16S Biopsy Sample M2008CSC2_BP
16S rRNA gene compositional analysis provides a summary of the composition and structure of the bacterial component of the microbiome. Genomic bacterial DNA extraction methods were optimized to maximize the yield of bacterial DNA while keeping background amplification to a minimum. 16S rRNA gene sequencing methods were adapted from the methods developed for the Earth Microbiome Project and NIH-Human Microbiome Project. Briefly, bacterial genomic DNA was extracted from the total mass of the biopsied specimens using the MoBIO PowerLyzer Tissue and Cells DNA isolation kit and sterile spatulas for tissue transfer. The 16S rDNA V4 region was amplified from the extracted DNA by PCR and sequenced in the MiSeq platform (Illumina) using the 2x250 bp paired-end protocol yielding pair-end reads that overlap almost completely. The primers used for amplification contain adapters for MiSeq sequencing and single-index barcodes so that the PCR products may be pooled and sequenced directly, targeting at least 10,000 reads per sample