Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations
Open accessAbstract
Dietary fibre impacts the growth dynamics of human gut microbiota, yet we lack a detailed and quantitative understanding of how these nutrients shape microbial interaction networks and responses to perturbations. By building human gut communities coupled with computational modelling, we dissect the effects of fibres that vary in chemical complexity and each of their constituent sugars on community assembly and response to perturbations. We demonstrate that the degree of chemical complexity across different fibres limits microbial growth and the number of species that can utilize these nutrients. The prevalence of negative interspecies interactions is reduced in the presence of fibres compared with their constituent sugars. Carbohydrate chemical complexity enhances the reproducibility of community assembly and resistance of the community to invasion. We demonstrate that maximizing or minimizing carbohydrate competition between resident and invader species enhances resistance to invasion. In sum, the quantitative effects of carbohydrate chemical complexity on microbial interaction networks could be exploited to inform dietary and bacterial interventions to modulate community resistance to perturbations.
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Dietary fiber promotes resistance of human gut microbiota to perturbations by limiting microbial growth and balancing positive and negative interspecies interactions.
“dietary fiber also promotes resistance of human gut microbiota to perturbations by limiting microbial growth and balancing the positive and negative interspecies interactions.”
From Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases (2024) · cites this paper as [638]
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Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · 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
The carbohydrate-active enzymes database (CAZy) in 2013
Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,355 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
Gut microbiota in human metabolic health and disease
Fan, Y., & Pedersen, O. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0433-9 · Cited by 4,724 · see citing works
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497 · see citing works
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,138 · see citing works
Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805 · see citing works
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 2,728 · see citing works
The impact of dietary fiber on gut microbiota in host health and disease
Makki, K., Deehan, E. C., Walter, J., & Bäckhed, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.05.012 · Cited by 2,517 · see citing works
Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421 · see citing works
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works
Fiber and prebiotics: Mechanisms and health benefits
Slavin, J. (2013) · Nutrients · doi:10.3390/nu5041417 · Cited by 2,340 · see citing works
Fundamentals of Microbial Community Resistance and Resilience
Shade, A. L., Peter, H., Allison, S., Baho, D. L., Berga, M., Bürgmann, H., Huber, D. H., Langenheder, S., Lennon, J. T., Martiny, J. B. H., et al. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00417 · Cited by 1,728 · see citing works
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
Kaoutari, A. E., Armougom, F., Gordon, J. I., Raoult, D., & Henrissat, B. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3050 · Cited by 1,683 · see citing works
Carbohydrate quality and human health: a series of systematic reviews and meta-analyses
Reynolds, A., Mann, J., Cummings, J., Winter, N., Mete, E., & Te Morenga, L. (2019) · The Lancet · doi:10.1016/s0140-6736(18)31809-9 · Cited by 1,630 · see citing works
Diet, gut microbiota and immune responses
Maslowski, K. M., & Mackay, C. R. (2011) · Nature Immunology · doi:10.1038/ni0111-5 · Cited by 1,261 · see citing works
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134 · see citing works
Species packing and competitive equilibrium for many species
MacArthur, R. H. (1970) · Theoretical Population Biology · doi:10.1016/0040-5809(70)90039-0 · Cited by 1,093 · see citing works
All of Statistics: A Concise Course in Statistical Inference
Wasserman, L. (2004) · Springer Texts in Statistics · doi:10.1007/978-0-387-21736-9 · Cited by 1,090 · see citing works
Antibiotics as Major Disruptors of Gut Microbiota
Ramirez, J., Guarner, F., Fernández, L. B., Saito, A. M., Sdepanian, V. L., & Cohen, H. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.572912 · Cited by 936 · see citing works
Colonization resistance of the digestive tract in conventional and antibiotic-treated mice
van der Waaij, D., Vries, J. M. B.-D., & der Wees, J. E. C. L.-V. (1971) · Journal of Hygiene · doi:10.1017/s0022172400021653 · Cited by 907 · see citing works
Antibiotic-Induced Changes in the Intestinal Microbiota and Disease
Becattini, S., Taur, Y., & Pamer, E. G. (2016) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2016.04.003 · Cited by 901 · see citing works
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
Recovery of gut microbiota of healthy adults following antibiotic exposure
Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, T., Hansen, T. H., Liang, S., Feng, Q., Zhang, C., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0257-9 · Cited by 875 · see citing works
The Human Gut Microbiome: From Association to Modulation
Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845 · see citing works
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D. A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3703 · Cited by 798 · see citing works
Feedback Systems: An Introduction for Scientists and Engineers
Aström, K. J., & Murray, R. M. (2008) · Princeton University Press eBooks · doi:10.1515/9781400828739 · Cited by 760 · see citing works
Shifting the balance: antibiotic effects on host–microbiota mutualism
Willing, B. P., Russell, S. L., & Finlay, B. B. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2536 · Cited by 747 · see citing works
Sonnenburg, E. D., Zheng, H., Joglekar, P., Higginbottom, S. K., Firbank, S. J., Bolam, D. N., & Sonnenburg, J. L. (2010) · Cell · doi:10.1016/j.cell.2010.05.005 · Cited by 745 · see citing works
Haiser, H. J., Gootenberg, D. B., Chatman, K., Sirasani, G., Balskus, E. P., & Turnbaugh, P. J. (2013) · Science · doi:10.1126/science.1235872 · Cited by 704 · see citing works
Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon
Salyers, A. A., Vercellotti, J. R., West, S. E. H., & Wilkins, T. D. (1977) · Applied and Environmental Microbiology · doi:10.1128/aem.33.2.319-322.1977 · Cited by 691 · see citing works
Regulated virulence controls the ability of a pathogen to compete with the gut microbiota
Kamada, N., Kim, Y.-G., Sham, H. P., Vallance, B. A., Puente, J. L., Martens, E. C., & Núñez, G. (2012) · Science · doi:10.1126/science.1222195 · Cited by 682 · see citing works
Complex pectin metabolism by gut bacteria reveals novel catalytic functions
Ndeh, D. A., Rogowski, A., Cartmell, A., Luis, A. S., Baslé, A., Gray, J., Venditto, I., Briggs, J. A., Zhang, X., Labourel, A., et al. (2017) · Nature · doi:10.1038/nature21725 · Cited by 642 · see citing works
Strength of species interactions determines biodiversity and stability in microbial communities
Ratzke, C., Barrere, J., & Gore, J. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1099-4 · Cited by 626 · see citing works
The evolution of cooperation within the gut microbiota
Rakoff-Nahoum, S., Foster, K. R., & Comstock, L. E. (2016) · Nature · doi:10.1038/nature17626 · Cited by 616 · see citing works
Hamaker, B. R., & Tuncil, Y. E. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.07.028 · Cited by 584 · see citing works
Polysaccharide Utilization Loci: Fueling Microbial Communities
Grondin, J. M., Tamura, K., Déjean, G., Abbott, D. W., & Brumer, H. (2017) · Journal of Bacteriology · doi:10.1128/jb.00860-16 · Cited by 554 · see citing works
Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism
Cuskin, F., Lowe, E. C., Temple, M. J., Zhu, Y., Cameron, E. A., Pudlo, N. A., Porter, N. T., Urs, K., Thompson, A. J., Cartmell, A., et al. (2015) · Nature · doi:10.1038/nature13995 · Cited by 550 · 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
Self-citationDysregulated Microbial Fermentation of Soluble Fiber Induces Cholestatic Liver Cancer
Singh, V., Yeoh, B. S., Chassaing, B., Xiao, X., Saha, P., Aguilera Olvera, R., Lapek, J. D., Zhang, L., Wang, W.-B., Hao, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.004 · Cited by 532 · see citing works
Maldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517 · see citing works
Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides
Luis, A. S., Briggs, J. A., Zhang, X., Farnell, B., Ndeh, D. A., Labourel, A., Baslé, A., Cartmell, A., Terrapon, N., Stott, K. M., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0079-1 · Cited by 431 · see citing works
Glycan complexity dictates microbial resource allocation in the large intestine
Rogowski, A., Briggs, J. A., Mortimer, J. C., Tryfona, T., Terrapon, N., Lowe, E. C., Baslé, A., Morland, C., Day, A. M., Zheng, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms8481 · Cited by 424 · see citing works
Metabolic niche of a prominent sulfate-reducing human gut bacterium
Rey, F. E., Gonzalez, M. D., Cheng, J., Wu, M., Ahern, P. P., & Gordon, J. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1312524110 · Cited by 412 · see citing works
An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts
Rakoff-Nahoum, S., Coyne, M. J., & Comstock, L. E. (2013) · Current Biology · doi:10.1016/j.cub.2013.10.077 · Cited by 410 · see citing works
Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults
Tap, J., Furet, J., Bensaada, M., Philippe, C., Roth, H., Rabot, S., Lakhdari, O., Lombard, V., Henrissat, B., Corthier, G., et al. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13006 · Cited by 397 · see citing works
Fabich, A. J., Jones, S. A., Chowdhury, F. Z., Cernosek, A., Anderson, A., Smalley, D., McHargue, J. W., Hightower, G. A., Smith, J. T., Autieri, S. M., et al. (2008) · Infection and Immunity · doi:10.1128/iai.01386-07 · Cited by 380 · see citing works
An exclusive metabolic niche enables strain engraftment in the gut microbiota
Shepherd, E. S., DeLoache, W. C., Pruss, K. M., Whitaker, W. R., & Sonnenburg, J. L. (2018) · Nature · doi:10.1038/s41586-018-0092-4 · Cited by 367 · see citing works
Microbial nutrient niches in the gut
Pereira, F. C., & Berry, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13659 · Cited by 365 · see citing works
Short-Term Effect of Antibiotics on Human Gut Microbiota
Panda, S., khader, I. E., Casellas, F., Vivancos, J., Cors, M. G., Santiago, A., Cuenca, S., Guarner, F., & Manichanh, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095476 · Cited by 350 · see citing works
Patnode, M. L., Beller, Z. W., Han, N. D., Cheng, J., Peters, S. L., Terrapon, N., Henrissat, B., Le Gall, S., Saulnier, L., Hayashi, D. K., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.011 · Cited by 329 · see citing works
Sorbara, M. T., & Pamer, E. G. (2018) · Mucosal Immunology · doi:10.1038/s41385-018-0053-0 · Cited by 325 · see citing works
Systems biology: parameter estimation for biochemical models
Ashyraliyev, M., Fomekong‐Nanfack, Y., Kaandorp, J. A., & Blom, J. G. (2009) · The FEBS Journal · doi:10.1111/j.1742-4658.2008.06844.x · Cited by 323 · see citing works
Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
Raue, A., Schilling, M., Bachmann, J., Matteson, A., Schelke, M., Kaschek, D., Hug, S., Kreutz, C., Harms, B. D., Theis, F. J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074335 · Cited by 307 · see citing works
Presence of Inulin and Oligofructose in the Diets of Americans
Moshfegh, A. J., Friday, J., Goldman, J., & Ahuja, J. K. C. (1999) · Journal of Nutrition · doi:10.1093/jn/129.7.1407s · Cited by 306 · see citing works
PULDB: the expanded database of Polysaccharide Utilization Loci
Terrapon, N., Lombard, V., Drula, É., Lapébie, P., Almasaudi, S. B., Gilbert, H. J., & Henrissat, B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1022 · Cited by 292 · see citing works
Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S., & Conway, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053957 · Cited by 285 · 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
Microbial interspecies interactions: recent findings in syntrophic consortia
Kouzuma, A., Kato, S., & Watanabe, K. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00477 · Cited by 258 · see citing works
Automatic prediction of polysaccharide utilization loci in Bacteroidetes species
Terrapon, N., Lombard, V., Gilbert, H. J., & Henrissat, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu716 · Cited by 235 · see citing works
Leatham, M. P., Banerjee, S., Autieri, S. M., Mercado–Lubo, R., Conway, T., & Cohen, P. S. (2009) · Infection and Immunity · doi:10.1128/iai.00059-09 · Cited by 233 · see citing works
Bello, M. D., Lee, H., Goyal, A., & Gore, J. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01535-8 · Cited by 225 · see citing works
The plant cell wall as a source of dietary fiber: chemistry and structure
Selvendran, R. R. (1984) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/39.2.320 · Cited by 219 · see citing works
Walter, J., Maldonado-Gómez, M. X., & Martínez, I. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.08.008 · Cited by 198 · see citing works
Design of synthetic human gut microbiome assembly and butyrate production
Clark, R. L., Connors, B., Stevenson, D. M., Hromada, S. E., Hamilton, J. J., Amador‐Noguez, D., & Venturelli, O. S. (2021) · Nature Communications · doi:10.1038/s41467-021-22938-y · Cited by 197 · see citing works
Self-citationSchwiertz, A., Hold, G. L., Duncan, S. H., Gruhl, B., Collins, M. D., Lawson, P. A., Flint, H. J., & Blaut, M. (2002) · Systematic and Applied Microbiology · doi:10.1078/0723-2020-00096 · Cited by 194 · see citing works
Pichler, M. J., Yamada, C., Shuoker, B., Silva, M. C. A., Gotoh, A., Leth, M. L., Schoof, E. M., Katoh, T., Sakanaka, M., Katayama, T., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17075-x · Cited by 185 · see citing works
Gut microbiome variation modulates the effects of dietary fiber on host metabolism
Murga-Garrido, S. M., Hong, Q., Cross, T.-W., Hutchison, E. R., Han, J. H., Thomas, S. P., Vivas, E. I., Denu, J. M., Ceschin, D. G., Tang, Z.-Z., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01061-6 · Cited by 184 · see citing works
Feng, J., Qian, Y., Zhou, Z., Sarah, E., Vivas, E. I., Lan, F., Hamilton, J. J., Rey, F. E., Anantharaman, K., & Venturelli, O. S. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.006 · Cited by 170 · see citing works
Self-citationNew View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota
Cantu-Jungles, T. M., & Hamaker, B. R. (2020) · mBio · doi:10.1128/mbio.02179-19 · Cited by 164 · see citing works
Cartmell, A., Muñoz-Muñoz, J., Briggs, J. A., Ndeh, D. A., Lowe, E. C., Baslé, A., Terrapon, N., Stott, K. M., Heunis, T. D. J., Gray, J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0258-8 · Cited by 163 · see citing works
Stability criteria for complex microbial communities
Butler, S., & O’Dwyer, J. P. (2018) · Nature Communications · doi:10.1038/s41467-018-05308-z · Cited by 152 · see citing works
Refining the stress gradient hypothesis in a microbial community
Hammarlund, S. P., & Harcombe, W. R. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1910420116 · Cited by 147 · see citing works
Laminarin in the dietary fibre concept
Devillé, C., Damas, J., Forget, P., Dandrifosse, G., & Peulen, O. (2004) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.1754 · Cited by 146 · see citing works
Jenior, M. L., Leslie, J. L., Young, V. B., & Schloss, P. D. (2017) · mSystems · doi:10.1128/msystems.00063-17 · Cited by 144 · see citing works
Ravcheev, D. A., Godzik, A., Osterman, A. L., & Rodionov, D. A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-873 · Cited by 140 · see citing works
Bernalier, A., Willems, A. L., Leclerc, M., Rochet, V., & Collins, M. D. (1996) · Archives of Microbiology · doi:10.1007/s002030050373 · Cited by 133 · see citing works
It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome
Morrison, K. E., Jašarević, E., Howard, C. D., & Bale, T. L. (2020) · Microbiome · doi:10.1186/s40168-020-0791-6 · Cited by 127 · see citing works
Respondek, F., Gérard, P., Bossis, M., Boschat, L., Bruneau, A., Rabot, S., Wagner, A., & Martin, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071026 · Cited by 115 · see citing works
Synergistic growth in bacteria depends on substrate complexity
Deng, Y., & Wang, S. Y. (2016) · The Journal of Microbiology · doi:10.1007/s12275-016-5461-9 · Cited by 114 · see citing works
Despres, J., Forano, É., Lepercq, P., Comtet-Marre, S., Jubelin, G., Chambon, C., Yeoman, C. J., Miller, M. E. B., Fields, C. J., Martens, E. C., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2680-8 · Cited by 109 · see citing works
Momose, Y., Hirayama, K., & Itoh, K. (2008) · Antonie van Leeuwenhoek · doi:10.1007/s10482-008-9222-6 · Cited by 107 · see citing works
Cantu-Jungles, T. M., Bulut, N., Chambry, E., Ruthes, A. C., Iacomini, M., Keshavarzian, A., Johnson, T. A., & Hamaker, B. R. (2021) · mBio · doi:10.1128/mbio.01028-21 · Cited by 106 · see citing works
Freter, R. (1962) · The Journal of Infectious Diseases · doi:10.1093/infdis/110.1.38 · Cited by 98 · see citing works
Topological sensitivity analysis for systems biology
Babtie, A. C., Kirk, P., & Stumpf, M. P. H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414026112 · Cited by 97 · see citing works
Jenior, M. L., Leslie, J. L., Young, V. B., & Schloss, P. D. (2018) · mSphere · doi:10.1128/msphere.00261-18 · Cited by 96 · see citing works
Déjean, G., Tamura, K., Cabrera, A., Jain, N., Pudlo, N. A., Pereira, G. V., Viborg, A. H., Petegem, F. V., Martens, E. C., & Brumer, H. (2020) · mBio · doi:10.1128/mbio.00095-20 · Cited by 96 · see citing works
Deng, Y., & Wang, S. Y. (2017) · FEMS Microbiology Letters · doi:10.1093/femsle/fnx019 · Cited by 90 · see citing works
Non-additive microbial community responses to environmental complexity
Pacheco, A. R., Osborne, M. L., & Segrè, D. (2021) · Nature Communications · doi:10.1038/s41467-021-22426-3 · Cited by 90 · see citing works
Li, S., Tan, J., Yang, X., Ma, C., & Jiang, L. (2018) · The ISME Journal · doi:10.1038/s41396-018-0283-x · Cited by 84 · see citing works
Litvak, Y., & Bäumler, A. J. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007563 · Cited by 80 · see citing works
Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics
Baranwal, M., Clark, R. L., Thompson, J. C., Sun, Z., Hero, A. O., & Venturelli, O. S. (2022) · eLife · doi:10.7554/elife.73870 · Cited by 75 · see citing works
Self-citationFluctuating resource availability increases invasibility in microbial microcosms
Li, W., & Stevens, M. H. H. (2011) · Oikos · doi:10.1111/j.1600-0706.2011.19762.x · Cited by 68 · see citing works
Devendran, S., Shrestha, R., Alves, J. M. P., Wolf, P. G., Ly, L. K., Hernández, Á. G., Méndez–García, C., Inboden, A. M., Wiley, J., Paul, O., et al. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.00052-19 · Cited by 59 · see citing works
Modulation of microbial community dynamics by spatial partitioning
Wu, F., Ha, Y., Weiss, A., Wang, M., Letourneau, J., Wang, S., Luo, N., Huang, S., Lee, C. T., David, L. A., et al. (2022) · Nature Chemical Biology · doi:10.1038/s41589-021-00961-w · Cited by 57 · see citing works
Stone, L. (2020) · Nature Communications · doi:10.1038/s41467-020-16474-4 · Cited by 53 · see citing works
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities
Hromada, S. E., Qian, Y., Jacobson, T. B., Clark, R. L., Watson, L., Safdar, N., Amador‐Noguez, D., & Venturelli, O. S. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110355 · Cited by 53 · see citing works
Self-citationPublic good exploitation in natural bacterioplankton communities
Pollak, S., Gralka, M., Sato, Y., Schwartzman, J. A., Lu, L., & Cordero, O. X. (2021) · Science Advances · doi:10.1126/sciadv.abi4717 · Cited by 47 · see citing works
Sun, X., Liu, Y., Jiang, P., Song, S., & Ai, C. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.12.024 · Cited by 40 · see citing works
Benítez‐Páez, A., Moreno, F. J., Sanz, M. L., & Sanz, Y. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00624 · Cited by 14 · see citing works
Gut Microbiome Variation Modulates the Effects of Dietary Fiber on Host MetabolismPreprint
Murga-Garrido, S. M., Hong, Q., Cross, T.-W., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-97357/v1 · Cited by 5 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- [59]Bishop CM Pattern Recognition and Machine Learning (Information Science and Statistics). (Springer-Verlag, 2006).
- [90]Maindonald J. Pattern Recognition and Machine Learning. Journal of Statistical Software 17, (Springer-Verlag, 2007).
- [92]Munsky B Hlavacek William S., Tsimring Lev S., Quantitative biology. Theory, computational methods, and models (The MIT Press, 2018).
Cited by
Sorted by citations
Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases
Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works
- Authors
- Ostrem Loss, E., Thompson, J., Cheung, P. L. K., Qian, Y., & Venturelli, O. S.
- Affiliations
- University of Wisconsin–Madison (US)
- Corresponding author
- Venturelli, Ophelia S.
- Venue
- Nature Ecology & Evolution
- Published
- 2023-01-05
- Volume
- 7
- Issue
- 1
- Pages
- 127-142
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC10268929
- OpenAlex
- W4313562045
- Cited by
- 38
- References
- 102
- Citations by year
- 2026: 9 · 2025: 16 · 2024: 9 · 2023: 4
- FWCI
- 3.39
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (R35GM124774)
- United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (W911NF1910269)
- U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (R01EB030340)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Keywords
- dietary fiber, human gut microbiome, microbial growth, community assembly, invasion resistance, interspecies interactions, negative interactions, synthetic microbial communities
- MeSH terms
- Gastrointestinal Microbiome, Sugars, Bacteria, Carbohydrates, Humans, Reproducibility of Results
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