Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans
Open accessAbstract
Development of microbiota-directed foods (MDFs) that selectively increase the abundance of beneficial human gut microbes, and their expressed functions, requires knowledge of both the bioactive components of MDFs and the mechanisms underlying microbe-microbe interactions. Here, gnotobiotic mice were colonized with a defined consortium of human-gut-derived bacterial strains and fed different combinations of 34 food-grade fibers added to a representative low-fiber diet consumed in the United States. Bioactive carbohydrates in fiber preparations targeting particular Bacteroides species were identified using community-wide quantitative proteomic analyses of bacterial gene expression coupled with forward genetic screens. Deliberate manipulation of community membership combined with administration of retrievable artificial food particles, consisting of paramagnetic microscopic beads coated with dietary polysaccharides, disclosed the contributions of targeted species to fiber degradation. Our approach, including the use of bead-based biosensors, defines nutrient-harvesting strategies that underlie, as well as alleviate, competition between Bacteroides and control the selectivity of MDF components.
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?
Dietary addition of a single type of fiber can cause dramatic changes in the expression of genes required for bacterial metabolism of fiber glycans.
“This is demonstrated in recent work showing that dietary addition of a single type of fiber can cause dramatic changes in the expression of genes required for bacterial metabolism of fiber glycans16.”
From Gut microbiota and cardiovascular disease. (2020) · cites this paper as [16]
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
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · see citing works
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Self-citationSearch and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829 · see citing works
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155 · see citing works
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R. D., Mills, D. A., & Caporaso, J. G. (2012) · Nature Methods · doi:10.1038/nmeth.2276 · Cited by 4,406 · see citing works
Self-citationGut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works
Self-citationPersonalized nutrition by prediction of glycemic responses
Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.001 · Cited by 2,929 · 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
Self-citationBacterial competition: surviving and thriving in the microbial jungle
Hibbing, M. E., Fuqua, C., Parsek, M. R., & Peterson, S. B. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2259 · Cited by 2,658 · see citing works
Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes
Zhao, L., Zhang, F., Ding, X., Wu, G., Lam, Y. Y., Wang, X., Fu, H., Xue, X., Lu, C., Ma, J., et al. (2018) · Science · doi:10.1126/science.aao5774 · Cited by 2,304 · see citing works
The 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 · see citing works
Self-citationBlundell, J. E., Baker, J. L., Boyland, E. J., Blaak, E. E., Charzewska, J., Henauw, S. D., Frühbeck, G., González‐Gross, M., Hebebrand, J., Holm, L., et al. (2017) · Obesity Facts · doi:10.1159/000455952 · Cited by 1,980 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
Measurement of uronic acids without interference from neutral sugars
Filisetti-Cozzi, T. M. C. C., & Carpita, N. C. (1991) · Analytical Biochemistry · doi:10.1016/0003-2697(91)90372-z · Cited by 1,446 · see citing works
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Martens, E. C., Lowe, E. C., Chiang, H. C., Pudlo, N. A., Wu, M., McNulty, N. P., Abbott, D. W., Henrissat, B., Gilbert, H. J., Bolam, D. N., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001221 · Cited by 847 · see citing works
Self-citationDetermining the polysaccharide composition of plant cell walls
Pettolino, F. A., Walsh, C. T., Fincher, G. B., & Bacic, A. (2012) · Nature Protocols · doi:10.1038/nprot.2012.081 · Cited by 775 · 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
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Goodman, A. L., McNulty, N. P., Zhao, Y., Leip, D., Mitra, R. D., Lozupone, C., Knight, R. D., & Gordon, J. I. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.08.003 · Cited by 713 · see citing works
Self-citationEvolving Views of Pectin Biosynthesis
Atmodjo, M. A., Hao, Z., & Mohnen, D. (2013) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042811-105534 · Cited by 625 · see citing works
Adey, A., Morrison, H. G., Asan, Xu, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-12-r119 · Cited by 566 · see citing works
Tabb, D. L., Fernando, C., & Chambers, M. (2007) · Journal of Proteome Research · doi:10.1021/pr0604054 · Cited by 548 · 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
Self-citationGlycan 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
Self-citationImproved Method for Measurement of Dietary Fiber as Non-Starch Polysaccharides in Plant Foods
Englyst, H. N., & Cummings, J. H. (1988) · Journal of AOAC INTERNATIONAL · doi:10.1093/jaoac/71.4.808 · Cited by 415 · see citing works
Faith, J. J., Ahern, P. P., Ridaura, V. K., Cheng, J., & Gordon, J. I. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008051 · Cited by 373 · see citing works
Self-citationAn 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
Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain
Menni, C., Jackson, M. A., Pallister, T., Steves, C. J., Spector, T. D., & Valdes, A. M. (2017) · International Journal of Obesity · doi:10.1038/ijo.2017.66 · Cited by 343 · see citing works
IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
Ma, Z.-Q., Dasari, S., Chambers, M., Litton, M. D., Sobecki, S. M., Zimmerman, L. J., Halvey, P. J., Schilling, B., Drake, P. M., Gibson, B. W., et al. (2009) · Journal of Proteome Research · doi:10.1021/pr900360j · Cited by 328 · see citing works
McNulty, N. P., Wu, M., Erickson, A. R., Pan, C., Erickson, B. K., Martens, E. C., Pudlo, N. A., Muegge, B. D., Henrissat, B., Hettich, R. L., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001637 · Cited by 295 · see citing works
Self-citationPULDB: 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
Self-citationAUTOMATISATION DU DOSAGE DES SUBSTANCES PECTIQUES PAR LA METHODE AU METAHYDROXYDIPHENYL
Thibault, J. (1979) · Cited by 258 · see citing works
The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology
Porter, N. T., & Martens, E. C. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095316 · Cited by 251 · see citing works
Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides
Wu, M., McNulty, N. P., Rodionov, D. A., Khoroshkin, M., Griffin, N. W., Cheng, J., Latreille, P., Kerstetter, R. A., Terrapon, N., Henrissat, B., et al. (2015) · Science · doi:10.1126/science.aac5992 · Cited by 245 · see citing works
Self-citationStructural basis for nutrient acquisition by dominant members of the human gut microbiota
Glenwright, A. J., Pothula, K. R., Bhamidimarri, S. P., Chorev, D. S., Baslé, A., Firbank, S. J., Zheng, H., Robinson, C. V., Winterhalter, M., Kleinekathöfer, U., et al. (2017) · Nature · doi:10.1038/nature20828 · Cited by 227 · see citing works
The effects of micronutrient deficiencies on bacterial species from the human gut microbiota
Hibberd, M. C., Wu, M., Rodionov, D. A., Li, X., Cheng, J., Griffin, N. W., Barratt, M. J., Giannone, R. J., Hettich, R. L., Osterman, A. L., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aal4069 · Cited by 221 · see citing works
Self-citationLevigne, S., Thomas, M., Ralet, M., Quéméner, B., & Thibault, J.-F. (2002) · Food Hydrocolloids · doi:10.1016/s0268-005x(02)00015-2 · Cited by 174 · see citing works
Links between environment, diet, and the hunter-gatherer microbiome
Fragiadakis, G. K., Smits, S. A., Sonnenburg, E. D., Treuren, W. V., Reid, G., Knight, R. D., Manjurano, A. M., Changalucha, J. M., Domínguez-Bello, M. G., Leach, J. D., et al. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1494103 · Cited by 164 · see citing works
Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling
Pattathil, S., Avcı, U., Miller, J. S., & Hahn, M. G. (2012) · Humana Press eBooks · doi:10.1007/978-1-61779-956-3_6 · Cited by 162 · see citing works
The structure of Cryptococcus neoformans galactoxylomannan contains β-d-glucuronic acid
Heiß, C., Klutts, J. S., Wang, Z., Doering, T. L., & Azadi, P. (2009) · Carbohydrate Research · doi:10.1016/j.carres.2009.03.003 · Cited by 137 · see citing works
Ting, L., Cowley, M. J., Hoon, S. L., Guilhaus, M., Raftery, M. J., & Cavicchioli, R. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800462-mcp200 · Cited by 129 · see citing works
Santander, J., Martin, T. E., Loh, A., Pohlenz, C., Gatlin, D. M., & Curtiss, R. (2013) · Microbiology · doi:10.1099/mic.0.066639-0 · Cited by 124 · see citing works
Lynch, J. B., & Sonnenburg, J. L. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08123.x · Cited by 72 · see citing works
Schwalm, N. D., Townsend, G. E., & Groisman, E. A. (2016) · mBio · doi:10.1128/mbio.01342-16 · Cited by 71 · see citing works
Kotarski, S. F., & Salyers, A. A. (1984) · Journal of Bacteriology · doi:10.1128/jb.158.1.102-109.1984 · Cited by 66 · see citing works
Clarkson, S. M., Giannone, R. J., Kridelbaugh, D. M., Elkins, J. G., Guss, A. M., & Michener, J. K. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01313-17 · Cited by 64 · see citing works
Self-citationBuffetto, F., Cornuault, V., Rydahl, M. G., Ropartz, D., Alvarado, C., Echasserieau‐Laporte, V., Gall, S. L., Bouchet, B., Tranquet, O., Verhertbruggen, Y., et al. (2015) · Plant and Cell Physiology · doi:10.1093/pcp/pcv128 · Cited by 39 · see citing works
Tauzin, A. S., Laville, É., Xiao, Y., Nouaille, S., Bourgeois, P., Heux, S., Portais, J., MONSAN, P. F., Martens, E. C., Potocki-Véronèse, G., et al. (2016) · Molecular Microbiology · doi:10.1111/mmi.13480 · Cited by 31 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Gut microbiota and cardiovascular disease.
Witkowski, M., Weeks, T. L., & Hazen, S. L. (2020) · Circulation Research · doi:10.1161/circresaha.120.316242 · Cited by 1,051 · see citing works
Dietary fibre in gastrointestinal health and disease
Gill, S. K., Rossi, M., Bajka, B., & Whelan, K. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00375-4 · Cited by 979 · see citing works
Sorbara, M. T., & Pamer, E. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00667-9 · Cited by 468 · see citing works
Hodgkinson, K. M., Abbar, F. E., Dobranowski, P., Manoogian, J., Butcher, J., Figeys, D., Mack, D. R., & Stintzi, A. P. (2022) · Clinical Nutrition · doi:10.1016/j.clnu.2022.10.024 · Cited by 446 · see citing works
Living Bacterial Hydrogels for Accelerated Infected Wound Healing
Ming, Z., Lin, H., Bao, M., Zhu, H., Qiang, S., Xue, S., & Liu, W. (2021) · Advanced Science · doi:10.1002/advs.202102545 · Cited by 318 · see citing works
Design, construction, and in vivo augmentation of a complex gut microbiome
Cheng, A. G., Ho, P.-Y., Aranda-Díaz, A., Jain, S., Yu, F. B., Meng, X., Wang, M., Iakiviak, M., Nagashima, K., Zhao, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.003 · Cited by 273 · see citing works
Guo, C., Wang, Y., Zhang, S., Zhang, X., Du, Z., Li, M., & Ding, K. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.03.137 · Cited by 270 · see citing works
Wei, W., Wong, C. C., Jia, Z., Liu, W., Liu, C., Ji, F., Pan, Y., Wang, F., Wang, G., Zhao, L., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01418-7 · Cited by 252 · 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
Dietary Factors Modulating Colorectal Carcinogenesis
Vernia, F., Longo, S. A., Stefanelli, G., Viscido, A., & Latella, G. (2021) · Nutrients · doi:10.3390/nu13010143 · Cited by 198 · see citing works
Wu, D., Nie, X.-R., Gan, R., Guo, H., Fu, Y., Yuan, Q., Zhang, Q. R., & Qin, W. (2020) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2020.106577 · Cited by 193 · see citing works
Gálvez, E. J. C., Iljazović, A., Amend, L., Lesker, T. R., Renault, T. T., Thiemann, S., Hao, L., Roy, U., Gronow, A., Charpentier, E., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.09.012 · Cited by 188 · see citing works
New 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
Towards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors
Simpson, R. C., Shanahan, E. R., Scolyer, R. A., & Long, G. V. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00803-9 · Cited by 153 · see citing works
Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans
Delannoy-Bruno, O., Desai, C., Raman, A. S., Chen, R. Y., Hibberd, M. C., Cheng, J., Han, N., Castillo, J. J., Couture, G., Lebrilla, C. B., et al. (2021) · Nature · doi:10.1038/s41586-021-03671-4 · Cited by 136 · see citing works
Self-citationMa, Y., Jiang, S., & Zeng, M. (2021) · Food Research International · doi:10.1016/j.foodres.2021.110646 · Cited by 143 · see citing works
Ecological dynamics of the gut microbiome in response to dietary fiber
Liu, H., Liao, C., Wu, L. H., Tang, J., Chen, J., Lei, C., Zheng, L., Zhang, C., Liu, Y., Xavier, J. B., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01253-4 · Cited by 138 · see citing works
Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications
van Leeuwen, P. T., Brul, S., Zhang, J., & Wortel, M. T. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad012 · Cited by 125 · see citing works
Dietary protein and the intestinal microbiota: An understudied relationship
Bartlett, A., & Kleiner, M. (2022) · iScience · doi:10.1016/j.isci.2022.105313 · Cited by 124 · see citing works
Gut microbiota and old age: Modulating factors and interventions for healthy longevity
Coman, V., & Vodnar, D. C. (2020) · Experimental Gerontology · doi:10.1016/j.exger.2020.111095 · Cited by 124 · 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
Metabolic control by the microbiome
Cox, T. O., Lundgren, P., Nath, K., & Thaiss, C. A. (2022) · Genome Medicine · doi:10.1186/s13073-022-01092-0 · Cited by 113 · see citing works
Customized materials-assisted microorganisms in tumor therapeutics
Chen, Q., Qiao, J., Liu, X., Zhang, C., & Zhang, X. (2021) · Chemical Society Reviews · doi:10.1039/d0cs01571g · Cited by 109 · see citing works
Gut Microbiota Interaction with the Central Nervous System throughout Life
Ojeda, J., Ávila, A., & Vidal, P. M. (2021) · Journal of Clinical Medicine · doi:10.3390/jcm10061299 · Cited by 107 · see citing works
Communal living: glycan utilization by the human gut microbiota
Briggs, J. A., Grondin, J. M., & Brumer, H. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15317 · Cited by 103 · see citing works
Biogeography of microbial bile acid transformations along the murine gut
Marion, S., Desharnais, L., Studer, N., Dong, Y., Notter, M. D., Poudel, S., Menin, L., Janowczyk, A. R., Hettich, R. L., Hapfelmeier, S., et al. (2020) · Journal of Lipid Research · doi:10.1194/jlr.ra120001021 · Cited by 101 · see citing works
Self-citationMicrobial transformation of dietary xenobiotics shapes gut microbiome composition
Culp, E. J., Nelson, N. T., Verdegaal, A. A., & Goodman, A. L. (2024) · Cell · doi:10.1016/j.cell.2024.08.038 · Cited by 104 · see citing works
Yeast β-glucan, a potential prebiotic, showed a similar probiotic activity to inulin
Wang, H., Chen, G., Li, X., Zheng, F., & Zeng, X. (2020) · Food & Function · doi:10.1039/d0fo02224a · Cited by 97 · see citing works
Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut
Michalak, L., Gaby, J. C., Lagos, L. X., Rosa, S. L. L., Hvidsten, T. R., Tétard‐Jones, C., Willats, W. G. T., Terrapon, N., Lombard, V., Henrissat, B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19585-0 · Cited by 97 · see citing works
Self-citationZhu, K., Mao, G., Wu, D., Yu, C., Cheng, H., Xiao, H., Ye, X., Linhardt, R. J., Orfila, C., & Chen, S. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c02654 · Cited by 95 · see citing works
Not All Fibers Are Born Equal; Variable Response to Dietary Fiber Subtypes in IBD
Armstrong, H., Mander, I. K., Zhang, Z., Armstrong, D. W. J., & Wine, E. (2021) · Frontiers in Pediatrics · doi:10.3389/fped.2020.620189 · Cited by 92 · see citing works
Salvato, F., Hettich, R. L., & Kleiner, M. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009245 · Cited by 93 · see citing works
Self-citationHigh pressure processing accelarated the release of RG-I pectic polysaccharides from citrus peel
Hou, Z., Chen, S., & Ye, X. (2021) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2021.118005 · Cited by 88 · see citing works
Elkrief, A., Pidgeon, R., Vareki, S. M., Messaoudene, M., Castagner, B., & Routy, B. (2025) · Nature Reviews Drug Discovery · doi:10.1038/s41573-025-01211-7 · Cited by 92 · see citing works
The human microbiome encodes resistance to the antidiabetic drug acarbose
Balaich, J. N., Estrella, M. A., Wu, G. G., Jeffrey, P. D., Biswas, A. G., Zhao, L., Korennykh, A. V., & Donia, M. S. (2021) · Nature · doi:10.1038/s41586-021-04091-0 · Cited by 84 · see citing works
Jin, H., You, L., Zhao, F.-Y., Li, S., Ma, T., Kwok, L., Xu, H.-Y., & Sun, Z.-H. (2022) · Gut microbes · doi:10.1080/19490976.2021.2021790 · Cited by 69 · 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
Considerations for constructing a protein sequence database for metaproteomics
Blakeley‐Ruiz, J. A., & Kleiner, M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.01.018 · Cited by 83 · see citing works
Park, S.-Y., Rao, C., Coyte, K. Z., Kuziel, G. A., Zhang, Y., Huang, W., Franzosa, E. A., Weng, J., Huttenhower, C., & Rakoff-Nahoum, S. (2022) · Cell · doi:10.1016/j.cell.2022.01.002 · Cited by 85 · see citing works
Dietary pectic substances enhance gut health by its polycomponent: A review
Wu, D., Ye, X., Linhardt, R. J., Liu, X., Zhu, K., Yu, C., Ding, T., Liu, D., He, Q., & Chen, S. (2021) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12723 · Cited by 83 · see citing works
Hu, W., Di, Q., Liang, T., Zhou, N., Chen, H., Zeng, Z., Luo, Y., & Shaker, M. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.124188 · Cited by 83 · see citing works
Brown, H. M., & Esterházy, D. (2021) · Mucosal Immunology · doi:10.1038/s41385-021-00420-8 · Cited by 83 · see citing works
Can we harness the microbiota to enhance the efficacy of cancer immunotherapy?
Finlay, B. B., Goldszmid, R., Honda, K., Trinchieri, G., Wargo, J., & Zitvogel, L. (2020) · Nature Reviews Immunology · doi:10.1038/s41577-020-0374-6 · Cited by 81 · see citing works
Glycan processing in gut microbiomes
Rosa, S. L. L., Ostrowski, M. P., de León, A. V., McKee, L. S., Larsbrink, J., Eijsink, V. G. H., Lowe, E. C., Martens, E. C., & Pope, P. B. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102143 · Cited by 80 · see citing works
Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study
Olendzki, B. C., Bucci, V., Cawley, C., Maserati, R., McManus, M. M., Olednzki, E., Madziar, C., Chiang, D., Ward, D. V., Pellish, R. S., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2046244 · Cited by 77 · see citing works
The microbiologist's guide to metaproteomics
Bossche, T. V. D., Armengaud, J., Benndorf, D., Blakeley‐Ruiz, J. A., Brauer, M., Cheng, K., Creskey, M., Figeys, D., Grenga, L., Griffin, T. J., et al. (2025) · iMeta · doi:10.1002/imt2.70031 · Cited by 81 · see citing works
Self-citationBacteroides vulgatus SNUG 40005 Restores Akkermansia Depletion by Metabolite Modulation
You, H. J., Si, J., Kim, J., Yoon, S.-H., Cha, K. H., Yoon, H. S., Lee, G., Yu, J., Choi, J.-S., Jung, M.-K., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.09.040 · Cited by 77 · see citing works
Han, G., & Vaishnava, S. (2023) · Experimental & Molecular Medicine · doi:10.1038/s12276-023-01120-y · Cited by 77 · see citing works
Dietary Selection Pressures and Their Impact on the Gut Microbiome
Ecklu-Mensah, G., Gilbert, J. A., & Devkota, S. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2021.07.009 · Cited by 76 · see citing works
Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome
Wang, M., Osborn, L. J., Jain, S., Meng, X., Weakley, A. M., Yan, J., Massey, W. J., Varadharajan, V., Horak, A. J., Banerjee, R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.05.037 · Cited by 74 · see citing works
Yu, C., Wu, D., Zhu, K., Hou, L., Xiao, H., Ding, T., Liu, D., Ye, X., Linhardt, R. J., & Chen, S. (2021) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2021.118377 · Cited by 72 · see citing works
Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans
Han, N. D., Cheng, J., Delannoy-Bruno, O., Webber, D. M., Terrapon, N., Henrissat, B., Rodionov, D. A., Arzamasov, A. A., Osterman, A. L., Hayashi, D. K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.004 · Cited by 71 · see citing works
Self-citationAL-Ayadhi, L. Y., Zayed, N., Bhat, R. S., Moubayed, N., Al-Muammar, M. N., & El-Ansary, A. (2021) · Gut Pathogens · doi:10.1186/s13099-021-00448-y · Cited by 70 · see citing works
Synthetic glycans control gut microbiome structure and mitigate colitis in mice
Tolonen, A. C., Beauchemin, N., Bayne, C. F., Li, L., Tan, J., Lee, J., Meehan, B. M., Meisner, J. S., Millet, Y. A., LeBlanc, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28856-x · Cited by 70 · see citing works
Polysaccharides influence human health via microbiota-dependent and -independent pathways
Gan, L., Wang, J., & Guo, Y. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.1030063 · Cited by 69 · see citing works
Gough, E. K., Edens, T. J., Geum, H. M., Baharmand, I., Gill, S. K., Robertson, R. C., Mutasa, K., Ntozini, R., Smith, L. E., Chasekwa, B., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103421 · Cited by 65 · see citing works
Zhou, J., Wang, M., Bäuerl, C., Cortés-Macías, E., Calvo‐Lerma, J., Collado, M. C., & Barba, F. J. (2022) · Food Chemistry · doi:10.1016/j.foodchem.2022.134083 · Cited by 64 · see citing works
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
Bisanz, J. E., Soto-Perez, P., Noecker, C. A., Aksenov, A. A., Lam, K. N., Kenney, G. E., Bess, E. N., Haiser, H. J., Kyaw, T. S., Yu, F. B., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.04.006 · Cited by 63 · see citing works
A 90-day dietary study with fibrillated cellulose in Sprague-Dawley rats
Ong, K. J., Ede, J. D., Pomeroy-Carter, C. A., Sayes, C. M., Mulenos, M. R., & Shatkin, J. A. (2020) · Toxicology Reports · doi:10.1016/j.toxrep.2020.01.003 · Cited by 62 · see citing works
Outlook on next-generation probiotics from the human gut
Filippis, F. D., Esposito, A., & Ercolini, D. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04080-6 · Cited by 66 · see citing works
Asthma in the Precision Medicine Era: Biologics and Probiotics
Chiu, C.-J., & Huang, M.-T. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094528 · Cited by 60 · see citing works
Living Bacterial Microneedles for Fungal Infection Treatment
Wang, F., Zhang, X., Chen, G., & Zhao, Y. (2020) · Research · doi:10.34133/2020/2760594 · Cited by 59 · see citing works
A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems
Li, J., Gálvez, E. J. C., Amend, L., Almási, É. D. H., Iljazović, A., Lesker, T. R., Bielecka, A. A., Schorr, E., & Strowig, T. (2021) · The EMBO Journal · doi:10.15252/embj.2021108287 · Cited by 57 · see citing works
Oxidative Stress and Gut Microbiome in Inflammatory Skin Diseases
Ni, Q., Zhang, P., Li, Q., & Han, Z. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.849985 · Cited by 57 · see citing works
Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae
Hecht, A. L., Harling, L. C., Friedman, E. S., Tanes, C., Lee, J., Firrman, J., Hao, F., Tu, V., Liu, L., Patterson, A. D., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci174726 · Cited by 57 · see citing works
Chapkin, R. S., Navarro, S. L., Hullar, M. A. J., & Lampe, J. W. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06106-8 · Cited by 57 · see citing works
Strong pathogen competition in neonatal gut colonisation
Mäklin, T., Thorpe, H. A., Pöntinen, A. K., Gladstone, R. A., Shao, Y., Pesonen, M., McNally, A., Johnsen, P. J., Samuelsen, Ø., Lawley, T. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35178-5 · Cited by 54 · see citing works
Dietary protein source alters gut microbiota composition and function
Blakeley‐Ruiz, J. A., Bartlett, A., McMillan, A. S., Awan, A., Vanhoy, M. E., Meyerhoffer, A. K., Vintila, S., Maier, J. L., Richie, T. G., Theriot, C. M., et al. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf048 · Cited by 54 · see citing works
Yue, B., Zong, G., Tao, R., Wei, Z., & Lu, Y. (2022) · Phytotherapy Research · doi:10.1002/ptr.7607 · Cited by 53 · see citing works
Identifying determinants of bacterial fitness in a model of human gut microbial succession
Feng, L., Raman, A. S., Hibberd, M. C., Cheng, J., Griffin, N. W., Peng, Y., Leyn, S. A., Rodionov, D. A., Osterman, A. L., & Gordon, J. I. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1918951117 · Cited by 53 · see citing works
Self-citationChristensen, L. H., Sørensen, C. V., Wøhlk, F. U., Kjølbæk, L., Astrup, A. V., Sanz, Y., Hjorth, M. F., & Benítez‐Páez, A. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1847627 · Cited by 52 · see citing works
Patnode, M. L., Guruge, J. L., Castillo, J. J., Couture, G., Lombard, V., Terrapon, N., Henrissat, B., Lebrilla, C. B., & Gordon, J. I. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.007 · Cited by 51 · see citing works
Self-citationHarness the functions of gut microbiome in tumorigenesis for cancer treatment
Lee, M. (2021) · Cancer Communications · doi:10.1002/cac2.12200 · Cited by 50 · see citing works
Fan, S., Ding, Y., Hu, Z., Zhang, Z., Fu, L., Zhang, J., Zhu, Y., Bai, J., & Xiao, X. (2024) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2024.111034 · Cited by 50 · see citing works
How Food Affects Colonization Resistance Against Enteropathogenic Bacteria
Kreuzer, M., & Hardt, W. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-020420-013457 · Cited by 43 · see citing works
Dietary fibre complexity and its influence on functional groups of the human gut microbiota
Louis, P., Solvang, M., Duncan, S. H., Walker, A. W., & Mukhopadhya, I. (2021) · Proceedings of The Nutrition Society · doi:10.1017/s0029665121003694 · Cited by 48 · see citing works
Ede, J. D., Ong, K. J., Mulenos, M. R., Pradhan, S. H., Gibb, M., Sayes, C. M., & Shatkin, J. A. (2020) · Toxicology Research · doi:10.1093/toxres/tfaa082 · Cited by 46 · see citing works
Kastl, A., Zong, W., Gershuni, V. M., Friedman, E. S., Tanes, C., Boateng, A., Mitchell, W. J., O’Connor, K., Bittinger, K. L., Terry, N. A., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2083417 · Cited by 46 · see citing works
Yuan, S., Du, H., Zhao, D., Qiao, Z., Zheng, J., Yu, X., & Xu, Y. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05103-22 · Cited by 45 · see citing works
Guo, Y., Chen, X., Gong, P., Wang, M., Yao, W., Yang, W., & Chen, F. (2022) · Food & Function · doi:10.1039/d2fo01776h · Cited by 44 · see citing works
Effects of aging on the fine structure, chain conformation, and morphology of Chenpi polysaccharides
Xu, G., Zhao, J., Yao, J., Xu, Y., Yuan, X., & Pan, S. (2024) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2024.122970 · Cited by 44 · see citing works
Lindemann, S. R. (2020) · Current Opinion in Chemical Engineering · doi:10.1016/j.coche.2020.08.004 · Cited by 44 · see citing works
Nanocrystalline Cellulose Cures Constipation via Gut Microbiota Metabolism
Wang, M., Cha, R., Hao, W., Du, R., Zhang, P., Hu, Y., & Jiang, X. (2022) · ACS Nano · doi:10.1021/acsnano.2c05809 · Cited by 43 · see citing works
Qu, D., Sun, F., Feng, S., Yu, L., Tian, F., Zhang, H., Chen, W., & Zhai, Q. (2021) · Food & Function · doi:10.1039/d1fo03073f · Cited by 43 · see citing works
Effects of Oral Glucose-Lowering Agents on Gut Microbiota and Microbial Metabolites
Wang, D., Liu, J. Y., Zhou, L., Zhang, Q., Li, M., & Xiao, X. (2022) · Frontiers in Endocrinology · doi:10.3389/fendo.2022.905171 · Cited by 46 · see citing works
Ge, T., Yang, C., Li, B., Huang, X., Zhao, L., Zhang, X., Tian, L., & Zhang, E. (2023) · BMC Veterinary Research · doi:10.1186/s12917-023-03592-6 · Cited by 46 · see citing works
Gerrick, E. R., Zlitni, S., West, P. T., Carter, M. M., Mechler, C. M., Olm, M. R., Caffrey, E. B., Li, J. A., Higginbottom, S. K., Severyn, C. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.11.018 · Cited by 42 · see citing works
Ye, Z., Yu, L., Zhang, C., Gao, Y., Zhao, J., Narbad, A., Chen, W., Zhai, Q., & Tian, F. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.139309 · Cited by 42 · see citing works
Zhou, T., Wang, M., Ma, H., Li, X., Heianza, Y., & Qi, L. (2020) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaa740 · Cited by 42 · see citing works
Mordant, A. L., & Kleiner, M. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01877-21 · Cited by 40 · see citing works
Plant extracts as natural modulators of gut microbiota community structure and functionality
Pérez-Burillo, S., Hinojosa-Nogueira, D., Pastoriza, S., & Rufián‐Henares, J. Á. (2020) · Heliyon · doi:10.1016/j.heliyon.2020.e05474 · Cited by 40 · see citing works
Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization
Nishiyama, K., Yokoi, T., Sugiyama, M., Osawa, R., Mukai, T., & Okada, N. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.754819 · Cited by 40 · see citing works
Fan, S., Zhang, Z., Zhao, Y., Daglia, M., Zhang, J., Zhu, Y., Bai, J., Zhu, L., & Xiao, X. (2022) · Current Opinion in Food Science · doi:10.1016/j.cofs.2022.100959 · Cited by 39 · see citing works
Culture-Delivery Live Probiotics Dressing for Accelerated Infected Wound Healing
Sun, Y., Liu, M., Tang, X., Zhou, Y., Zhang, J., & Yang, B. (2023) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.3c12845 · Cited by 39 · see citing works
Hu, Y., He, J., Zheng, P., Mao, X., Huang, Z., Yan, H., Luo, Y., Yu, J., Luo, J., Yu, B., et al. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1955654 · Cited by 39 · see citing works
Ostrem Loss, E., Thompson, J., Cheung, P. L. K., Qian, Y., & Venturelli, O. S. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01930-9 · Cited by 38 · see citing works
The role of gut microbiota in tumorigenesis and treatment
Xu, J., Liu, M.-T., Tao, T., Zhu, X. M., & Fei, F. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.111444 · Cited by 37 · see citing works
He, L., Li, J., Sun, M., Wang, X., Zhao, J., Zhang, W., Lv, G., Wang, Y., & Lin, Z. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.128538 · Cited by 37 · see citing works
Diet and cancer risk reduction: The role of diet-microbiota interactions and microbial metabolites
Weir, T. L., Trikha, S. R. J., & Thompson, H. J. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.06.007 · Cited by 37 · see citing works
Gut microbiota and its roles in the pathogenesis and therapy of endocrine system diseases
Wu, Z., Tian, E., Chen, Y., Dong, Z., & Peng, Q. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127291 · Cited by 39 · see citing works
- Authors
- 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., Meynier, A., Vinoy, S., Giannone, R. J., Hettich, R. L., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- Oak Ridge National Laboratory (US)
- Centre National de la Recherche Scientifique (FR)
- Biopolymères Interactions Assemblages (FR)
- Mondelēz International (United States) (US)
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-09
- Volume
- 179
- Issue
- 1
- Pages
- 59-73.e13
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6760872
- OpenAlex
- W2974099250
- Cited by
- 329
- References
- 49
- Citations by year
- 2026: 30 · 2025: 45 · 2024: 48 · 2023: 46 · 2022: 71 · 2021: 46 · 2020: 34 · 2019: 6
- FWCI
- 13.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Microbial Metabolites in Food Biotechnology
- Health Sciences › Nursing › Nutrition and Dietetics › Food composition and properties
- Keywords
- human gut microbiome, interspecific competition, dietary fiber, Bacteroides, bioactive carbohydrates, microbial gene expression, gnotobiotic mice, polysaccharide degradation, forward genetic screen
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteroides, Diet, Dietary Fiber, Feces, Germ-Free Life, Humans, Male, Mice, Inbred C57BL, Polysaccharides, Gene Expression Regulation, Bacterial, Proteomics, Mice, 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
