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.