16S rRNA Gene Amplicon Dataset
This dataset is comprised of 83 samples, which have previously been described, analyzed, and archived on the NCBI SRA . The DNA extraction protocol for these samples is identical to the one used to create the Nextera XT prepared deep shotgun metagenomic dataset (described above). As above, we quantified DNA using Qubit dsDNA Broad Range Assays. Next, we standardized DNA concentration to 20 ng/μl and PCR amplified the v3–v4 region of the 16S rRNA gene using the 341f forward and 805r reverse universal primers. PCR products were sequenced on an Illumina MiSeq platform (v3 chemistry: 2 × 300 base-pair reads) by the University of Calgary Centre for Health Genomics and Informatics, to a target depth of >120,000 read pairs per sample.