The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Stability of the human faecal microbiome in a cohort of adult men
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Study of short-term longitudinal samplings from half the donors found that individuals are more similar to themselves over time compared with others (Costello et al., 2009; Flores et al., 2014; Mehta et al., 2018).”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Mehta et al., 2018
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“It is possible that higher intake of fiber could reduce the carcinogenic effects of F nucleatum by restoring effective immunosurveillance.173”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [173]
Experimental — accuracy not yet measuredIn the citing paper
“Although stability was the norm, the degree of species stability (quantified as 1 − BC distance; Mehta et al., 2018) was variable across the 413 donors (Fig. 6, B and C)”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Mehta et al., 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533
Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.024 · Cited by 3,283
Stool form scale as a useful guide to intestinal transit time
Lewis, S. J., & Heaton, K. W. (1997) · Scandinavian Journal of Gastroenterology · doi:10.3109/00365529709011203 · Cited by 3,244
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231
The diversity–stability debate
McCann, K. S. (2000) · Nature · doi:10.1038/35012234 · Cited by 3,220
The ecology of the microbiome: Networks, competition, and stability
Coyte, K. Z., Schlüter, J., & Foster, K. R. (2015) · Science · doi:10.1126/science.aad2602 · Cited by 2,812
Repeatability for Gaussian and non-Gaussian data: a practical guide for biologists.
Nakagawa, S., & Schielzeth, H. (2010) · Biological Reviews · doi:10.1111/j.1469-185x.2010.00141.x · Cited by 2,584
Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421
Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400
A microbial symbiosis factor prevents intestinal inflammatory disease
Mazmanian, S. K., Round, J. L., & Kasper, D. L. (2008) · Nature · doi:10.1038/nature07008 · Cited by 2,340
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185
Self-citationThe Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., et al. (2016) · Science · doi:10.1126/science.aad3369 · Cited by 1,914
Self-citationLloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891
Self-citationPopulation diversity and the portfolio effect in an exploited species
Schindler, D. E., Hilborn, R., Chasco, B., Boatright, C. P., Quinn, T. P., Rogers, L. A., & Webster, M. S. (2010) · Nature · doi:10.1038/nature09060 · Cited by 1,605
Zoetendal, E. G., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3854-3859.1998 · Cited by 1,360
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160
Moving pictures of the human microbiome
Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r50 · Cited by 1,138
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,076
Self-citationHost lifestyle affects human microbiota on daily timescales
David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J. (2014) · Genome biology · doi:10.1186/gb-2014-15-7-r89 · Cited by 950
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907
Faecalibacterium prausnitzii : from microbiology to diagnostics and prognostics
López‐Siles, M., Duncan, S. H., Garcia-Gil, L. J., & Martínez-Medina, M. (2017) · The ISME Journal · doi:10.1038/ismej.2016.176 · Cited by 892
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013) · Cell · doi:10.1016/j.cell.2012.10.052 · Cited by 811
Relating the metatranscriptome and metagenome of the human gut
Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J. A., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319284111 · Cited by 731
Self-citationAntibiotics and the Gut Microbiota
Modi, S. R., Collins, J. J., & Relman, D. A. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72333 · Cited by 667
McNulty, N. P., Yatsunenko, T., Hsiao, A., Faith, J. J., Muegge, B. D., Goodman, A. L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002701 · Cited by 559
Identifying personal microbiomes using metagenomic codes
Franzosa, E. A., Huang, K. H., Meadow, J. F., Gevers, D., Lemon, K. P., Bohannan, B. J. M., & Huttenhower, C. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1423854112 · Cited by 526
Self-citationTemporal variability is a personalized feature of the human microbiome
Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala, D., Chase, J., Leff, J. W., Vázquez-Baeza, Y., Gonzalez, A., Knight, R., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0531-y · Cited by 446
Composition and temporal stability of the gut microbiota in older persons
Jeffery, I. B., Lynch, D. B., & O’Toole, P. W. (2016) · The ISME Journal · doi:10.1038/ismej.2015.88 · Cited by 421
Simultaneous generation of many RNA-seq libraries in a single reaction
Shishkin, A. A., Giannoukos, G., Küçükural, A., Ciulla, D., Busby, M., Surka, C., Chen, J., Bhattacharyya, R. P., Rudy, R. F., Patel, M. M., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3313 · Cited by 288
Microbiota, Disease, and Back to Health: A Metastable Journey
Blumberg, R. S., & Powrie, F. M. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004184 · Cited by 287
Long‐term monitoring of the human intestinal microbiota composition
Rajilić-Stojanović, M. D., Heilig, H. G. H. J., Tims, S., Zoetendal, E. G., & de Vos, W. M. (2012) · Environmental Microbiology · doi:10.1111/1462-2920.12023 · Cited by 286
Effects of bowel cleansing on the intestinal microbiota
Jalanka, J., Salonen, A., Salojärvi, J., Ritari, J., Immonen, O., Marciani, L., Gowland, P. A., Hoad, C. L., Garsed, K. C., Lam, C., et al. (2014) · Gut · doi:10.1136/gutjnl-2014-307240 · Cited by 277
Metatranscriptome of human faecal microbial communities in a cohort of adult men
Abu-Ali, G., Mehta, R. S., Lloyd‐Price, J., Mallick, H., Branck, T. A., Ivey, K. L., Drew, D. A., DuLong, C. R., Rimm, E. B., Izard, J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0084-4 · Cited by 238
Self-citationREVERSIBLE CHANGES IN THE SUSCEPTIBILITY OF MICE TO BACTERIAL INFECTIONS
Dubos, R. J., & Schaedler, R. W. (1956) · The Journal of Experimental Medicine · doi:10.1084/jem.104.1.53 · Cited by 152
Impact of Colonoscopy Bowel Preparation on Intestinal Microbiota
O'Brien, C. L., Allison, G. E., Grimpen, F., & Pavli, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062815 · Cited by 114
Jenkins, A. H., Schyns, G., Potot, S., Sun, G., & Begley, T. P. (2007) · Nature Chemical Biology · doi:10.1038/nchembio.2007.13 · Cited by 111
Bussiere, D. E., Muchmore, S. W., Dealwis, C. G., Schluckebier, G., Nienaber, V. L., Edalji, R. P., Walter, K. A., Ladror, U. S., Holzman, T. F., & Abad‐Zapatero, C. (1998) · Biochemistry · doi:10.1021/bi973113c · Cited by 109
Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria
Mahony, J., McDonnell, B., Casey, E., & van Sinderen, D. (2016) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-041715-033322 · Cited by 60
Malojcic, G., Owen, R. L., Grimshaw, J. P. A., Brozzo, M. S., Dreher‐Teo, H., & Glockshuber, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806997105 · Cited by 58
Kim, D., Konishi, L., & Kobashi, K. (1986) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/0167-4838(86)90144-5 · Cited by 54
REVERSIBLE CHANGES IN THE SUSCEPTIBILITY OF MICE TO BACTERIAL INFECTIONS
Schaedler, R. W., & Dubos, R. J. (1956) · The Journal of Experimental Medicine · doi:10.1084/jem.104.1.67 · Cited by 43
Cited by
Sorted by citations
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Shaffer, M., Borton, M., McGivern, B. B., Zayed, A. A., Rosa, S. L. L., Solden, L., Liu, P., Narrowe, A. B., Rodríguez-Ramos, J. A., Bolduc, B., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa621 · Cited by 1,163
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752
Self-citationThe person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449
Wang, D. D., Nguyen, L. H., Li, Y., Yan, Y., Ma, W., Rinott, E., Ivey, K. L., Shai, I., Willett, W. C., Hu, F. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01223-3 · Cited by 386
Self-citationBacterial antagonism in host-associated microbial communities
García-Bayona, L., & Comstock, L. E. (2018) · Science · doi:10.1126/science.aat2456 · Cited by 372
Metadata
- 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
- Venue
- Nature Microbiology
- Published
- 2018-01-15
- Volume
- 3
- Issue
- 3
- Pages
- 347-355
- ISSN
- 2058-5276 (ISSN-L)
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
