Statistical analysis of taxonomical and clinical features
Sequence data were analyzed using the phyloseqR (version 1.28.0) (Abundance raw-data counts were normalized using the cumulative sum scaling (CSS) method (To evaluate alpha diversity of bacterial communities, Shannon’s index and OTUs (Observed species) were calculated using the phyloseqR package. The proportion and composition of the most abundant species in the data was aggregated at both Phylum and Family levels. The beta diversity was computed under the Bray-Curtis dissimilarity index (Spearman’s rank correlation was also used to investigate associations between normalized microbial abundance counts, at a species level, with reported clinical variables. P-values were then adjusted with the false rate discovery method. Correlations and adjusted P-values were computed with R package stats (version 4.0.5).