Bacterial DNA Extraction and 16S rRNA Sequencing

Bacterial DNA was extracted using the NucliSENS^® easyMAG^® system (BioMèrieux, Gorman, NC, United States), following the manufacturer’s instructions, starting from 500 μl and with a final elution volume of 50 μl. Briefly, a 500-base-pair region of the V1–V3 portion of the 16S rRNA gene and, subsequently, the 200-base-pair region of the V3 portion was amplified, as elsewhere described (Campisciano et al., 2018 (link)). The V3 amplicon was used for template preparation by the Ion PGM Hi-Q View kit on the Ion OneTouch^TM 2 System (Life Technologies, Grand Island, NY, United States) and sequenced using the Ion PGM Hi-Q View sequencing kit (Life Technologies, Grand Island, NY, United States) with the Ion PGM^TM System technology. Negative controls, including a no-template control, were processed with the clinical samples.

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De Seta F., Campisciano G., Zanotta N., Ricci G, & Comar M. (2019). The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis. Frontiers in Microbiology, 10, 2451.

Publication 2019

Ion PGM Hi-Q View kit Ion OneTouchTM 2 System Ion PGM Hi-Q View sequencing kit

16s rrna A gene Bacterial dna Base pair

Corresponding Organization : IRCCS Materno Infantile Burlo Garofolo

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Variable analysis

independent variables

DNA extraction method: NucliSENS® easyMAG® system
Amplification of 500-base-pair region of the V1–V3 portion of the 16S rRNA gene
Amplification of 200-base-pair region of the V3 portion of the 16S rRNA gene
Template preparation by the Ion PGM Hi-Q View kit on the Ion OneTouch™ 2 System
Sequencing using the Ion PGM Hi-Q View sequencing kit with the Ion PGM™ System technology

dependent variables

Not explicitly mentioned

control variables

Negative controls, including a no-template control, were processed with the clinical samples

controls

Negative controls, including a no-template control, were processed with the clinical samples

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