2.9. Analysis of 16S rDNA Gene Sequencing

The 16S rDNA sequences were analyzed by the Quantitative Insights into Microbial Ecology (QIIME) pipeline version 1.9.1 [40]. The 16S rDNA sequences, which were filtered for quality, were divided into operational taxonomic units (OTU) based on whether they had 97% homology with the UCLUST algorithm [41]. These sequences were then compared to reference sequence collections in the Greengenes database (August 2013 version). A total of 4,901,162 reads were obtained from 80 samples. On average, 61,264.53 ± 4,964.184 sequences were obtained per sample. By using the QIIME pipeline, these sequences were analyzed to produce a taxonomy summary from the phylum to the genus level, the alpha diversity (Simpson diversity index), the beta diversity, and a principal coordinate analysis (PCoA). Principal coordinate analyses were calculated using weighted UniFrac distances.