The DOI matches its Crossref record; 50 of the 51 references it cites were found in a registry or an index.
Understanding Competition and Cooperation within the Mammalian Gut Microbiome
Open accessAbstract
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.
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?
In the citing paper
“Bacteria compete for carbon and nitrogen sources that are essential to support their growth within the intestine [66–68].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [67]
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
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913
The Human Intestinal Microbiome in Health and Disease
Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637
The Competitive Exclusion Principle
Hardin, G. (1960) · Science · doi:10.1126/science.131.3409.1292 · Cited by 3,456
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
Self-citationPrecision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Kurtz, Z. D., Müller, C. L., Miraldi, E. R., Littman, D. R., Blaser, M. J., & Bonneau, R. A. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004226 · Cited by 1,799
Pukatzki, S. U., Ma, A. T., Sturtevant, D., Krastins, B., Sarracino, D. A., Nelson, W. C., Heidelberg, J. F., & Mekalanos, J. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510322103 · Cited by 1,116
A Virulence Locus of Pseudomonas aeruginosa Encodes a Protein Secretion Apparatus
Mougous, J. D., Cuff, M. E., Raunser, S., Shen, A., Zhou, M., Gifford, C. A., Goodman, A. L., Joachimiak, G., Ordoñez, C. L., Lory, S. J., et al. (2006) · Science · doi:10.1126/science.1128393 · Cited by 1,105
Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043
Flagged first, then by citations
1 of the 51 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 301–329 of 329
Joulain, C., Bessoles, S., Pozuelo, M., Chiron, A., Abina, A. M., Sarrabayrouse, G., & Hacein‐Bey‐Abina, S. (2026) · Cytokine · doi:10.1016/j.cyto.2026.157138
Sharma, V., Kumar, S., Kasana, D., & Roy, R. P. (2026) · Indian Journal of Community Medicine · doi:10.4103/ijcm.ijcm_78_25
Les communautés microbiennes au sein des populations de tiques : origine, diversité et structure
Binetruy, F. (2019) · theses.fr (ABES) · doi:10.70675/bbc486a6z72faz4bfazb023zc92b9ecfbbe9
Gaillard, J. (2023) · theses.fr (ABES) · doi:10.70675/8c3e1078zf49ez4662z893ezbf256ef32bc5
The Coreoidea-Caballeronia gut symbiosis : specificity and bacterial fitness determinants
Lextrait, G. (2024) · theses.fr (ABES) · doi:10.70675/94a6f8f1z54e1z45d0z8a2bzeb19476f092a
Čepić, A., Rausch, P., Geese, T., Dempfle, A., Graßl, G. A., & Baines, J. F. (2026) · mSystems · doi:10.1128/msystems.01640-25
Griffin, T. W., Scott, M., Holohan, B. A., & Ward, J. E. (2026) · Marine Ecology Progress Series · doi:10.3354/meps15193
The Human Microbiota: Composition and Functions
Sobti, R. C., Negi, R. K., & Rana, A. (2026) · Springer eBooks · doi:10.1007/978-981-95-9031-5_2
Han, J., Liu, J., Wang, T. T., Dong, B., Zhang, F., Li, S., Zou, Q., & Li, D. (2026) · Animal Microbiome · doi:10.1186/s42523-026-00580-7
Li, H., Li, N., Wang, C., Yang, J., Dong, Z., Cai, Z., Li, J., Chen, Y., Zheng, J., & Zhu, J. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1753665
Metabolic set theory: a generalized model of microbial interactions
Jyoti, J., Zoller, H., zu Castell, W., & Hütt, M. ‐. (2026) · npj Systems Biology and Applications · doi:10.1038/s41540-026-00774-4
Sarkar, S., Sharma, A., Gulati, L., Banerjee, A., & Vuree, S. (2026) · Bacteria · doi:10.3390/bacteria5030039
Alanazi, A. (2026) · Journal of Clinical Laboratory Analysis · doi:10.1002/jcla.70307
Erokhina, K., Quon, H., Kajale, S. C., Djordjevic, S. P., Wyrsch, E. R., Hamilton, K. A., & Cytryn, E. J. (2026) · Water Research · doi:10.1016/j.watres.2026.126534
The type VI secretion system governs strain maintenance in a wild mammalian gut microbiomePreprint
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.110200.2
Huang, Z., McGrath, P. M., Ferdinand, D., McCormick, B. A., Ward, D. V., Bucci, V., & Haran, J. P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.12.743985
Deciphering microbial community dynamics using cross-sectional data-informed NeuralODE
Xue, F., Tan, X., Zhang, C., Zhao, H., & Wang, T. (2026) · Microbiome · doi:10.1186/s40168-026-02458-x
Díaz, A., Garcı́a, G., & Cano, R. J. (2026) · Microorganisms · doi:10.3390/microorganisms14092001
Ghezzi, H., Wolff, R., Jain, A., Burckhardt, J. C., Hunter, M., Ng, K. M., Carasso, S., Geva‐Zatorsky, N., Garud, N. R., & Tropini, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.08.750096
Kumar, B., Lorusso, E., Fosso, B., & Pesole, G. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1925500
Dietary Fiber Structural Diversity Shapes Gut Microbiome Function: A Glycocentric Perspective
Vilaplana, F. (2026) · JACS Au · doi:10.1021/jacsau.6c01032
Host genetics determines the fate of the Lactobacillaceae population in the small intestinePreprint
Beilinson, H. A., Coyne, M. J., Bass, K., Maslyar, M., Cullum, E., Villalobos, J., Chervonsky, A. V., & Golovkina, T. V. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.25.754556
Streb, L.-M., Assane, I. M., de Souza, G. F. P., Pilarski, F., Queiroga, A. P., Kublik, S., Rath, S., & Schloter, M. (2026) · Scientific Reports · doi:10.1038/s41598-026-75240-6
Atuahene, P. Y., Stevenson, B., & Sang, Y. (2026) · Microorganisms · doi:10.3390/microorganisms14102360
Small RNAs as emerging regulators of commensal adaptation in the mammalian gut
Fansler, R. T., & Zhu, W. (2026) · Infection and Immunity · doi:10.1128/iai.00292-26
Abaidullah, M., Ji, Y., 黄, 勤., Scarpa, M., Li, J., Xiao, X., & Xu, D. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1883529
Metadata
- Authors
- Coyte, K. Z., & Rakoff-Nahoum, S.
- Affiliations
- Boston Children's Hospital (US)
- Corresponding author
- 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)
- 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
- 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
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