Links between diet, gut microbiota composition and gut metabolism
Open accessAbstract
The gut microbiota and its metabolic products interact with the host in many different ways, influencing gut homoeostasis and health outcomes. The species composition of the gut microbiota has been shown to respond to dietary change, determined by competition for substrates and by tolerance of gut conditions. Meanwhile, the metabolic outputs of the microbiota, such as SCFA, are influenced both by the supply of dietary components and via diet-mediated changes in microbiota composition. There has been significant progress in identifying the phylogenetic distribution of pathways responsible for formation of particular metabolites among human colonic bacteria, based on combining cultural microbiology and sequence-based approaches. Formation of butyrate and propionate from hexose sugars, for example, can be ascribed to different bacterial groups, although propionate can be formed via alternative pathways from deoxy-sugars and from lactate by a few species. Lactate, which is produced by many gut bacteria in pure culture, can also be utilised by certain Firmicutes to form butyrate, and its consumption may be important for maintaining a stable community. Predicting the impact of diet upon such a complex and interactive system as the human gut microbiota not only requires more information on the component groups involved but, increasingly, the integration of such information through modelling approaches.
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Bifidobacterium and Lactobacillus spp. produce lactate and acetate and can increase butyrate production through cross-feeding interactions with butyrate-producing species such as Eubacterium rectale.
“Bifidobacterium and Lactobacillus spp. produce lactate and acetate and can also increase production of butyrate through cross-feeding interactions with the butyrate-producing species, such as Eubacterium rectale.130–132”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [130]
Important factors such as age, birth method or delivery route, antibiotic use, and diet shape the gut microbiota.
“Important factors such as age, birth method, antibiotic use, and diet have been established as formative factors that shape the gut microbiota.”
From The athletic gut microbiota (2020) · cites this paper as [9]
Beneficial microbes that produce butyrate include F. prausnitzii, E. rectale, E. hallii, and R. bromii.
“This group of beneficial microbes include the taxa Faecalibacterium prausnitzii (F. prausnitzii), Eubacterium rectale (E. rectale), E. hallii, and Ruminococcus bromii (R. bromii) [36].”
From Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders (2022) · cites this paper as [36]
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Cites
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
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
Richness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works
Energy conservation in chemotrophic anaerobic bacteria
Thauer, R. K., Jungermann, K., & Decker, K. (1977) · Bacteriological Reviews · doi:10.1128/br.41.1.100-180.1977 · Cited by 4,146 · 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
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
Belenguer, A., Duncan, S. H., Calder, A. G., Holtrop, G., Louis, P., Lobley, G. E., & Flint, H. J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3593-3599.2006 · Cited by 856 · see citing works
Self-citationWalker, A. W., Duncan, S. H., McWilliam Leitch, E. C., Child, M. W., & Flint, H. J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.3692-3700.2005 · Cited by 796 · see citing works
Self-citationRussell, W. R., Gratz, S. W., Duncan, S. H., Holtrop, G., Ince, J., Scobbie, L., Duncan, G., Johnstone, A. M., Lobley, G. E., Wallace, R. J., et al. (2011) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.002188 · Cited by 775 · see citing works
Self-citationDiversity of Bifidobacteria within the Infant Gut Microbiota
Turroni, F., Peano, C., Pass, D. A., Foroni, E., Severgnini, M., Claesson, M. J., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036957 · Cited by 647 · see citing works
Dietary fibre and the gut microbiota
Scott, K. P., Duncan, S. H., & Flint, H. J. (2008) · Nutrition Bulletin · doi:10.1111/j.1467-3010.2008.00706.x · Cited by 237 · see citing works
Self-citationPropionate. Anti-obesity and satiety enhancing factor?
Arora, T., Sharma, R., & Frost, G. (2011) · Appetite · doi:10.1016/j.appet.2011.01.016 · Cited by 205 · cited 1× · see citing works
“Butyrate has received much attention for its anti-inflammatory and anti-carcinogenic effects((31)) and more recently SCFA have been studied for their effects on systemic host metabolism, particularly as satiety-inducing agents((32,33)).”
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Flagged first, then by citations
Research works printed but not linked: 7
- Macfarlane GT & Gibson GR (1997) Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine. In Gastrointestinal Microbiology, vol. I, pp. 269-318 [RI Mackie and BA White, editors] London: Chapman and Hall.
- Salonen A, Lahti L, Salojärvi J et al. (2014) Impact of diet and individual variation on intestinal microbiota compo- sition and fermentation products in obese men. ISME J (In the Press).
- Frost G, Sleeth ML, Sahuri-Arisoylu M et al. (2014) The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun 5, available at http://www.nature.com/ncomms/2014/140429/ncomms4611/ full/ncomms4611.html.
- McBurney MI (2010) Dietary fibre: Insights and opportu- nities. In Dietary fibre: new frontiers for food and health. pp. 153-166.
- Falony G & De Vuyst L (2009) Ecological interactions of bacteria in the human gut. In Ecological Interactions of Bacteria in the Human Gut: Prebiotics and Probiotics Science and Technology, pp. 641-682 [
- Kettle H, Louis P, Holtrop G et al. (2014) Modelling the emergent dynamics and major metabolites of the human colonic microbiota. Environ Microbiol (In the Press).
- Shoaie S & Nielsen J (2014) Elucidating the interactions be- tween the human gut microbiota and its host through meta- bolic modeling. Front Genet 5, available at http://journal. frontiersin.org/Journal/10.3389/fgene.2014.00086/full. · DOI
Cited by
Sorted by citations
Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism
Morrison, D. J., & Preston, T. (2016) · Gut Microbes · doi:10.1080/19490976.2015.1134082 · Cited by 3,781 · see citing works
Formation of propionate and butyrate by the human colonic microbiota
Louis, P., & Flint, H. J. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13589 · Cited by 3,028 · see citing works
Self-citationGut 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
Probiotics and prebiotics in intestinal health and disease: from biology to the clinic
Sanders, M. E., Merenstein, D. J., Reid, G., Gibson, G. R., & Rastall, R. A. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0173-3 · Cited by 2,059 · see citing works
De Filippis, F., Pellegrini, N., Vannini, L., Jeffery, I. B., La Storia, A., Laghi, L., Serrazanetti, D. I., Di Cagno, R., Ferrocino, I., Lazzi, C., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-309957 · Cited by 1,638 · see citing works
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Brooks, G. A. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.03.008 · Cited by 1,486 · see citing works
Diet, microorganisms and their metabolites, and colon cancer
O'Keefe, S. J. D. (2016) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2016.165 · Cited by 1,100 · see citing works
Nogal, A., Valdes, A. M., & Menni, C. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1897212 · Cited by 917 · 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
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752 · see citing works
So, D., Whelan, K., Rossi, M., Morrison, M., Holtmann, G., Kelly, J. T., Shanahan, E. R., Staudacher, H. M., & Campbell, K. L. (2018) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqy041 · Cited by 683 · see citing works
Differences in gut microbiota profile between women with active lifestyle and sedentary women
Bressa, C., Bailén-Andrino, M., Pérez-Santiago, J., González-Soltero, R., Pérez, M., Montalvo-Lominchar, M. G., Maté-Muñoz, J. L., Domínguez, R., Moreno, D., & Larrosa, M. (2017) · PLOS ONE · doi:10.1371/journal.pone.0171352 · Cited by 501 · see citing works
Iljazovic, A., Roy, U., Gálvez, E. J. C., Lesker, T. R., Zhao, B., Gronow, A., Amend, L., Will, S. E., Hofmann, J. D., Pils, M. C., et al. (2021) · Mucosal Immunology · doi:10.1038/s41385-020-0296-4 · Cited by 454 · see citing works
The gut-bone axis: How bacterial metabolites bridge the distance
Zaiss, M. M., Jones, R. M., Schett, G., & Pacifici, R. (2019) · Journal of Clinical Investigation · doi:10.1172/jci128521 · Cited by 403 · 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
Environmental Factors, Gut Microbiota, and Colorectal Cancer Prevention
Song, M., & Chan, A. T. (2019) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.07.012 · Cited by 355 · see citing works
Rios-Covian, D., Gueimonde, M., Duncan, S. H., Flint, H. J., & de los Reyes-Gavilan, C. G. (2015) · FEMS Microbiology Letters · doi:10.1093/femsle/fnv176 · Cited by 371 · see citing works
Self-citationModulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet
Candela, M., Biagi, E., Soverini, M., Consolandi, C., Quercia, S., Severgnini, M., Peano, C., Turroni, S., Rampelli, S., Pozzilli, P., et al. (2016) · British Journal Of Nutrition · doi:10.1017/s0007114516001045 · Cited by 260 · see citing works
Cerdá, B., Pérez, M., Pérez-Santiago, J. D., Tornero-Aguilera, J. F., González-Soltero, R., & Larrosa, M. (2016) · Frontiers in Physiology · doi:10.3389/fphys.2016.00051 · Cited by 247 · see citing works
Modulation of bone remodeling by the gut microbiota: A new therapy for osteoporosis
Lyu, Z., Hu, Y., Guo, Y., & Liu, D. (2023) · Bone Research · doi:10.1038/s41413-023-00264-x · Cited by 207 · see citing works
Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders
Horn, J., Mayer, D. E., Chen, S., & Mayer, E. A. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-01922-0 · Cited by 193 · see citing works
Effects of metabolites derived from gut microbiota and hosts on pathogens
Li, Z., Quan, G., Jiang, X., Yang, Y., Ding, X., Zhang, D., Wang, X., Hardwidge, P. R., Ren, W., & Zhu, G. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00314 · Cited by 157 · see citing works
The impact of nutrition on intestinal bacterial communities
Flint, H. J., Duncan, S. H., & Louis, P. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.005 · Cited by 149 · see citing works
Self-citationJefferson, A., & Adolphus, K. (2019) · Frontiers in Nutrition · doi:10.3389/fnut.2019.00033 · Cited by 149 · see citing works
Chen, L., Xu, W., Chen, D., Chen, G., Liu, J., Zeng, X., Shao, R., & Zhu, H. (2018) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2018.01.183 · Cited by 140 · see citing works
Bioactivity of Food Melanoidins Is Mediated by Gut Microbiota
Pérez-Burillo, S., Rajakaruna, S., Pastoriza, S., Paliy, O., & Ángel Rufián-Henares, J. (2020) · Food Chemistry · doi:10.1016/j.foodchem.2020.126309 · Cited by 138 · see citing works
Mazhar, M., Zhu, Y., & Qin, L. (2023) · Foods · doi:10.3390/foods12051023 · Cited by 119 · see citing works
The Gut Microbiome and Individual-Specific Responses to Diet
Leshem, A., Segal, E., & Elinav, E. (2020) · mSystems · doi:10.1128/msystems.00665-20 · Cited by 109 · see citing works
Grimaldi, R., Cela, D., Swann, J. R., Vulevic, J., Gibson, G. R., Tzortzis, G., & Costabile, A. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw233 · Cited by 109 · see citing works
Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota
Lobach, A. R., Roberts, A., & Rowland, I. R. (2019) · Food and Chemical Toxicology · doi:10.1016/j.fct.2018.12.005 · Cited by 104 · see citing works
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Han, Y., & Xiao, H. (2020) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-111519-014337 · Cited by 101 · see citing works
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Wang, Y., Alkhalidy, H., & Liu, D. (2021) · Molecules · doi:10.3390/molecules26030703 · Cited by 88 · see citing works
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Debnath, N., Kumar, R., Kumar, A., Mehta, P. K., & Yadav, A. K. (2021) · Biotechnology and Genetic Engineering Reviews · doi:10.1080/02648725.2021.1989847 · Cited by 77 · see citing works
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Mu, C., Yang, Y., Luo, Z., & Zhu, W. (2017) · Anaerobe · doi:10.1016/j.anaerobe.2017.06.003 · Cited by 67 · see citing works
Davis, S. C., Yadav, J. S., Barrow, S. D., & Robertson, B. K. (2017) · MicrobiologyOpen · doi:10.1002/mbo3.476 · Cited by 69 · see citing works
Gallier, S., Van den Abbeele, P., & Prosser, C. (2020) · Frontiers in Nutrition · doi:10.3389/fnut.2020.608495 · Cited by 38 · see citing works
Sun, F., & Xu, Z. (2021) · Journal of Marine Science and Engineering · doi:10.3390/jmse9020104 · Cited by 35 · see citing works
Paturi, G., Butts, C. A., Stoklosinski, H., Herath, T. D., & Monro, J. A. (2017) · International Journal of Food Science & Technology · doi:10.1111/ijfs.13543 · Cited by 35 · see citing works
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Ni Lochlainn, M., Bowyer, R. C. E., & Steves, C. J. (2018) · doi:10.20944/preprints201806.0152.v1 · Cited by 138 · see citing works
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Matsuyama, M., Gomez-Arango, L. F., Fukuma, N. M., Morrison, M., Davies, P. S. W., & Hill, R. J. (2019) · Journal of Developmental Origins of Health and Disease · doi:10.1017/s2040174418000624 · Cited by 22 · see citing works
- Authors
- Flint, H. J., Duncan, S. H., Scott, K. P., & Louis, P.
- Affiliations
- University of Aberdeen (GB)
- Corresponding author
- Flint, Harry J.
- Venue
- Proceedings of the Nutrition Society
- Publisher
- Cambridge University Press (CUP)
- Published
- 2014-09-30
- Volume
- 74
- Issue
- 1
- Pages
- 13-22
- ISSN
- 0029-6651 (ISSN-L)
- 1475-2719
- OpenAlex
- W2159924324
- Cited by
- 1,020
- References
- 12
- Citations by year
- 2026: 63 · 2025: 100 · 2024: 120 · 2023: 116 · 2022: 106 · 2021: 128 · 2020: 108 · 2019: 90 · 2018: 95 · 2017: 39 · 2016: 37 · 2015: 12
- FWCI
- 12.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of The Nutrition Society (publishedVersion)
- PubMed (publishedVersion)
- 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
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- gut microbiota, diet, intestinal metabolism, short-chain fatty acids, butyrate, propionate, lactate, colonic bacteria, bacterial metabolic pathways, intestinal homeostasis, Firmicutes, microbial community stability
- MeSH terms
- Butyrates, Feeding Behavior, Fermentation, Humans, Intestinal Mucosa, Intestines, Propionates, Lactic Acid, Microbiota
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