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A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities

Author

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  • Jacob T. Barlow

    (California Institute of Technology)

  • Said R. Bogatyrev

    (California Institute of Technology)

  • Rustem F. Ismagilov

    (California Institute of Technology
    California Institute of Technology)

Abstract

A fundamental goal in microbiome studies is determining which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative, rather than absolute abundances. Moreover, studies often analyze only stool, despite microbial diversity differing substantially among gastrointestinal (GI) locations. Here, we develop a quantitative framework to measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compare microbial loads in lumenal and mucosal samples along the GI tract. Quantitative measurements of absolute (but not relative) abundances reveal decreases in total microbial loads on the ketogenic diet and enable us to determine the differential effects of diet on each taxon in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework, appropriate for diverse GI locations enables mapping microbial biogeography of the mammalian GI tract and more accurate analyses of changes in microbial taxa in microbiome studies.

Suggested Citation

  • Jacob T. Barlow & Said R. Bogatyrev & Rustem F. Ismagilov, 2020. "A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16224-6
    DOI: 10.1038/s41467-020-16224-6
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    Cited by:

    1. Dennis Metze & Jörg Schnecker & Alberto Canarini & Lucia Fuchslueger & Benjamin J. Koch & Bram W. Stone & Bruce A. Hungate & Bela Hausmann & Hannes Schmidt & Andreas Schaumberger & Michael Bahn & Chri, 2023. "Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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