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Gut microbiota functions: metabolism of nutrients and other food components
Open accessAbstract
The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.
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![Fig. 1 Pathways of carbohydrate metabolism [156]](/paper-figures/0789d3a4c19c4826a07200a7a76066fa/gut-microbiota-functions-metabolism-of-nutrients-and-other-food-components-figure-1.jpg)
![Fig. 2 Pathways of gut microbial protein degradation [46]](/paper-figures/cc1b510fc88248d78c4eeb15d54318eb/gut-microbiota-functions-metabolism-of-nutrients-and-other-food-components-figure-2.jpg)
![Fig. 3 Bile acid metabolism (adapted from [167])](/paper-figures/ba744a3c7e1f4717903bbb3e1936901d/gut-microbiota-functions-metabolism-of-nutrients-and-other-food-components-figure-3.jpg)
![Fig. 4 Scheme of gut microbial degradation of rutin [90]](/paper-figures/8a34bd7457774af6aff71c65303483d0/gut-microbiota-functions-metabolism-of-nutrients-and-other-food-components-figure-4.jpg)
![Fig. 5 Gut bacterial metabolism of the lignan secoisolariciresinol diglucoside (after Clavel et al. [92]). Abbreviations of bacterial genus names: B.—Bacteroides; Bu.—Butyribacterium; Bl—Blautia; C.—Clostridium; E.—Eubacterium; Eg.—Eggerthella; Lact.—Lactonifactor; P.—Peptostreptococcus](/paper-figures/b5fcfbb105914698aca541b8f73a9c65/gut-microbiota-functions-metabolism-of-nutrients-and-other-food-components-figure-5.jpg)
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“The intricate role of the gut microbiota in breaking down complex carbohydrates, proteins, and lipids enhances the digestive process, facilitating the absorption of essential nutrients.”
From Unveiling the therapeutic symphony of probiotics, prebiotics, and postbiotics in gut-immune harmony (2024) · cites this paper as [15]
Experimental — accuracy not yet measuredIn the citing paper
“The gut microbiota is an important factor that shapes both energy harvest and storage through metabolism of proteins and production of several metabolites including SCFAs, ammonia, sulfur-containing metabolites such as hydrogen sulfide and methanethiol, and neuroactive compounds such as tryptamine, serotonin, phenethylamine, tryptophan, and histamine [137, 138].”
From The athletic gut microbiota (2020) · cites this paper as [138]
In the citing paper
“It is well appreciated that the gut microbiota can synthesize certain vitamins, most notably vitamin K and B-group vitamins [e.g., cobalamin (B 12 ), folate, and riboflavin (144, 145)], some of which might be directly absorbed.”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [145]
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Association of gut microbiota with obesity in children and adolescents
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Zou, T., Xie, F., Liang, P., Chen, J., Wang, Z., Du, ., & You, J. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.114034 · Cited by 53
Functional constipation and the effect of prebiotics on the gut microbiota: a review
Erhardt, R., Harnett, J., Steels, E., & Steadman, K. J. (2022) · British Journal Of Nutrition · doi:10.1017/s0007114522003853 · Cited by 54
“The gut microbiota, with an estimated 3 million genes, is 150 times larger than the human genome and contributes to such an extent to our metabolic capacity that it is considered by many as fulfilling the functions of another organ(32,33).”
Yu, H., Sun, T., He, X., Wang, Z., Zhao, K., An, J., Wen, L., Li, J., Li, W., & Feng, J. (2022) · Aging and Disease · doi:10.14336/ad.2022.0325 · Cited by 56
“In the presence of gut microbiota-caused dysbiosis, harmful metabolites and proinflammatory cytokines can damage the intestinal barrier, causing systematic inflammation and pancreatic β-cell dysfunction and further damaging the brain-blood barrier to cause neuroinflammation, immune activation, and oxidative stress [10…”
BackgroundEffects of gut microbiota on neurodegenerative diseases
Khatoon, S., Kalam, N., Rashid, S., & Bano, G. (2023) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2023.1145241 · Cited by 55
“These metabolites exerts various physiological activities in the brain, including cognitive function, mood, and appetite (Kennedy et al., 2017; Lin and Zhang, 2017; Rowland et al., 2018).”
BackgroundClemente‐Suárez, V. J., Redondo-Flórez, L., Rubio-Zarapuz, A., Martín-Rodríguez, A., & Tornero-Aguilera, J. F. (2024) · Biomedicines · doi:10.3390/biomedicines12010221 · Cited by 59
“The microbiota aids in digestion, synthesizes essential vitamins, modulates the immune system, and provides a line of defense against pathogenic organisms [9].”
BackgroundThe dark side of the gut: Virome–host interactions in intestinal homeostasis and disease
Li, Y., Handley, S. A., & Baldridge, M. T. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20201044 · Cited by 55
Gut microbiome strain-sharing within isolated village social networks
Beghini, F., Pullman, J., Alexander, M., Shridhar, S. V., Prinster, D., Singh, A., Matute Juárez, R., Airoldi, E. M., Brito, I. L., & Christakis, N. A. (2025) · Nature · doi:10.1038/s41586-024-08222-1 · Cited by 51
Yin, H., Ma, J., Han, J., Li, M., & Shang, J. (2019) · PeerJ · doi:10.7717/peerj.6665 · Cited by 50
“3) came from different individual rats, there existed transformations between Qr, IQ, and QG in vivo, and the metabolism and transformation between these three compounds would be affect by many factors, such as gastric emptying rate and intestinal flora (Rowland et al., 2018; Yuan et al., 2016).”
BackgroundThe chemistry of gut microbiome in health and diseases
Lau, A., Tan, L. T., Mutalib, N. A., Wong, S. H., Letchumanan, V., & Lee, L. (2021) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000175 · Cited by 55
“Some probiotics strains can increase antiinflammatory mediators' concentration, such as tumor necrosis factors, which can abate diseases([276,284]).”
BackgroundWu, Y., Zhang, X., Han, D., Pi, Y., Tao, S., Zhang, S., Wang, S., Zhao, J., Chen, L., & Wang, J. (2021) · Animal nutrition · doi:10.1016/j.aninu.2020.07.012 · Cited by 51
“Intestinal microbiota have vital functions on gut barriers, metabolic reactions, nutritional effects and the maturation of the host's immune responses (Rowland et al., 2017; Ma et al., 2018; Valdes et al., 2018).”
BackgroundTurchini, G. M., Francis, D. S., Du, Z., Olsen, R. E., Ringø, E., & Tocher, D. R. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819587-1.00003-3 · Cited by 60
Guizzo, M. G., Tirloni, L., González, S., Farber, M. D., Braz, G. R. C., Parizi, L. F., Silva, L. A. D. E., Vaz, I. D. S., & de Oliveira, P. L. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.868575 · Cited by 50
Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition
Zarei, I., Koistinen, V., Kokla, M., Klåvus, A., Babu, A. F., Lehtonen, M., Auriola, S. O. K., & Hanhineva, K. (2022) · Scientific Reports · doi:10.1038/s41598-022-19327-w · Cited by 49
Microbiota of the gastrointestinal tract: Friend or foe?
Senchukova, M. A. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i1.19 · Cited by 56
Liu, C., Gan, R., Chen, D., Zheng, L., Ng, S. B., & Rietjens, I. M. C. M. (2023) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2023.2180478 · Cited by 50
“…tools to study the microbial conversion of a wide array of substances, including dietary ingredients, e.g., polysaccharides, polyphenols, dietary fibers, proteins, pathogens, pharmaceuticals, and toxins, without ethical constraints (Aura et al. 2002; Rowland et al. 2018; Titgemeyer et al. 1991).”
Gut microbiota dependant trimethylamine N-oxide and hypertension
Mutengo, K. H., Masenga, S. K., Mweemba, A., Mutale, W., & Kirabo, A. (2023) · Frontiers in Physiology · doi:10.3389/fphys.2023.1075641 · Cited by 53
“On the other hand, Bacteroidetes break down complex polysaccharides and play a role in vitamin production and regulating inflammation in the gut (Belkaid and Hand, 2014; Rowland et al., 2018).”
BackgroundBiomarkers in aquatic systems: Advancements, applications and future directions
Sikaily, A. E., & Shabaka, S. H. (2024) · The Egyptian Journal of Aquatic Research · doi:10.1016/j.ejar.2024.05.002 · Cited by 56
Xu, M., Zhou, E. Y., & Shi, H. (2025) · Cells · doi:10.3390/cells14050384 · Cited by 58
“…LPSs, SCFAs, polyamines (e.g., putrescine, spermidine, spermine), bile salts (produced by the liver and modified in the gut lumen by the microbiota), and certain essential vitamins, as well as gas, toxins, and virulence factors, as has been shown in both preclinical and clinical studies [208–210].”
Composition of the Intestinal Microbiota Determines the Outcome of Virus-Triggered Colitis in Mice
Bolsega, S., Basic, M., Smoczek, A., Büettner, M., Eberl, C., Ahrens, D., Odum, K. A., Stecher, B., & Bleich, A. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01708 · Cited by 50
“production of short chain fatty acids (SCFA), bioconversion of complex molecules, degradation of xenobiotic substances, and also in the development and maturation of the mucosal immune system (3, 4).”
BackgroundMetabolomic Signatures of Long-term Coffee Consumption and Risk of Type 2 Diabetes in Women
Hang, D., Zeleznik, O. A., He, X., Guasch‐Ferré, M., Jiang, X., Li, J., Liang, L., Eliassen, A. H., Clish, C. B., Chan, A. T., et al. (2020) · Diabetes Care · doi:10.2337/dc20-0800 · Cited by 50
Fu, Y., Yin, R., Liu, Z., Niu, Y., Guo, E., Cheng, R., Diao, X., Xue, Y., & Shen, Q. (2020) · Nutrients · doi:10.3390/nu12113452 · Cited by 50
“In particular, gut microbiota in the small and large intestine also play a role in dietary protein metabolism, including promoting protein digestion to produce short peptides and amino acids, which are then fermented to exert regulatory effects back on the gut microbiota [21,22].”
Effects of the l-tyrosine-derived bacterial metabolite p-cresol on colonic and peripheral cells
Blachier, F., & Andriamihaja, M. (2021) · Amino Acids · doi:10.1007/s00726-021-03064-x · Cited by 53
Metabolomic signatures after bariatric surgery – a systematic review
Vaz, M. E. D. L., Pereira, S. S., & Monteiro, M. P. (2021) · Reviews in Endocrine and Metabolic Disorders · doi:10.1007/s11154-021-09695-5 · Cited by 53
“Gut microbiota plays an important role in various physiological processes, including metabolism of dietary components and some host-generated substances, with an impact on the use and storage of energy [71].”
BackgroundDeandra, F. A., Ketherin, K., Rachmasari, R., Sulijaya, B., & Takahashi, N. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e13475 · Cited by 49
Influence of the gut microbiota on satiety signaling
Bastings, J. J. A. J., Venema, K., Blaak, E. E., & Adam, T. C. (2023) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2023.02.003 · Cited by 48
Matin, S., & Dadkhah, M. (2024) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2024.110882 · Cited by 50
Shin, J., Jung, S., Kim, S.-A., Kang, M., Kim, M. S., Joung, H., Hwang, G., & Shin, D. (2019) · Nutrients · doi:10.3390/nu11102450 · Cited by 49
“The gut microbiota influences the uptake and metabolism of dietary components, such as fermentation of dietary fiber, synthesis of specific vitamins, and transformation of cholesterol [8].”
BackgroundCognitive-Behavioural Correlates of Dysbiosis: A Review
Luca, M., Chattipakorn, S. C., Sriwichaiin, S., & Luca, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21144834 · Cited by 46
Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis
Chen, C., Zhang, Y., Yao, X., Li, S., Wang, G., Huang, Y., Yang, Y., Zhang, A., Liu, C., Zhu, D., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01711-22 · Cited by 49
“makes an important contribution to human metabolic homeostasis (26) and is closely”
BackgroundOliveira, R. A., & Pamer, E. G. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.002 · Cited by 51
Bioactive Dairy-Fermented Products and Phenolic Compounds: Together or Apart
Wróblewska, B., Kuliga, A., & Wnorowska, K. (2023) · Molecules · doi:10.3390/molecules28248081 · Cited by 55
“The microbiota in the large intestine enables the metabolization of polyphenols that end up in the colon [25].”
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Antibiotic use and the risk of rheumatoid arthritis: a population-based case-control study
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“Soybean oligosaccharides have been demonstrated to contribute to the growth of beneficial bacteria and improve the intestinal microenvironment, thus resulting in the change of VFAs concentrations.”
BackgroundInfluentialLiver Cirrhosis and Sarcopenia from the Viewpoint of Dysbiosis
Nishikawa, H., Enomoto, H., Nishiguchi, S., & Iijima, H. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21155254 · Cited by 49
“Glutathione has an auxiliary role in protecting cells from reactive oxygen species such as free radicals and peroxides [68,69].”
BackgroundInsight into the Possible Use of the Predator Bdellovibrio bacteriovorus as a Probiotic
Bonfiglio, G., Neroni, B., Radocchia, G., Marazzato, M., Pantanella, F., & Schippa, S. (2020) · Nutrients · doi:10.3390/nu12082252 · Cited by 50
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BackgroundG protein-coupled receptors as potential targets for nonalcoholic fatty liver disease treatment
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Butyrate: A Link between Early Life Nutrition and Gut Microbiome in the Development of Food Allergy
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“Although SCFAs can also be derived from dietary proteins and glycoprotein metabolism, carbohydrates represent the main sources [41].”
BackgroundImpacts of polyphenols on laying hens' productivity and egg quality: A review
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Microbiota-mediated metabolic perturbations in the gut and brain of mice after microplastic exposure
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Milk-derived extracellular vesicles and gut health
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Arginine accelerates intestinal health through cytokines and intestinal microbiota
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Metadata
- Authors
- Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K.
- Affiliations
- University of Reading (GB)
- University of Luxembourg (LU)
- University of Aberdeen (GB)
- Imperial College London (GB)
- Fondazione Edmund Mach (IT)
- Corresponding author
- Rowland, Ian
- Venue
- European Journal of Nutrition
- Published
- 2017-04-09
- Volume
- 57
- Issue
- 1
- Pages
- 1-24
- ISSN
- 1436-6207 (ISSN-L)
- 1436-6215
- PMC
- PMC5847071
- OpenAlex
- W2604323123
- Cited by
- 2,878
- References
- 166
- Citations by year
- 2026: 317 · 2025: 393 · 2024: 431 · 2023: 382 · 2022: 424 · 2021: 365 · 2020: 305 · 2019: 173 · 2018: 65 · 2017: 17
- FWCI
- 14.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- European Journal of Nutrition (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CentAUR (University of Reading) (acceptedVersion, other-oa)
- ePrints Soton (University of Southampton) (acceptedVersion)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion, other-oa)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- Funders
- International Life Sciences Institute Europe
- 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, host-microbe interactions, nutrient metabolism, dietary carbohydrates, short-chain fatty acids, protein metabolism, plant polyphenols, bile acids, vitamin metabolism, microbial metabolic pathways, enzyme activity assay
- MeSH terms
- Gastrointestinal Microbiome, Bacteria, Bile Acids and Salts, Diet, Dietary Carbohydrates, Dietary Proteins, Fatty Acids, Food, Health Promotion, Humans, Models, Theoretical, Plants, Edible, Vitamins, Proteomics, Metagenomics, Polyphenols, Phytochemicals
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