2.10. Bioinformatics analysis
Alpha diversity was calculated using the Shannon, Simpson, Chao1, and OTU diversity matrices. Beta diversity was determined by principal coordinate analysis (PcoA) using unweighted and weighted UniFrac metrics. Emperor 3D viewer was used to visualize the plots. Taxon differential abundance across the groups was performed in QIIME (QIIME: group significance.py) to examine whether observation counts (i.e., OTUs and Microbial taxon) are significantly different between the groups at baseline and final visit. Before the final community quality control, the OTU table was collapsed at each taxonomic level (i.e., Phylum–nus; QIIME: collapse_taxonomy.py), with counts representing the relative abundance of each microbial taxon. Differences in the mean abundance of taxa between sample groups were calculated using Kruskal–Wallis nonparametric statistical tests. The taxon was ranked with 