA) and
hierarchical tree analysis based on the Bray-Curtis dissimilarity
matrix, which were performed with “vegan” package in R (Dixon, 2003).
To show the special characteristics of the gut microbiome of SNM, the
taxonomic (phylum and genus) and function (COGs, KOs and CAZymes) terms
present in 90% of individuals in each gene catalog were used for
comparison and visualization with UpSet Venn (Xie et al., 2021). Then,
we calculated the differences among 12 species by the Wilcoxon rank-sum
test or Kruskal–Wallis test, and the p values were adjusted using the
Benjamini–Hochberg false discovery rate (FDR) (Yoav Benjamini, 1995).