2.4 | Deep sequencing data processing
Raw deep sequencing data were processed using Quantitative Insights Into Microbial Ecology software (http://www.qiime.org, QIIME version 1.9.0; (Caporaso et al., 2010)) with the default parameters unless otherwise noted. After all chimeric and low-quality reads were removed, qualified sequences were clustered into operational taxonomic units (OTUs) at the 97% identity threshold level, and the most abundant sequence from each OTU was chosen as a representative sequence for that OTU. Taxonomic classification of each OTU was assigned using the Ribosomal Database Project classifier. The average relative abundance (%) of predominant genus-level taxonomic groups in each sample was estimated by comparing the number of sequences assigned to a specific taxon versus the total number of sequences obtained for that sample.