Cited by 329Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

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Understanding Competition and Cooperation within the Mammalian Gut Microbiome

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Coyte, Katharine Z., Rakoff-Nahoum, Seth·2019·Current Biology

DOI 10.1016/j.cub.2019.04.017PMC PMC6935513

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Abstract

The mammalian gut harbors a vast community of microorganisms - termed the microbiota - whose composition and dynamics are considered to be critical drivers of host health. These factors depend, in part, upon the manner in which microbes interact with one another. Microbes are known to engage in a myriad of different ways, ranging from unprovoked aggression to actively feeding each other. However, the relative extent to which these different interactions occur between microbes within the gut is unclear. In this minireview we assess our current knowledge of microbe-microbe interactions within the mammalian gut microbiota, and the array of methods used to uncover them. In particular, we highlight the discrepancies between different methodologies: some studies have revealed rich networks of cross-feeding interactions between microbes, whereas others suggest that microbes are more typically locked in conflict and actively cooperate only rarely. We argue that to reconcile these contradictions we must recognize that interactions between members of the microbiota can vary across condition, space, and time - and that only through embracing this dynamism will we be able to comprehensively understand the ecology of our gut communities.

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Additional file 6 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720358
Additional file 1 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720343
Additional file 5 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720355
Additional file 8 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720364
Additional file 3 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720349
Additional file 1 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
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Additional file 1 of Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome
Mataigne, A., Vannier, N., Vandenkoornhuyse, P., & Hacquard, S. (2024) · Figshare · doi:10.6084/m9.figshare.26552077
Additional file 2 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720346
Additional file 7 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720361
Additional file 1 of Effect of stress urinary incontinence on vaginal microbial communities
Zhang, M., Zhou, Y., Yao, S., Zhao, Y., Batool, S. S., Huang, J., Jiang, L., Yan, D., Yan, W., & Yu, Z. P. (2024) · Figshare · doi:10.6084/m9.figshare.25546993
Additional file 4 of Early-life factors shaping the gut microbiota of Common buzzard nestlings
Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K.-P., Tobias, B., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Figshare · doi:10.6084/m9.figshare.26720352
Additional file 1 of Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions
Martínez-Álvaro, M., Mattock, J., Auffret, M. D., Weng, Z., Duthie, C.-A., Dewhurst, R. J., Cleveland, M. A., Watson, M., & Roehe, R. (2022) · Figshare · doi:10.6084/m9.figshare.21285704
Author response: The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome
Shen, B. A., Asfahl, K. L., Lim, B., Bertolli, S. K., Minot, S. S., Radey, M. C., Penewit, K. M., Ngo, B., Salipante, S. J., Johnston, C. D., et al. (2026) · eLife · doi:10.7554/elife.110200.1.sa0
eLife Assessment: The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome
Antunes, C. (2026) · eLife · doi:10.7554/elife.110200.1.sa4
Generalized dynamics of cross-feeding bacteria
Massing, J. C., Groß, T., Yeakel, J. D., & Fahimipour, A. K. (2026) · Journal of The Royal Society Interface · doi:10.1098/rsif.2025.0437

Authors: Coyte, K. Z., & Rakoff-Nahoum, S.
Affiliations: Boston Children's Hospital (US)
Corresponding author: Coyte, Katharine Z.
Rakoff-Nahoum, Seth
ORCID: Coyte, Katharine Z.
Rakoff-Nahoum, Seth
Venue: Current Biology
Publisher: Elsevier BV
Published: 2019-06
Volume: 29
Issue: 11
Pages: R538-R544
ISSN: 0960-9822 (ISSN-L)
DOI: 10.1016/j.cub.2019.04.017
PMC: PMC6935513
OpenAlex: W2948909067
Cited by: 329
References: 51
Citations by year: 2026: 43 · 2025: 57 · 2024: 69 · 2023: 57 · 2022: 48 · 2021: 34 · 2020: 18 · 2019: 2
FWCI: 2.31
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 368 d)
Locations: Current Biology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Research Explorer (The University of Manchester) (submittedVersion, other-oa)
Funders: March of Dimes Foundation
Wellcome Trust (201341/A/16/Z, 201341/Z/16/Z)
National Institute of Allergy and Infectious Diseases (K08AI130392)
National Institute of Diabetes and Digestive and Kidney Diseases (P30DK040561)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords: gut microbiota, microbial interactions, competition (biology), cooperation, cross-feeding, microbial ecology, microbial community dynamics, host-microbe interactions
MeSH terms: Gastrointestinal Microbiome, Animals, Mammals, Microbial Interactions

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Understanding Competition and Cooperation within the Mammalian Gut Microbiome

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