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Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans
Abstract
PURPOSE: Exercise is associated with altered gut microbial composition, but studies have not investigated whether the gut microbiota and associated metabolites are modulated by exercise training in humans. We explored the impact of 6 wk of endurance exercise on the composition, functional capacity, and metabolic output of the gut microbiota in lean and obese adults with multiple-day dietary controls before outcome variable collection. METHODS: Thirty-two lean (n = 18 [9 female]) and obese (n = 14 [11 female]), previously sedentary subjects participated in 6 wk of supervised, endurance-based exercise training (3 d·wk) that progressed from 30 to 60 min·d and from moderate (60% of HR reserve) to vigorous intensity (75% HR reserve). Subsequently, participants returned to a sedentary lifestyle activity for a 6-wk washout period. Fecal samples were collected before and after 6 wk of exercise, as well as after the sedentary washout period, with 3-d dietary controls in place before each collection. RESULTS: β-diversity analysis revealed that exercise-induced alterations of the gut microbiota were dependent on obesity status. Exercise increased fecal concentrations of short-chain fatty acids in lean, but not obese, participants. Exercise-induced shifts in metabolic output of the microbiota paralleled changes in bacterial genes and taxa capable of short-chain fatty acid production. Lastly, exercise-induced changes in the microbiota were largely reversed once exercise training ceased. CONCLUSION: These findings suggest that exercise training induces compositional and functional changes in the human gut microbiota that are dependent on obesity status, independent of diet and contingent on the sustainment of exercise.
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“To date, one study showed that exercise induced compositional changes in the human gut microbiota that were more pronounced in lean than in obese (Allen et al., 2017).”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“The authors concluded that the shifts were dependent on the obesity status and were reversed after cessation of the training.”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“It was recently demonstrated by targeted gene amplification, not metagenomics, that in addition to the influence on the gut microbiota composition, exercise training increased the gene encoding butyrate forming Butyryl CoA: Acetate CoA transferase (Allen et al., 2017)”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“while in a human study it increased after cessation of the training and not in response to exercise (Allen et al., 2017).”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“But interestingly, contradictory findings from the human exercise interventions have been recently presented (Allen et al., 2017; Cronin et al., 2018).”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“On the other hand, similar to our results, Allen and co-workers reported compositional and β-diversity changes of the microbiota in response to six-weeks endurance training that resembled the intervention of our study (Allen et al., 2017).”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Allen et al., 2017
In the citing paper
“Notably, the study also found that a return to sedentary lifestyle for 6 weeks reversed changes in the gut microbiota observed after exercise training, again indicating the sensitivity of the gut microbiome to physical activity.”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [113]
In the citing paper
“Exercise training is a well-known modulator of gut microbiota composition, improving biodiversity and representation of taxa with purported health-promoting significance [26,131].”
From Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia (2019) · cites this paper as [131]
In the citing paper
“After the washout period, exercise-induced changes in the microbiota were largely reversed once exercise training ceased.”
From The athletic gut microbiota (2020) · cites this paper as [98]
In the citing paper
“In a longitudinal research design, Allen et al. [98] reported for the first time that exercise training can modulate the composition and metabolic capacity of the human gut microbiota in previously sedentary individuals.”
From The athletic gut microbiota (2020) · cites this paper as [98]
In the citing paper
“Exercise-induced modulations of the gut microbiota and SCFA were strongly associated with changes in body composition in lean participants and VO2max in obese participants, independent of diet.”
From The athletic gut microbiota (2020) · cites this paper as [98]
In the citing paper
“Of note, the exercise induced shifts in SCFA-producing taxa (Faecalibacterium species [spp.] and Lachnospira spp.) and genetic machinery (butyrate-regulating gene, BCoAT) were more substantial in lean versus obese participants.”
From The athletic gut microbiota (2020) · cites this paper as [98]
In the citing paper
“Once these participants ceased training, exercise-induced changes in the microbiota were largely reversed when re-measured after a 6-week sedentary period109.”
From Exerkines in health, resilience and disease (2022) · cites this paper as [109]
In the citing paper
“In humans, chronic exercise altered the gut microbiome to increase availability of short chain fatty acids, particularly butyrate109.”
From Exerkines in health, resilience and disease (2022) · cites this paper as [109]
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“Higher levels of butyrate have been suggested as the mechanism linking dietary fibre intake with higher percentage of whole body lean mass and physical functioning in older adult men.(39,40) Importantly, SCFAs produced by Lachnospiraceae have also been associated with reduction in inflammatory bowel disease via intera…”
BackgroundHome-based exercise training influences gut bacterial levels in multiple sclerosis
Mokhtarzade, M., Shamsi, M. M., Abolhasani, M., Bakhshi, B., Sahraian, M. A., Quinn, L. S., & Negaresh, R. (2021) · Complementary Therapies in Clinical Practice · doi:10.1016/j.ctcp.2021.101463 · Cited by 38
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“In addition, experiments were conducted on obese and thin subjects, and it was found that exercise training could cause changes in the intestinal flora and increase the number of butyrate-producing bacteria, but this change depends on the change in body mass index (131, 132).”
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“without exhaustive exercise, during a 6-week trial conducted on four groups of mice: (1) no intervention; (2) PEMF treatment; (3) exercise; (4)”
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“These changes are independent of diet and may rapidly disappear once exercise training is ceased [68].”
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“Among lean participants, exercise significantly increases the concentration of SCFAs in fecal matter (37).”
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“This variability is not surprising given the “individualized and varying response” to exercise previously reported between lean individuals and those with obesity [77,78].”
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“butyrate, which are metabolized by gut microbiota (Allen et al., 2018).”
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Targeting the Gut Microbiota for Prevention and Management of Type 2 Diabetes
Zeppa, S. D., Gervasi, M., Bartolacci, A., Ferrini, F., Patti, A., Sestili, P., Stocchi, V., & Agostini, D. (2024) · Nutrients · doi:10.3390/nu16223951 · Cited by 33
“Nevertheless, the washout period was associated with a decline in the gut microbiome’s capacity to produce SCFAs in the obese group, as evidenced by a decrease in the relative abundances of butyrate-and propionate-regulating genes [164].”
Health Impact and Therapeutic Manipulation of the Gut Microbiome
Daliri, E. B., Ofosu, F. K., Chelliah, R., Lee, B. H., & Oh, D. (2020) · Microarrays · doi:10.3390/ht9030017 · Cited by 28
“Other important factors that account for the variations in the gut microbiota and their functions include drugs [63], antibiotic use [64], sex hormones [65], toxicants [66], age [67], and exercise [68,69].”
BackgroundOrtega‐Santos, C. P., Al‐Nakkash, L., & Whisner, C. M. (2020) · Nutrients · doi:10.3390/nu12113410 · Cited by 28
“Exercise interventions also have an impact on the gut microbial communities of obese and lean individuals; the beta-diversity of obese individuals, after a 6-week exercise intervention, no longer differed from lean individuals [36].”
BackgroundLee, M., Jhang, W.-L., Lee, C., Kan, N., Hsu, Y.-J., Ho, C.-S., Chang, C.-H., Cheng, Y.-C., Lin, J., & Huang, C. (2021) · Metabolites · doi:10.3390/metabo11030136 · Cited by 29
“The link between exercise and the composition of the gut microbiota seems to be two-way [7].”
BackgroundSuo, H., Shishir, M. R. I., Xiao, J., Wang, M., Chen, F., & Cheng, K. (2021) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.1c03158 · Cited by 28
The Relationship among Physical Activity, Intestinal Flora, and Cardiovascular Disease
Yan, Q., Zhai, W., Yang, C., Li, Z., Mao, L., Zhao, M., & Wu, X. (2021) · Cardiovascular Therapeutics · doi:10.1155/2021/3364418 · Cited by 28
Li, R., Liu, R., Chen, L., Wang, G., Qin, L., Yu, Z., & Wan, Z. (2023) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2023/2766250 · Cited by 30
“For example, it has been reported that a 6-week moderate to intense aerobic exercise induced a shift in the SCFA-producing bacteria and elevated fecal SCFAs in lean subjects [11].”
BackgroundPhysical activity‐induced alterations of the gut microbiota are BMI dependent
Shah, S., Mu, C., Moossavi, S., Shen‐Tu, G., Schlicht, K., Rohmann, N., Geisler, C., Laudes, M., Franke, A., Züllig, T., et al. (2023) · The FASEB Journal · doi:10.1096/fj.202201571r · Cited by 34
Carter, S. J., Hunter, G. R., Blackston, J. W., Liu, N., Lefkowitz, E. J., Pol, W. J. V. D., Morrow, C. D., Paulsen, J. A., & Rogers, L. Q. (2019) · Experimental Physiology · doi:10.1113/ep087404 · Cited by 30
Möller, G. B., Goulart, M. J. V. D. C., Nicoletto, B. B., Alves, F. D., & Schneider, C. D. (2019) · International Journal of Sport Nutrition and Exercise Metabolism · doi:10.1123/ijsnem.2018-0227 · Cited by 27
Macrophages in the pathophysiology of NAFLD: The role of sex differences
Ministrini, S., Montecucco, F., Sahebkar, A., & Carbone, F. (2020) · European Journal of Clinical Investigation · doi:10.1111/eci.13236 · Cited by 26
Effects of Low-Carbohydrate Diet and Exercise Training on Gut Microbiota
Sun, S., Lei, O. K., Nie, J., Shi, Q., Xu, Y., & Kong, Z. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.884550 · Cited by 27
“Studies both in rodents (18, 19) and humans (20, 21) showed that the traditional endurancebased exercise training or called moderate-intensity continuous training (MICT) could increase gut microbial diversity, enrich beneficial microbial members and fecal metabolites, and modify gut physiology to a favorable way.”
BackgroundCai, Y., Liu, Y., Wu, Z., Wang, J., & Zhang, X. (2023) · Nutrients · doi:10.3390/nu15122743 · Cited by 29
“Depending on the different metabolic states of the host (normal individuals [13], diabetes [14], obesity [15], hypertension [16], anxiety and cog‐ nitive impairment [17]), exercise can have different positive effects on the intestinal flora to promote host health.”
BackgroundExercise, the Gut Microbiome, and Frailty
Shin, H. E., Kwak, S. E., Lee, J., Zhang, D., Bae, J. H., & Song, W. J. (2019) · Annals of Geriatric Medicine and Research · doi:10.4235/agmr.19.0014 · Cited by 28
“Allen et al.17) showed that exercise can induce compositional and functional alterations in the human gut microbiome.”
BackgroundInflammatory Bowel Diseases: The Role of Gut Microbiota
Musis, C. D., Granata, L., Dallio, M., Miranda, A., Gravina, A. G., & Romano, M. (2020) · Current Pharmaceutical Design · doi:10.2174/1381612826666200420144128 · Cited by 27
Bielik, V., Hric, I., Ugrayová, S., Kubáňová, L., Putala, M., Grznár, Ľ., Penesová, A., Havranová, A., Šardzíková, S., Grendár, M., et al. (2022) · Sports Medicine - Open · doi:10.1186/s40798-022-00453-8 · Cited by 29
“[33] did not observe statistical differences between the α-diversity of lean and of obese participants at baseline or after 6 weeks of endurance-based exercise training [33].”
BackgroundPhysical inactivity and knee osteoarthritis in guinea pigs
Wallace, I. J., Bendele, A. M., Riew, G. J., et al. (2019) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2019.07.005 · Cited by 26
Warbeck, C. B., Dowd, A. J., Kronlund, L. J., Parmar, C., Daun, J. T., Wytsma-Fisher, K., Millet, G. Y., Schick, A., Reimer, R. A., Fung, T. S., et al. (2020) · Applied Physiology, Nutrition, and Metabolism · doi:10.1139/apnm-2020-0459 · Cited by 27
“A 6-week endurance exercise program was shown to alter the abundance of bacterial genera such as Faecalibacterium and Bacteroides, but in opposite directions depending on whether the subjects were lean or obese (Allen et al., 2018).”
BackgroundBoisseau, N., Barnich, N., & Koechlin‐Ramonatxo, C. (2022) · Nutrients · doi:10.3390/nu14050924 · Cited by 32
“and by reducing Bacteroides members [117].”
BackgroundGut Microbiota – A Potential Contributor in the Pathogenesis of Bipolar Disorder
Zhang, P., Kong, L., Huang, H., Pan, Y., Zhang, D., Jiang, J., Shen, Y., Xi, C., Lai, J., Ng, C. H., et al. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.830748 · Cited by 26
McLeod, A., Bernabé, B. P., Xia, Y., Sanchez-Flack, J., Lamar, M., Schiffer, L. A., Castellanos, K., Fantuzzi, G., Maki, P. M., Fitzgibbon, M., et al. (2023) · PLoS ONE · doi:10.1371/journal.pone.0280211 · Cited by 27
Gut check: Unveiling the influence of acute exercise on the gut microbiota
Grosicki, G. J., Langan, S. P., Bagley, J. R., Galpin, A. J., Garner, D., Hampton‐Marcell, J., Allen, J. M., & Robinson, A. T. (2023) · Experimental Physiology · doi:10.1113/ep091446 · Cited by 27
Self-citationChbeir, S., & Carrión, V. (2023) · World Journal of Psychiatry · doi:10.5498/wjp.v13.i5.144 · Cited by 25
The role of the gut microbiome in gastrointestinal cancers
Mishra, Y., Ranjan, A., Mishra, V. K., Chattaraj, A., Aljabali, A. A. A., El‐Tanani, M., Hromić‐Jahjefendić, A., Uversky, V. N., & Tambuwala, M. M. (2023) · Cellular Signalling · doi:10.1016/j.cellsig.2023.111013 · Cited by 28
Microbiota–gut–brain axis: the mediator of exercise and brain health
Kang, P., & Wang, A. (2024) · Psychoradiology · doi:10.1093/psyrad/kkae007 · Cited by 31
“Later, in 2018, a controlled longitudinal study was carried out to further assess the influence of exercise on the intestinal flora (Allen et al. , 2018 ).”
BackgroundGut microbiota regulates exercise-induced hormetic modulation of cognitive function
Cintado, E., Muela, P., Rodriguez, L., Alcaide, I., Tezanos, P., Vlčková, K., Valderrama, B., Bastiaanssen, T. F. S., Rodríguez-Muñoz, M., CEBALLOS, M. L. D., et al. (2025) · EBioMedicine · doi:10.1016/j.ebiom.2025.105876 · Cited by 28
“68,69 In contrast, moderate exercise was linked to increased pectin degradation activity (SF.7d).”
Plissonneau, C., Capel, F., Chassaing, B., Dupuit, M., Maillard, F., Wawrzyniak, I., Combaret, L., Dutheil, F., Etienne, M., Mairesse, G., et al. (2021) · Nutrients · doi:10.3390/nu13030788 · Cited by 26
“Gut microbiota composition and function could be influenced by regular physical activity, and also by n-3 PUFAs intake [17,27].”
BackgroundPaton, S. E. J., Solano, J. L., Coulombe-Rozon, F., Lebel, M., & Ménard, C. (2023) · Journal of Psychiatry and Neuroscience · doi:10.1503/jpn.220218 · Cited by 24
Wei, J., Liu, Q., Yuen, H.-Y., Lam, A. C.-H., Jiang, Y., Yang, Y., Liu, Y., Zhao, X., & Xiao, L. (2025) · Journal of Orthopaedic Translation · doi:10.1016/j.jot.2024.11.003 · Cited by 28
“These findings implied that the exercise-induced alterations in the SCFA-producing capacity were largely dependent on obesity status, and the microbiome of lean individuals could be more responsive to exercise compared to over-weight or obese ones [187].”
Eslami, M., Adampour, Z., Dowlat, B. F., Yaghmayee, S., Tabaei, F. M., Oksenych, V., & Naderian, R. (2025) · Biomedicines · doi:10.3390/biomedicines13040915 · Cited by 27
“However, these beneficial microbial shifts were not observed in obese participants, suggesting that individual physiological differences may mediate exercise-induced microbiota changes [101].”
Exercise, Diet, and Brain Health: From the Perspective of Gut Microbiota Regulation
Zhang, L., Liu, R., Song, Z., & Zhang, X. (2025) · Nutrients · doi:10.3390/nu17101686 · Cited by 24
“A previous study demonstrated that endurance exercise upregulates key SCFA-producing pathways, including butyrate synthesis via the BCoAT gene and propionate production through mmDA gene modulation, thereby enhancing the gut microbiome’s SCFA-generating capacity [35].”
Yan, X., & He, B. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1695448 · Cited by 30
Wang, W., Zhong, M., Yu, T., Chen, L., Shi, L., Zong, J., & Wang, S. (2020) · Nutrition & Metabolism · doi:10.1186/s12986-020-00442-2 · Cited by 24
Microbiome-liver crosstalk: A multihit therapeutic target for liver disease
Kirundi, J., Moghadamrad, S., & Urbaniak, C. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i11.1651 · Cited by 24
Niemiro, G. M., Allen, J. M., Mailing, L. J., Khan, N. A., Holscher, H. D., Woods, J. A., & Lisio, M. D. (2018) · The Journal of Physiology · doi:10.1113/jp276023 · Cited by 24
“This study was an additional analysis of some participants previously described (Allen et al. 2018).”
BackgroundMethodResultInfluentialSelf-citationQin, X., Chen, M., He, B., Chen, Y., & Zheng, Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1539972 · Cited by 32
Thomas, B., Smallwood, S., Clarke, C., & Bescós, R. (2019) · Nitric Oxide · doi:10.1016/j.niox.2019.03.001 · Cited by 24
“From this viewpoint, recent studies on the gut microbiome have shown a positive association between exercise levels and the diversity of bacteria (13-16), however no previous study has investigated a possible link between oral bacteria and exercise capacity.”
BackgroundShamsi, M. M., Maryam, J., Bakhshi, B., Neda, F., Mokhtarzade, M., Mahboobeh, B., Quinn, L. S., & Kalani, B. S. (2021) · Archives of Physiology and Biochemistry · doi:10.1080/13813455.2021.1871763 · Cited by 26
Cheng, H. T., Yen, G., Huang, S., Chen, S., & Hsu, C. (2022) · Journal of Food and Drug Analysis · doi:10.38212/2224-6614.3396 · Cited by 24
Graybeal, A. J., Kreutzer, A., Willis, J. L., Moss, K., Braun-Trocchio, R., & Shah, M. (2022) · Journal of Dietary Supplements · doi:10.1080/19390211.2022.2056670 · Cited by 24
“However, while OA may be more exposed to sleep deprivation, increased exercise favorably changes gut microbiota (79) unless exercise becomes excessive (80).”
BackgroundYu, C., Liu, S., Niu, Y., & Fu, L. (2022) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2022.109059 · Cited by 23
Lee, J. E., Walton, D. M., O’Connor, C. P., Wammes, M., Burton, J. P., & Osuch, E. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23126643 · Cited by 27
“’s study, after a six-week exercise intervention, the abundance of butyrateproducing taxa and fecal acetate and butyrate concentrations were only increased in lean subjects but not in obese subjects [62].”
BackgroundBoytar, A. N., Nitert, M. D., Morrison, M., Skinner, T. L., & Jenkins, D. G. (2022) · The Journal of Physiology · doi:10.1113/jp283702 · Cited by 28
Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients.
Himbert, C., Stephens, W. Z., Gigic, B., Hardikar, S. S., Holowatyj, A. N., Lin, T., Ose, J., Swanson, E., Ashworth, A., Warby, C. A., et al. (2022) · PubMed Central · Cited by 24
Diet Quality and the Fecal Microbiota in Adults in the American Gut Project
Baldeon, A. D., McDonald, D. T., González, A., Knight, R. D., & Holscher, H. D. (2023) · Journal of Nutrition · doi:10.1016/j.tjnut.2023.02.018 · Cited by 49
Self-citation
Metadata
- Authors
- ALLEN, J. M., MAILING, L. J., NIEMIRO, G. M., MOORE, R., COOK, M. D., WHITE, B. A., HOLSCHER, H. D., & WOODS, J. A.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- ORCID
- Venue
- Medicine & Science in Sports & Exercise
- Published
- 2018-04
- Volume
- 50
- Issue
- 4
- Pages
- 747-757
- ISSN
- 0195-9131 (ISSN-L)
- OpenAlex
- W2770212191
- Semantic Scholar
- 174d28f947e411c5265cc65ec9ba4d74f60b5bc0
- Cited by
- 820
- References
- 42
- Citations by year
- 2026: 121 · 2025: 84 · 2024: 111 · 2023: 106 · 2022: 107 · 2021: 124 · 2020: 85 · 2019: 51 · 2018: 30
- FWCI
- 18.53
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Medicine & Science in Sports & Exercise (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Illinois at Urbana-Champaign
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- exercise training, gut microbiota, obesity, endurance exercise, short-chain fatty acids, fecal microbiota, beta diversity, sedentary lifestyle
- MeSH terms
- Gastrointestinal Microbiome, Adult, Bacteria, Fatty Acids, Volatile, Feces, Female, Humans, Longitudinal Studies, Male, Obesity, Oxygen Consumption, RNA, Ribosomal, 16S, Exercise, Body Mass Index, Young Adult, Sedentary Behavior
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