OTU (operational taxonomic unit) cluster and species annotation

OTUs were clustered by Usearch (UPARSE-OTU algorithm, http://www.drive5.com/usearch/) with default parameters (97 % identity) [56]. For each OTU representative sequence, the Silva (https://www.arb-silva.de) database was used to annotate taxonomic information via usearch-sintax (the confidence threshold was set to default, ≥0.8). The taxonomy of the species annotation was divided into seven levels: kingdom, phylum, class, order, family, genus and species. During the clustering, Usearch was able to remove chimaera sequences and singleton OTUs at the same time. The OTUs that were annotated as chloroplasts or mitochondria (16S amplicons) and could not be annotated to the kingdom level were removed.