2.6. 16S Amplicon Sequencing and Taxonomic Assignments
PCR amplification was carried out using primers specific for the V3-V4 hypervariable regions of the 16S rDNA gene. The resulting amplicons were quantified, pooled at equimolar ratios, and sequenced using the MiSeq System Guide (Illumina, San Diego, CA, USA). The paired-end reads that overlapped were merged into longer reads covering the 16S rRNA V3-V4 region. Chimeric sequences were identified using VSEARCH against the SILVA gold database. The high-quality reads that were filtered and trimmed were clustered into operational taxonomic units (OTUs) using VSEARCH with a de novo clustering algorithm with a 97% sequence similarity threshold [