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 .