Assessment of microbial DNA enrichment techniques from sino-nasal swab samples for metagenomics

Abstract

Methods: In this study, three techniques were assessed for microbial DNA enrichment: 1. A series of centrifugation steps, 2. Enrichment of microbial DNA using the NEBNext® Microbiome DNA Enrichment kit, and 3. Whole-genome amplification following the previous enrichment strategies. A no-treatment control and a whole-genome amplified control were also included. Swab samples from three adult patients undergoing functional endoscopic sinus surgery for chronic rhinosinusitis (CRS) were collected intraoperatively for this study. Paired-end shotgun metagenome sequencing was conducted using Illumina HiSeq and bacterial 16S rRNA gene amplicon sequencing using Illumina MiSeq to assess bacterial community composition.