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Cited by 97Reproductive tract infections researchGut microbiota and healthMicrobial Community Ecology and Physiology

Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

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Tettamanti Boshier, Florencia A., Srinivasan, Sujatha, Lopez, Anthony, Hoffman, Noah G., Proll, Sean, Fredricks, David N., Schiffer, Joshua T.·2020·mSystems
DOI 10.1128/msystems.00777-19PMC PMC7141891

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Abstract

Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

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  • Compositional data are still useful and can correlate well with absolute quantifications obtained with techniques such as qPCR.

    “Compositional data are still useful, and can correlate well with absolute quantifications obtained with techniques such as qPCR 28,29 .”

    From Human microbiome myths and misconceptions (2023) · cites this paper as [28]

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Cited by

Sorted by citations

Authors
Tettamanti Boshier, F. A., Srinivasan, S., Lopez, A., Hoffman, N. G., Proll, S., Fredricks, D. N., & Schiffer, J. T.
Affiliations
  • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
  • Fred Hutch Cancer Center (US)
  • University of Washington (US)
ORCID
Venue
mSystems
Publisher
American Society for Microbiology
Published
2020-04-28
Volume
5
Issue
2
ISSN
2379-5077 (ISSN-L)
DOI
10.1128/msystems.00777-19
PMC
PMC7141891
OpenAlex
W3014416553
Cited by
97
References
3
Citations by year
2026: 13 · 2025: 15 · 2024: 16 · 2023: 25 · 2022: 10 · 2021: 16 · 2020: 2
FWCI
9.77
Type
journal article
Language
en
Open access
Licence
Locations
  • mSystems (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
HHS | National Institutes of Health (U19 AI 113173)
Topics
  • Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
vaginal microbiota, 16S rRNA gene amplicon sequencing, relative abundance, bacterial community composition

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