Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics
Open accessAbstract
Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human feces to uncover simple assembly rules and develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Community membership was largely determined by the donor feces, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient, due to the ability of fast-growing organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that community assembly follows simple rules of nutrient utilization dynamics and provides a predictive framework for manipulating gut commensal communities through nutritional perturbations.
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
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 gut microbiota can participate in cross-feeding, where metabolic intermediates (such as acetate, lactate, succinate and formate) produced by gut commensals can act as nutrients to support the growth of other gut commensals.
“The gut microbiota can also participate in cross-feeding, where metabolic intermediates (such as acetate, lactate, succinate and formate) that are produced by gut commensals can act as nutrients to support the growth of other gut commensals [20, 21].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [21]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
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 · see citing works
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858 · see citing works
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
The gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works
The rhizosphere microbiome and plant health
Berendsen, R. L., Pieterse, C. M. J., & Bakker, P. A. H. M. (2012) · Trends in Plant Science · doi:10.1016/j.tplants.2012.04.001 · Cited by 5,347 · see citing works
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · see citing works
The impact of the gut microbiota on human health: an integrative view
Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710 · see citing works
Decoupling function and taxonomy in the global ocean microbiome
Louca, S., Parfrey, L. W., & Doebeli, M. (2016) · Science · doi:10.1126/science.aaf4507 · Cited by 3,543 · see citing works
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
Tsugawa, H., Čajka, T., Kind, T., Ma, Y., Higgins, B. T., Ikeda, K., Kanazawa, M., VanderGheynst, J. S., Fiehn, O., & Arita, M. (2015) · Nature Methods · doi:10.1038/nmeth.3393 · Cited by 3,423 · see citing works
The Microbial Engines That Drive Earth's Biogeochemical Cycles
Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008) · Science · doi:10.1126/science.1153213 · Cited by 3,379 · see citing works
Lozupone, C., Hamady, M., Kelley, S. T., & Knight, R. D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01996-06 · Cited by 2,717 · see citing works
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378 · see citing works
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., & Palsson, B. Ø. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.65 · Cited by 1,006 · see citing works
Emergent simplicity in microbial community assembly
Goldford, J. E., Lu, N., Bajić, D., Estrela, S., Tikhonov, M., Sánchez-Gorostiaga, A., Segrè, D., Mehta, P., & Sánchez, Á. (2018) · Science · doi:10.1126/science.aat1168 · Cited by 1,002 · see citing works
Self-citationTsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0531-2 · Cited by 895 · see citing works
Competitive and cooperative metabolic interactions in bacterial communities
Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., Gophna, U., Sharan, R., & Ruppin, E. (2011) · Nature Communications · doi:10.1038/ncomms1597 · Cited by 557 · see citing works
Deciphering microbial interactions in synthetic human gut microbiome communities
Venturelli, O. S., Carr, A. V., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S. E., Northen, T. R., & Arkin, A. P. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178157 · Cited by 539 · see citing works
Personalized Mapping of Drug Metabolism by the Human Gut Microbiome
Javdan, B., Lopez, J. G., Chankhamjon, P., Lee, Y.-C. J., Hull, R., Wu, Q., Wang, X., Chatterjee, S., & Donia, M. S. (2020) · Cell · doi:10.1016/j.cell.2020.05.001 · Cited by 486 · see citing works
Separating host and microbiome contributions to drug pharmacokinetics and toxicity
Zimmermann, M., Zimmermann‐Kogadeeva, M., Wegmann, R., & Goodman, A. L. (2019) · Science · doi:10.1126/science.aat9931 · Cited by 427 · see citing works
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
Han, S., Treuren, W. V., Fischer, C. R., Merrill, B. D., DeFelice, B. C., Sánchez, J. M., Higginbottom, S. K., Guthrie, L., Fall, L. A., Dodd, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03707-9 · Cited by 400 · see citing works
Deciphering functional redundancy in the human microbiome
Tian, L., Wang, X.-W., Wu, A.-K., Fan, Y., Friedman, J., Dahlin, A., Waldor, M. K., Weinstock, G. M., Weiss, S. T., & Liu, Y.-Y. (2020) · Nature Communications · doi:10.1038/s41467-020-19940-1 · Cited by 380 · see citing works
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Tramontano, M., Andrejev, S., Pruteanu, M., Klünemann, M., Kuhn, M., Galardini, M., Jouhten, P., Zelezniak, A., Zeller, G., Bork, P., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0123-9 · Cited by 295 · see citing works
Ng, K. M., Aranda-Díaz, A., Tropini, C., Frankel, M. R., Treuren, W. V., O’Loughlin, C. T., Merrill, B. D., Yu, F. B., Pruss, K. M., Oliveira, R. A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.10.011 · Cited by 270 · see citing works
Self-citationNOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES
Harcombe, W. R. (2010) · Evolution · doi:10.1111/j.1558-5646.2010.00959.x · Cited by 267 · see citing works
Massively parallel screening of synthetic microbial communities
Kehe, J., Kulesa, A. B., Lopez, A. O., Ackerman, C. M., Thakku, S. G., Sellers, D., Kuehn, S., Gore, J., Friedman, J., & Blainey, P. C. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1900102116 · Cited by 266 · see citing works
Microbiome: Focus on Causation and Mechanism
Fischbach, M. A. (2018) · Cell · doi:10.1016/j.cell.2018.07.038 · Cited by 251 · see citing works
de Vos, M. G. J., Zagórski, M., McNally, A., & Bollenbach, T. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1713372114 · Cited by 209 · see citing works
Strong inter-population cooperation leads to partner intermixing in microbial communities
Momeni, B., Brileya, K. A., Fields, M. W., & Shou, W. (2013) · eLife · doi:10.7554/elife.00230 · Cited by 199 · see citing works
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages
Ai, J., Wang, X., He, X., Zhao, X., Zhang, Y., Jiang, Y., Li, M., Cui, Y., Chen, Y., Qiao, R., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.05.001 · Cited by 179 · see citing works
Functional attractors in microbial community assembly
Estrela, S., Vila, J. C. C., Lu, N., Bajić, D., Rebolleda‐Gómez, M., Chang, C., Goldford, J. E., Sánchez-Gorostiaga, A., & Sánchez, Á. (2021) · Cell Systems · doi:10.1016/j.cels.2021.09.011 · Cited by 148 · see citing works
Self-citationSpecies Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes
Gutiérrez, N., & Garrido, D. A. (2019) · mSystems · doi:10.1128/msystems.00185-19 · Cited by 117 · see citing works
Aranda-Díaz, A., Ng, K. M., Thomsen, T., Real-Ramírez, I., Dahan, D., Dittmar, S., Gonzalez, C. G., Chavez, T. M., Vasquez, K. S., Nguyen, T. H., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.008 · Cited by 116 · see citing works
Self-citationNutrient dominance governs the assembly of microbial communities in mixed nutrient environments
Estrela, S., Sánchez-Gorostiaga, A., Vila, J. C. C., & Sánchez, Á. (2021) · eLife · doi:10.7554/elife.65948 · Cited by 112 · see citing works
Self-citationA multidimensional perspective on microbial interactions
Pacheco, A. R., & Segrè, D. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz125 · Cited by 105 · see citing works
Resource competition predicts assembly of gut bacterial communities in vitro
Ho, P.-Y., Nguyen, T. H., Sánchez, J. M., DeFelice, B. C., & Huang, K. C. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01625-w · Cited by 86 · see citing works
Self-citationBacterial interspecies interactions modulate pH-mediated antibiotic tolerance
Aranda-Díaz, A., Obadia, B., Dodge, R., Thomsen, T., Hallberg, Z. F., Güvener, Z. T., Ludington, W. B., & Huang, K. C. (2020) · eLife · doi:10.7554/elife.51493 · Cited by 75 · see citing works
Self-citationObesogenic diets alter metabolism in mice
Showalter, M. R., Nonnecke, E. B., Linderholm, A., Čajka, T., Michael, R., Lönnerdal, B. L., Kenyon, N. J., & Fiehn, O. (2018) · PLoS ONE · doi:10.1371/journal.pone.0190632 · Cited by 74 · see citing works
Interspecies nutrient extraction and toxin delivery between bacteria
Stempler, O., Baidya, A. K., Bhattacharya, S., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00344-7 · Cited by 67 · see citing works
Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth
Atolia, E., Cesar, S., Arjes, H. A., Rajendram, M., Shi, H., Knapp, B. D., Khare, S., Aranda-Díaz, A., Lenski, R. E., & Huang, K. C. (2020) · mBio · doi:10.1128/mbio.01378-20 · Cited by 67 · see citing works
Self-citationHo, P.-Y., Good, B. H., & Huang, K. C. (2022) · eLife · doi:10.7554/elife.75168 · Cited by 65 · see citing works
Self-citationThe impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro
Celis, A. I., Relman, D., & Huang, K. (2023) · Cell Chemical Biology · doi:10.1016/j.chembiol.2022.12.001 · Cited by 57 · see citing works
Self-citationNutrient levels and trade-offs control diversity in a serial dilution ecosystem
Erez, A., Lopez, J. G., Weiner, B., Meir, Y., & Wingreen, N. S. (2020) · eLife · doi:10.7554/elife.57790 · Cited by 49 · see citing works
Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition
Huus, K. E., Hoang, T. T., Creus-Cuadros, A., Cirstea, M. S., Vogt, S. L., Knuff-Janzen, K., Sansonetti, P. J., Vonaesch, P., & Finlay, B. B. (2021) · Nature Communications · doi:10.1038/s41467-021-27191-x · Cited by 49 · see citing works
Deciphering Functional Redundancy in the Human MicrobiomePreprint
Tian, L., Wang, X., Wu, A.-K., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/176313 · Cited by 39 · see citing works
Diversity begets diversity under microbial niche constructionPreprint
Estrela, S., Díaz‐Colunga, J., Vila, J. C. C., Sánchez-Gorostiaga, A., & Sánchez, Á. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.13.480281 · Cited by 28 · see citing works
Self-citationCelis, A. I., Aranda-Díaz, A., Culver, R. N., Xue, K. S., Relman, D. A., Shi, H., & Huang, K. C. (2022) · iScience · doi:10.1016/j.isci.2022.103907 · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 4
- was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
- was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
- which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
- which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Cited by
Sorted by citations
Horrocks, V., King, O. G., Yip, A. Y. G., Marques, I. M., & McDonald, J. A. K. (2023) · Microbiology · doi:10.1099/mic.0.001377 · Cited by 104 · see citing works
- Authors
- Aranda-Díaz, A., Willis, L., Nguyen, T. H., Ho, P.-Y., Vila, J., Thomsen, T., Chavez, T., Yan, R., Yu, F. B., Neff, N., Sanchez, A., Estrela, S., & Huang, K. C.
- Affiliations
- Stanford University (US)
- Yale University (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Corresponding author
- Estrela, Sylvie
- Huang, Kerwyn Casey
- ORCID
- Venue
- Cell Systems
- Publisher
- openRxiv
- Published
- 2023-01-14
- Volume
- 16
- Issue
- 4
- Pages
- 101240-101240
- ISSN
- 2405-4712 (ISSN-L)
- PMC
- PMC9882107
- OpenAlex
- W4409033846
- Cited by
- 35
- References
- 49
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 10 · 2023: 4
- FWCI
- 6.27
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Cell Systems (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Science Foundation (2125383, 2032985)
- National Institutes of Health (AI147023)
- Stanford Bio-X
- Allen Discovery Center
- National Institute of General Medical Sciences (RM1GM135102)
- National Institute of Allergy and Infectious Diseases (R01AI147023)
- 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 › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- carbon source supplementation, niche competition, central carbon metabolism, commensal bacteria
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
