5.7. Microbial community composition

Alpha diversity indices detailing microbial community composition within samples were calculated using vegan [67] in R. Shannon index was used for alpha diversity evaluation based on the relative abundance of each taxonomic level. Statistical comparisons of healthy controls vs. obese subjects and pre- vs. post-operative subjects were performed by Wilcoxon rank sum test and rank sum test paired Wilcoxon signed-rank test. For estimating community dissimilarities, Bray-Curtis distances were calculated by phyloseq [68] and vegan [67] and Aitchison distances were calculated by robCompositions [69] based on the relative abundance of each taxon at phylum, family, genus and species level. Adonis from vegan package [67] in R was used for PERMANOVA tests to evaluate differences among groups (number of permutation set to 999). Within-group distance (Bray-Curtis distance among samples from the same group) indicating the community divergence and between-group distances (Bray-Curtis distance among samples from each of the two groups) indicating the difference between two communities were determined and compared by Wilcoxon rank sum test, paired Wilcoxon signed-rank and Kruskal-Wallis tests, where appropriate.