Cited by 277Gut microbiota and healthOral microbiology and periodontitis researchMicrobial Community Ecology and Physiology

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Stability of the human faecal microbiome in a cohort of adult men

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Mehta, Raaj S., Abu-Ali, Galeb S., Drew, David A., Lloyd-Price, Jason, Subramanian, Ayshwarya, Lochhead, Paul, Joshi, Amit D., Ivey, Kerry L., Khalili, Hamed, Brown, Gordon T., DuLong, Casey, Song, Mingyang, Nguyen, Long H., Mallick, Himel, Rimm, Eric B., Izard, Jacques, Huttenhower, Curtis, Chan, Andrew T.·2018·Nature Microbiology

DOI 10.1038/s41564-017-0096-0PMC PMC6016839

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Abstract

Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.

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Authors: Mehta, R. S., Abu-Ali, G. S., Drew, D. A., Lloyd-Price, J., Subramanian, A., Lochhead, P., Joshi, A. D., Ivey, K. L., Khalili, H., Brown, G. T., DuLong, C., Song, M., Nguyen, L. H., Mallick, H., Rimm, E. B., Izard, J., Huttenhower, C., & Chan, A. T.
Affiliations: Harvard University (US)
Broad Institute (US)
Brigham and Women's Hospital (US)
University of Nebraska–Lincoln (US)
Corresponding author: Huttenhower, Curtis
Chan, Andrew T.
ORCID: Abu-Ali, Galeb S.
Drew, David A.
Lloyd-Price, Jason
Subramanian, Ayshwarya
Joshi, Amit D.
Ivey, Kerry L.
Khalili, Hamed
Brown, Gordon T.
Song, Mingyang
Nguyen, Long H.
Mallick, Himel
Rimm, Eric B.
Izard, Jacques
Huttenhower, Curtis
Chan, Andrew T.
Venue: Nature Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2018-01-15
Volume: 3
Issue: 3
Pages: 347-355
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-017-0096-0
PMC: PMC6016839
OpenAlex: W2783226215
Cited by: 273
References: 48
Citations by year: 2026: 16 · 2025: 29 · 2024: 43 · 2023: 36 · 2022: 31 · 2021: 43 · 2020: 43 · 2019: 17 · 2018: 15
FWCI: 10.30
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Microbiology (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Lincoln (University of Nebraska) (submittedVersion)
Funders: Massachusetts General Hospital
Crohn's and Colitis Foundation (454674, 563526)
National Heart, Lung, and Blood Institute (R01HL035464)
National Cancer Institute (R01CA202704, L30 CA209764, U01CA152904, UM1CA167552)
National Institute of Diabetes and Digestive and Kidney Diseases (K01DK110267, K24DK098311, P30DK043351)
National Institute of Dental and Craniofacial Research (U54DE023798)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: fecal microbiota, within-person variability, between-person variation, metatranscriptomics, metagenomics, Health Professionals Follow-up Study, adult male, biomarkers
MeSH terms: Gastrointestinal Microbiome, Adult, Aged, Bacteria, Feces, Follow-Up Studies, Health Personnel, Humans, Male, Middle Aged, Prospective Studies, Cohort Studies, Gene Expression, Gene Expression Profiling, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota

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