Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract

Simon Graspeuntner, Nathalie Loeper, Sven Künzel, John F. Baines, Jan Rupp*

*Corresponding author for this work

Abstract

Next-generation sequencing-based methods are extensively applied in studies of the human microbiota using partial 16 S rRNA gene amplicons. However, they carry drawbacks that are critical to consider when interpreting results, including differences in outcome based on the hypervariable region(s) used. Here, we show that primers spanning the V3/V4 region identify a greater number of taxa in the vaginal microbiota than those spanning the V1/V2 region. In particular, taxa such as Gardnerella vaginalis, Bifidobacterium bifidum and Chlamydia trachomatis, all species that influence vaginal health and disease, are not represented in V1/V2-based community profiles. Accordingly, missing or underestimating the frequency of these species overestimates the abundance of other taxa and fails to correctly assess the bacterial diversity in the urogenital tract. We elaborate that covering these taxa using the V3/V4 region leads to profound changes in the assignment of community state types. Altogether, we show that the choice of primers used for studying the vaginal microbiota has deep implications on the biological evaluation of the results.

Original languageEnglish
Article number9678
JournalScientific Reports
Volume8
Issue number1
ISSN2045-2322
DOIs
Publication statusPublished - 26.06.2018

Research Areas and Centers

  • Academic Focus: Center for Infection and Inflammation Research (ZIEL)

DFG Research Classification Scheme

  • 204-03 Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology

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