Analyses of sequenced samples

Sequencing data were analysed in R (v 3.3.2) using the packages ‘dada2’ , ‘phyloseq’  , and ‘vegan ’ . Using a full-stack workflow we estimated the error rates, inferred and merged sequences, constructed a sequence table, removed chimeric sequences, and assigned taxonomy to each amplicon sequence variant (ASV). Greengenes database provided the taxonomy information based on a previously published pipeline . The phylogenetic tree was estimated using the R package ‘phangorn ’ . We constructed a neighbour-joining tree, and then fit a Generalized time-reversible with Gamma rate variation maximum likelihood tree using the neighbour-joining tree as a starting point. We used UniFrac distance (weighted and unweighted) and Bray-Curtis as our measures of compositional dissimilarity . In case of alpha diversity, we calculated species richness and evenness .