The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
Abstract
Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.
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Fermentation of dietary fibre is one of the dominant microbial metabolic activities in the colon.
“the fermentation of dietary fibre represents one of the dominant microbial metabolic activities in the colon”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [36]
Dietary fiber passes undigested from the small intestine into the colonic environment, and the gut microbiota relies on these fibers for energy, targeting them for disassembly with a combined toolkit of thousands of enzymes.
“Dietary fiber passes undigested from the small intestine into the colonic environment [171] and the gut microbiota relies on these fibers for energy, which they target for disassembly with a combined ‘toolkit’ of thousands of enzymes [204].”
From The athletic gut microbiota (2020) · cites this paper as [204]
Cites
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
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
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 · see citing works
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
Self-citationHuman gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Self-citationEnterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548 · see citing works
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762 · see citing works
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176 · see citing works
Self-citationThe Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn663 · Cited by 5,947 · see citing works
Self-citationGut flora metabolism of phosphatidylcholine promotes cardiovascular disease
Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597 · see citing works
Interactions Between the Microbiota and the Immune System
Hooper, L. V., Littman, D. R., & Macpherson, A. J. (2012) · Science · doi:10.1126/science.1223490 · Cited by 4,173 · see citing works
A classification of glycosyl hydrolases based on amino acid sequence similarities.
Henrissat, B. (1991) · Biochemical Journal · doi:10.1042/bj2800309 · Cited by 3,188 · see citing works
Self-citationTopping, D. L., & Clifton, P. M. (2001) · Physiological Reviews · doi:10.1152/physrev.2001.81.3.1031 · Cited by 3,091 · see citing works
Review article: the role of butyrate on colonic function
HAMER, H. M., JONKERS, D., VENEMA, K., VANHOUTVIN, S., TROOST, F. J., & BRUMMER, R. ‐. (2008) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2007.03562.x · Cited by 2,721 · see citing works
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity
Henao-Mejia, J., Elinav, E., Jin, C., Hao, L., Mehal, W. Z., Strowig, T., Thaiss, C. A., Kau, A. L., Eisenbarth, S. C., Jurczak, M. J., et al. (2012) · Nature · doi:10.1038/nature10809 · Cited by 2,435 · see citing works
Self-citationGlycosyltransferases: Structures, Functions, and Mechanisms
Lairson, L. L., Henrissat, B., Davies, G. J., & Withers, S. G. (2007) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.76.061005.092322 · Cited by 2,073 · see citing works
Self-citationStructures and mechanisms of glycosyl hydrolases
Davies, G. J., & Henrissat, B. (1995) · Structure · doi:10.1016/s0969-2126(01)00220-9 · Cited by 2,036 · see citing works
Self-citationNew families in the classification of glycosyl hydrolases based on amino acid sequence similarities
Henrissat, B., & Bairoch, A. (1993) · Biochemical Journal · doi:10.1042/bj2930781 · Cited by 1,974 · see citing works
Self-citationPolysaccharide utilization by gut bacteria: potential for new insights from genomic analysis
Flint, H. J., Bayer, E. A., Rincón, M. T., Lamed, R., & White, B. A. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1817 · Cited by 1,710 · see citing works
Structural and sequence-based classification of glycoside hydrolases
Henrissat, B., & Davies, G. J. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80072-3 · Cited by 1,668 · see citing works
Self-citationHow glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works
Symptomatic atherosclerosis is associated with an altered gut metagenome
Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications · doi:10.1038/ncomms2266 · Cited by 1,371 · see citing works
Updating the sequence-based classification of glycosyl hydrolases
Henrissat, B., & Bairoch, A. (1996) · Biochemical Journal · doi:10.1042/bj3160695 · Cited by 1,362 · see citing works
Self-citationEffects of Dietary Fiber and Its Components on Metabolic Health
Lattimer, J. M., & Haub, M. D. (2010) · Nutrients · doi:10.3390/nu2121266 · Cited by 1,333 · see citing works
IMG: the integrated microbial genomes database and comparative analysis system
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Jacob, B., Huang, J., Williams, P. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1044 · Cited by 1,315 · see citing works
Glycan foraging in vivo by an intestine-adapted bacterial symbiont
Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works
Self-citationTransfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117 · see citing works
Ze, X., Duncan, S. H., Louis, P., & Flint, H. J. (2012) · The ISME Journal · doi:10.1038/ismej.2012.4 · Cited by 1,060 · see citing works
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,050 · see citing works
Self-citationBacterial peptidoglycan (murein) hydrolases
Vollmer, W., Joris, B., Charlier, P., & Foster, S. J. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2007.00099.x · Cited by 880 · 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-citationThe contribution of the large intestine to energy supplies in man
N I, M. (1984) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/39.2.338 · Cited by 691 · see citing works
Stam, M. R., Danchin, É., Rancurel, C., Coutinho, P. M., & Henrissat, B. (2006) · Protein Engineering Design and Selection · doi:10.1093/protein/gzl044 · Cited by 625 · see citing works
Self-citationA hierarchical classification of polysaccharide lyases for glycogenomics
Lombard, V., Bernard, T., Rancurel, C., Brumer, H., Coutinho, P. M., & Henrissat, B. (2010) · Biochemical Journal · doi:10.1042/bj20101185 · Cited by 384 · see citing works
Self-citationComplex Carbohydrate Utilization by the Healthy Human Microbiome
Cantarel, B. L., Lombard, V., & Henrissat, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0028742 · Cited by 378 · see citing works
Self-citationBjursell, M. K., Martens, E. C., & Gordon, J. I. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m606509200 · Cited by 338 · see citing works
Self-citationHehemann, J.-H., Kelly, A. G., Pudlo, N. A., Martens, E. C., & Boraston, A. B. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211002109 · Cited by 338 · see citing works
The concept of the α-amylase family: Structural similarity and common catalytic mechanism
Kuriki, T., & Imanaka, T. (1999) · Journal of Bioscience and Bioengineering · doi:10.1016/s1389-1723(99)80114-5 · Cited by 330 · see citing works
Human Gut Microbiota: Repertoire and Variations
Lagier, J., Million, M., Hugon, P., Armougom, F., & Raoult, D. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00136 · Cited by 329 · see citing works
Self-citationSelective colonization of insoluble substrates by human faecal bacteria
Leitch, E. C. M., Walker, A. W., Duncan, S. H., Holtrop, G., & Flint, H. J. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01186.x · Cited by 297 · see citing works
Short chain fatty acids and colonic health
Hijová, E., & Chmelařová, A. (2007) · Bratislavské lekárske listy/Bratislava medical journal · doi:10.1007/bf03656953 · Cited by 295 · see citing works
The integrated microbial genomes system: an expanding comparative analysis resource
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Anderson, I., Lykidis, A., Mavromatis, K., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp887 · Cited by 256 · see citing works
Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces
Zoetendal, E. G., Plugge, C. M., Akkermans, A. D. L., & de Vos, W. M. (2003) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.02362-0 · Cited by 145 · see citing works
Paliy, O., Kenche, H., Abernathy, F., & Michail, S. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02764-08 · Cited by 132 · see citing works
Low-Digestible Carbohydrates in Practice
Grabitske, H. A., & Slavin, J. L. (2008) · Journal of the American Dietetic Association · doi:10.1016/j.jada.2008.07.010 · Cited by 131 · see citing works
Gloster, T. M., Turkenburg, J. P., Potts, J. R., Henrissat, B., & Davies, G. J. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.09.005 · Cited by 112 · see citing works
Self-citationFermentative metabolism by the human gut microbiota
Bernalier‐Donadille, A. (2010) · Gastroentérologie Clinique et Biologique · doi:10.1016/s0399-8320(10)70016-6 · Cited by 99 · see citing works
Mirande, C., Kadlecikova, E., Matulová, M., Capek, P., Bernalier‐Donadille, A., Forano, É., & Béra‐Maillet, C. (2010) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2010.04671.x · Cited by 98 · see citing works
Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces
Kitahara, M., Sakamoto, M., Ike, M., Sakata, S., & Benno, Y. (2005) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.63788-0 · Cited by 93 · see citing works
Probiotics and functional foods in gastrointestinal disorders
Floch, M. H., & Hong-Curtis, J. (2002) · Current Treatment Options in Gastroenterology · doi:10.1007/s11938-002-0054-6 · Cited by 45 · see citing works
Robert, C., Del’Homme, C., & Bernalier‐Donadille, A. (2001) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2001.tb10949.x · Cited by 39 · see citing works
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Introduction to the human gut microbiota
Thursby, E., & Juge, N. (2017) · Biochemical Journal · doi:10.1042/bcj20160510 · Cited by 3,600 · 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
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Diet–microbiota interactions as moderators of human metabolism
Sonnenburg, J. L., & Bäckhed, F. (2016) · Nature · doi:10.1038/nature18846 · Cited by 2,257 · see citing works
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., & Yin, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky418 · Cited by 2,224 · 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
Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., Hallen, A., Martens, E., Björck, I., & Bäckhed, F. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.10.001 · Cited by 1,731 · see citing works
Dietary fiber and prebiotics and the gastrointestinal microbiota
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Rivière, A., Selak, M., Lantin, D., Leroy, F., & Vuyst, L. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00979 · Cited by 1,746 · see citing works
Chloroplast genomes: diversity, evolution, and applications in genetic engineering
Daniell, H., Lin, C., Yu, M., & Chang, W. (2016) · Genome biology · doi:10.1186/s13059-016-1004-2 · Cited by 1,731 · see citing works
Gut microbial metabolites as multi-kingdom intermediates
Krautkramer, K. A., Fan, J., & Bäckhed, F. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0438-4 · Cited by 1,398 · see citing works
Pelaseyed, T., Bergström, J. H., Gustafsson, J. K., Ermund, A., Birchenough, G. M. H., Schütte, A., van der Post, S., Svensson, F., Rodríguez‐Piñeiro, A. M., Nyström, E. E. L., et al. (2014) · Immunological Reviews · doi:10.1111/imr.12182 · Cited by 1,363 · see citing works
Potential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375 · see citing works
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
Zheng, J., Ge, Q., Yan, Y., Zhang, X., Huang, L., & Yin, Y. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad328 · Cited by 1,117 · see citing works
Chemical transformation of xenobiotics by the human gut microbiota
Koppel, N., Maini Rekdal, V., & Balskus, E. P. (2017) · Science · doi:10.1126/science.aag2770 · Cited by 1,080 · see citing works
Bifidobacteria and Their Role as Members of the Human Gut Microbiota
O’Callaghan, A. A., & van Sinderen, D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00925 · Cited by 1,108 · see citing works
Links between diet, gut microbiota composition and gut metabolism
Flint, H. J., Duncan, S. H., Scott, K. P., & Louis, P. (2015) · Proceedings of the Nutrition Society · doi:10.1017/s0029665114001463 · Cited by 1,020 · 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
Postler, T. S., & Ghosh, S. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.05.008 · Cited by 876 · see citing works
“Members of the Bacteroidetes provide most of the acetate and propionate, whereas Firmicutes, which tend to utilize polysaccharides less efficiently, are believed to be the primary producers of butyrate (Flint et al., 2015; El Kaoutari et al., 2013; Levy et al., 2016; Louis et al., 2010).”
BackgroundAmerican Gut: an Open Platform for Citizen-Science Microbiome Research
McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · doi:10.1101/277970 · Cited by 878 · see citing works
US immigration westernizes the human gut microbiome
Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794 · see citing works
Sonnenburg, E. D., & Sonnenburg, J. L. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.003 · Cited by 871 · see citing works
Microbiomes in light of traits: a phylogenetic perspective
Martiny, J. B. H., Jones, S. E., Lennon, J. T., & Martiny, A. C. (2015) · Science · doi:10.1126/science.aac9323 · Cited by 834 · see citing works
Gut Microbiota Orchestrates Energy Homeostasis during Cold
Chevalier, C., Stojanović, O., Colin, D. J., Suarez-Zamorano, N., Tarallo, V., Veyrat-Durebex, C., Rigo, D., Fabbiano, S., Stevanović, A., Hagemann, S., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.004 · Cited by 829 · see citing works
Actinobacteria: A relevant minority for the maintenance of gut homeostasis
Binda, C., Lopetuso, L. R., Rizzatti, G., Gibiino, G., Cennamo, V., & Gasbarrini, A. (2018) · Digestive and Liver Disease · doi:10.1016/j.dld.2018.02.012 · Cited by 814 · see citing works
Colonocyte metabolism shapes the gut microbiota
Litvak, Y., Byndloss, M. X., & Bäumler, A. J. (2018) · Science · doi:10.1126/science.aat9076 · Cited by 765 · see citing works
Schmidt, T. M., Baxter, N. T., Waldron, C., Alexander, S. W., Venkataraman, A., & Kim, K. (2019) · mBio · doi:10.1128/mbio.02566-18 · Cited by 773 · see citing works
Small molecules from the human microbiota
Donia, M. S., & Fischbach, M. A. (2015) · Science · doi:10.1126/science.1254766 · Cited by 760 · see citing works
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Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748 · see citing works
Schroeder, B. O., Birchenough, G. M. H., Ståhlman, M., Arike, L., Johansson, M. E. V., Hansson, G. C., & Bäckhed, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.004 · Cited by 713 · see citing works
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Mukherjee, A., Lordan, C., Ross, R. P., & Cotter, P. D. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1802866 · Cited by 703 · see citing works
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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
The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease
Zuo, T., & Ng, S. C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02247 · Cited by 590 · see citing works
Mucins: A biologically relevant glycan barrier in mucosal protection
Corfield, A. P. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.05.003 · Cited by 567 · 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
Microbial Fermentation of Dietary Protein: An Important Factor in Diet–Microbe–Host Interaction
Diether, N. E., & Willing, B. P. (2019) · Microorganisms · doi:10.3390/microorganisms7010019 · Cited by 574 · see citing works
Cockburn, D. W., & Koropatkin, N. M. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.06.021 · Cited by 542 · see citing works
Wang, X., Tsai, T.-C., Deng, F., Wei, X., Chai, J., Knapp, J., APPLE, J. K., Maxwell, C. V. V., Lee, J. A., Li, Y., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0721-7 · Cited by 528 · see citing works
A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes
Larsbrink, J., Rogers, T. E., Hemsworth, G. R., McKee, L. S., Tauzin, A. S., Oliver Spadiut, A., Klinter, S., Pudlo, N. A., Urs, K., Koropatkin, N. M., et al. (2014) · Nature · doi:10.1038/nature12907 · Cited by 527 · see citing works
Contribution of diet to the composition of the human gut microbiota
Gräf, D., Cagno, R. D., Fåk, F., Flint, H. J., NYMAN, M. E., Saarela, M., & Watzl, B. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26164 · Cited by 520 · see citing works
Research progress in the relationship between type 2 diabetes mellitus and intestinal flora
Ma, Q., Li, Y., Li, P., Wang, M., Wang, J., Tang, Z., Wang, T., Luo, L., Wang, C., Wang, T., et al. (2019) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2019.109138 · Cited by 436 · see citing works
The microbiome and gut homeostasis
Lee, J., Tsolis, R. M., & Bäumler, A. J. (2022) · Science · doi:10.1126/science.abp9960 · Cited by 430 · 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
Self-citationModulation of the human gut microbiota by dietary fibres occurs at the species level
Chung, W. S. F., Walker, A. W., Louis, P., Parkhill, J., Vermeiren, J., Bosscher, D., Duncan, S. H., & Flint, H. J. (2016) · BMC Biology · doi:10.1186/s12915-015-0224-3 · Cited by 409 · see citing works
Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes
Johnson, E. L., Heaver, S. L., Walters, W. A., & Ley, R. E. (2017) · Journal of Molecular Medicine · doi:10.1007/s00109-016-1492-2 · Cited by 389 · see citing works
Influence of Mediterranean Diet on Human Gut Microbiota
Merra, G., Noce, A., Marrone, G., Cintoni, M., Tarsitano, M. G., Capacci, A., & De Lorenzo, A. (2020) · Nutrients · doi:10.3390/nu13010007 · Cited by 417 · see citing works
Regulation of short-chain fatty acids in the immune system
Liu, X., Shao, J.-H., Liao, Y.-T., Wang, L., Yuan, J., Dong, P.-J., Liu, Z., He, D., Li, C., & Zhang, X. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1186892 · Cited by 435 · see citing works
Microbiota depletion promotes browning of white adipose tissue and reduces obesity
Suárez-Zamorano, N., Fabbiano, S., Chevalier, C., Stojanović, O., Colin, D. J., Stevanović, A., Veyrat-Durebex, C., Tarallo, V., Rigo, D., Germain, S., et al. (2015) · Nature Medicine · doi:10.1038/nm.3994 · Cited by 403 · see citing works
Precision Nutrition and the Microbiome, Part I: Current State of the Science
Mills, S., Stanton, C., Lane, J. A., Smith, G., & Ross, R. P. (2019) · Nutrients · doi:10.3390/nu11040923 · Cited by 406 · see citing works
Chung, W. S. F., Meijerink, M., Zeuner, B., Holck, J., Louis, P., Meyer, A. S., Wells, J. M., Flint, H. J., & Duncan, S. H. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix127 · Cited by 395 · see citing works
Mohr, A. E., Jäger, R., Carpenter, K. C., Kerksick, C. M., Purpura, M., Townsend, J. R., West, N. P., Black, K., Gleeson, M., Pyne, D. B., et al. (2020) · Journal of the International Society of Sports Nutrition · doi:10.1186/s12970-020-00353-w · Cited by 378 · see citing works
Dietary Fibre from Whole Grains and Their Benefits on Metabolic Health
P., N. P. V., & Joye, I. J. (2020) · Nutrients · doi:10.3390/nu12103045 · Cited by 387 · see citing works
Gut Microbiota, Short-Chain Fatty Acids, and Herbal Medicines
Feng, W., Ao, H., & Peng, C. Y. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.01354 · Cited by 368 · see citing works
Applying the core microbiome to understand host–microbe systems
Risely, A. (2020) · Journal of Animal Ecology · doi:10.1111/1365-2656.13229 · Cited by 370 · see citing works
Ramayo‐Caldas, Y., Mach, N., Lepage, P., Levenez, F., Denis, C., Lemonnier, G., Leplat, J. J. J. J., Billon, Y., Berri, M., Dore, J. M., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.77 · Cited by 359 · see citing works
The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases
Baldelli, V., Scaldaferri, F., Putignani, L., & CHIERICO, F. D. (2021) · Microorganisms · doi:10.3390/microorganisms9040697 · Cited by 358 · see citing works
Gut microbiome and its role in obesity and insulin resistance
Lee, C. J., Sears, C. L., & Maruthur, N. M. (2019) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14107 · Cited by 352 · see citing works
Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota
Xu, J., Chen, H., & Li, S. (2017) · Medicinal Research Reviews · doi:10.1002/med.21431 · Cited by 340 · see citing works
Soluble Dietary Fiber, One of the Most Important Nutrients for the Gut Microbiota
Guan, Z.-W., Yu, E.-Z., & Feng, Q. (2021) · Molecules · doi:10.3390/molecules26226802 · Cited by 348 · see citing works
<i>Ruminococcus gnavus</i> : friend or foe for human health
Crost, E. H., Coletto, E., Bell, A., & Juge, N. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad014 · Cited by 335 · see citing works
Selective maternal seeding and environment shape the human gut microbiomePreprint
Korpela, K., Costea, P. I., Coelho, L. P., Kandels-Lewis, S. E., Willemsen, G. A. H. M., Boomsma, D. I., Segata, N., & Peer Bork, B. (2018) · Genome Research · doi:10.1101/gr.233940.117 · Cited by 325 · see citing works
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation
Huang, L., Zhang, H., Wu, P., Entwistle, S., Li, X., Yohe, T., Yi, H., Yang, Z., & Yin, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx894 · Cited by 325 · see citing works
Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases
Jiao, Y., Wu, L., Huntington, N. D., & Zhang, X. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00282 · Cited by 321 · see citing works
Gut microbiota in neurodegenerative disorders
Sarkar, S. R., & Banerjee, S. (2019) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2019.01.004 · Cited by 319 · see citing works
Advancing human gut microbiota research by considering gut transit time
Procházková, N., Falony, G., Dragsted, L. O., Licht, T. R., Raes, J., & Roager, H. M. (2022) · Gut · doi:10.1136/gutjnl-2022-328166 · Cited by 322 · see citing works
Characterizing the mucin-degrading capacity of the human gut microbiota
Glover, J. S., Ticer, T. D., & Engevik, M. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-11819-z · Cited by 307 · see citing works
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome
Tanes, C., Bittinger, K. L., Gao, Y., Friedman, E. S., Nessel, L. A., Paladhi, U. R., Chau, L., Panfen, E., Fischbach, M. A., Braun, J. G., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.12.012 · Cited by 306 · see citing works
The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans
Rosa, S. L. L., Leth, M. L., Michalak, L., Ejby, M., Pudlo, N. A., Glowacki, R. W. P., Pereira, G. V., Workman, C. T., Arntzen, M. Ø., Pope, P. B., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08812-y · Cited by 308 · see citing works
Li, X. O., Li, X. O., Xia, B., Jin, X., Zou, Q., Zeng, Z., Zhao, W., Yan, S., Li, L., Yuan, S., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.02.002 · Cited by 303 · see citing works
Urbanization and the gut microbiota in health and inflammatory bowel disease
Zuo, T., Kamm, M. A., Colombel, J., & Ng, S. C. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0003-z · Cited by 294 · 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
Self-citationIntestinal mucus and their glycans: A habitat for thriving microbiota
Luis, A. S., & Hansson, G. C. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.05.026 · Cited by 290 · see citing works
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Milani, C., Lugli, G. A., Duranti, S., Turroni, F., Mancabelli, L., Ferrario, C., Mangifesta, M., Hevia, A., Viappiani, A., Scholz, M., et al. (2015) · Scientific Reports · doi:10.1038/srep15782 · Cited by 284 · see citing works
Xiao, Z., Aweya, J. J., Huang, Z.-X., Kang, Z.-Y., Bai, Z.-H., Li, K.-H., He, X., Liu, Y., Chen, X., & Cheong, K. (2020) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2020.115894 · Cited by 281 · see citing works
Sheridan, P. O., Martin, J. C., Lawley, T. D., Browne, H. P., Harris, H. M. B., Bernalier‐Donadille, A., Duncan, S. H., O’Toole, P. W., Scott, K. P., & Flint, H. J. (2015) · Microbial Genomics · doi:10.1099/mgen.0.000043 · Cited by 268 · see citing works
Interplay between food and gut microbiota in health and disease
Danneskiold‐Samsøe, N. B., Barros, H. D. D. F. Q., dos Santos, R., Bicas, J. L., Cazarin, C. B. B., Madsen, L., Kristiansen, K., Pastore, G. M., Brix, S., & Maróstica, M. R. (2018) · Food Research International · doi:10.1016/j.foodres.2018.07.043 · Cited by 271 · see citing works
The Sus operon: a model system for starch uptake by the human gut Bacteroidetes
Foley, M. H., Cockburn, D. W., & Koropatkin, N. M. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2242-x · Cited by 258 · see citing works
Glycan Utilization and Cross-Feeding Activities by Bifidobacteria
Turroni, F., Milani, C., Duranti, S., Mahony, J., van Sinderen, D., & Ventura, M. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2017.10.001 · Cited by 263 · see citing works
Ketogenic Diet and Microbiota: Friends or Enemies?
Paoli, A., Mancin, L., Bianco, A., Thomas, E., Mota, J. F., & Piccini, F. (2019) · Genes · doi:10.3390/genes10070534 · Cited by 265 · see citing works
Sang, T., Guo, C., Guo, D., Wu, J., Wang, Y., Wang, Y., Chen, J., Chen, C., Wu, K., Na, K., et al. (2021) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2020.117594 · Cited by 268 · see citing works
A critical review on interplay between dietary fibers and gut microbiota
Ye, S., Shah, B. R., Li, J., Liang, H., Zhan, F., Geng, F., & Li, B. (2022) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2022.04.010 · Cited by 266 · see citing works
Shang, Q., Song, G., Zhang, M., Shi, J., Xu, C., Hao, J., Li, G., & Yu, G. (2017) · Journal of Functional Foods · doi:10.1016/j.jff.2016.11.002 · Cited by 258 · see citing works
Zheng, L.-X., Chen, X., & Cheong, K. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.02.168 · Cited by 253 · 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
Shang, Q., Jiang, H., Cai, C., Hao, J., Li, G., & Yu, G. (2017) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2017.09.059 · Cited by 254 · see citing works
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas
Baniel, A., Amato, K. R., Beehner, J. C., Bergman, T. J., Mercer, A., Perlman, R. F., Petrullo, L. A., Reitsema, L. J., Sams, S. N., Lu, A., et al. (2021) · Microbiome · doi:10.1186/s40168-020-00977-9 · Cited by 249 · see citing works
Biomass Utilization by Gut Microbiomes
White, B. A., Lamed, R., Bayer, E. A., & Flint, H. J. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-092412-155618 · Cited by 217 · see citing works
Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice
Huang, Y., Chassard, C., Hausmann, M., von Itzstein, M., & Hennet, T. (2015) · Nature Communications · doi:10.1038/ncomms9141 · Cited by 242 · see citing works
Dietary Fibers from Fruits and Vegetables and Their Health Benefits via Modulation of Gut Microbiota
Cui, J., Lian, Y., Zhao, C., Du, H., Han, Y., Gao, W. Y., Xiao, H., & Zheng, J. (2019) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12489 · Cited by 243 · see citing works
Bacterial pectate lyases, structural and functional diversity
Hugouvieux‐Cotte‐Pattat, N., Condemine, G., & Shevchik, V. E. (2014) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12166 · Cited by 241 · see citing works
Liu, Y., Yu, X., Zhao, J., Zhang, H., Zhai, Q., & Chen, W. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.07.191 · Cited by 241 · 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
Self-citationMewis, K., Lenfant, N., Lombard, V., & Henrissat, B. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.03453-15 · Cited by 238 · see citing works
Self-citationSeo, B., Jeon, K., Moon, S., Lee, K., Kim, W.-K., Jeong, H., Cha, K. H., Lim, M. Y., Kang, W., Kweon, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.11.001 · Cited by 238 · see citing works
Martens, E. C., Kelly, A. G., Tauzin, A. S., & Brumer, H. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.06.022 · Cited by 235 · see citing works
Review: Enhancing gastrointestinal health in dairy cows
Plaizier, J. C. B., Mesgaran, M. D., Derakhshani, H., Golder, H. M., Khafipour, E., Kleen, J. L., Lean, I. J., Loor, J. J., Penner, G. B., & Zebeli, Q. (2018) · animal · doi:10.1017/s1751731118001921 · Cited by 239 · see citing works
Liu, X., Inda, M. E., Lai, Y., Lu, T. K., & Zhao, X. (2022) · Advanced Materials · doi:10.1002/adma.202201326 · Cited by 227 · see citing works
Loy, A., Pfann, C., Steinberger, M., Hanson, B. T., Herp, S., Brugiroux, S., Neto, J. C. G., Boekschoten, M. V., Schwab, C., Urich, T., et al. (2017) · mSystems · doi:10.1128/msystems.00171-16 · Cited by 229 · see citing works
- Authors
- Kaoutari, A. E., Armougom, F., Gordon, J. I., Raoult, D., & Henrissat, B.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Washington University in St. Louis (US)
- University of Copenhagen (DK)
- Corresponding author
- Henrissat, Bernard
- Venue
- Nature Reviews Microbiology
- Published
- 2013-06-10
- Volume
- 11
- Issue
- 7
- Pages
- 497-504
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W1991497480
- Cited by
- 1,683
- References
- 51
- Citations by year
- 2026: 111 · 2025: 156 · 2024: 206 · 2023: 167 · 2022: 198 · 2021: 226 · 2020: 153 · 2019: 127 · 2018: 100 · 2017: 84 · 2016: 70 · 2015: 41 · 2014: 38 · 2013: 6
- FWCI
- 4.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Enzyme Production and Characterization
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Keywords
- carbohydrate-active enzymes, human gut microbiome, polysaccharide digestion, bacterial carbohydrate metabolism, dietary polysaccharides, host-microbe interactions
- MeSH terms
- Bacteria, Glycoside Hydrolases, Humans, Polysaccharide-Lyases, Glycosyltransferases, Gastrointestinal Tract, Metagenome
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