DNA was extracted from the swabs using the NucliSENS® easyMAG® system (BioMèrieux, Gorman, North Carolina, CA, USA), following the manufacturer’s instructions, starting from 500 µL of sample and with an elution volume of 50 µL. All DNA samples were stored at −80 °C prior to further processing.
Firstly, a 500 base pair region of the V1-V3 portion of the 16S rRNA gene was amplified and subsequently the 200 base pair region of the V3 portion was amplified as well, as described elsewhere [12 (link)]. The V3 amplicon was used for template preparation by the Ion PGM Hi-Q View kit on the Ion OneTouch™ 2 System (Life Technologies, Gran Island, New York, NY, USA) and sequenced using the Ion PGM Hi-Q View sequencing kit (Life Technologies, New York, NY, USA) with the Ion PGM™ System technology. Negative controls, including a no template control, were processed with the clinical samples.
Firstly, a 500 base pair region of the V1-V3 portion of the 16S rRNA gene was amplified and subsequently the 200 base pair region of the V3 portion was amplified as well, as described elsewhere [12 (link)]. The V3 amplicon was used for template preparation by the Ion PGM Hi-Q View kit on the Ion OneTouch™ 2 System (Life Technologies, Gran Island, New York, NY, USA) and sequenced using the Ion PGM Hi-Q View sequencing kit (Life Technologies, New York, NY, USA) with the Ion PGM™ System technology. Negative controls, including a no template control, were processed with the clinical samples.
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