Operational Taxonomic Unit (OUT) Cluster and Species Annotation

Sequence analyses were performed using the UPARSE software (UPARSE v.7.0.1001, http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs. The representative sequence for each OTU was screened for further annotation.

For each representative sequence, the Silva Database (version 132; https://www.arb-silva.de/), based on the Ribosomal Database Project (RDP) classifier algorithm, was used (version 2.2; http://rdp.cme.msu.edu/) to annotate taxonomic information.

In order to study the phylogenetic relationship between different OTUs, as well as the differences among the dominant species in different samples (groups), multiple sequence alignments were conducted using the MUSCLE software (version 3.8; http://www.drive5.com/muscle/).

OTU abundance information was normalized using a standard sequence number corresponding to the sample with the lowest number of sequences. Subsequent analyses of the alpha diversity and beta diversity were all performed based on these normalized output data.