Diversity Analysis of Gut Microbiota

The vegan package was used for Pan/Core species analysis. Pan/Core species analysis was used to describe changes in total species and core species populations as the sample size increases. The mothur software (version 1.30) was used for alpha diversity analysis. The commonly used alpha diversity indices include sobs, chao, ace, shannon, simpson, shannoneven, coverage and phylogenetic diversity (PD). Sobs, chao and ace indices were used to reflect community richness. Shannon and simpson indices were used to reflect community diversity. Shannoneven indice was used to reflect community evenness. Coverage index was used to reflect community coverage. PD index was used to reflect community phylogenetic diversity. The Wilcoxon rank sum test was used to analyze the differences in alpha diversity indices between groups. Subsequently, beta diversity analysis was also performed. Principal coordinate analysis (PCoA) can be used to study the similarity or difference of sample community composition. The weighted UniFrac distance algorithm was used to calculate the distance between samples. The ANOSIM was used to test differences between groups. In addition, non-metric multidimensional scaling (NMDS) analysis was also performed.