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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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“98 Moreover, exercise elicited the alteration of intestinal microecology composition is varied in different populations.”
BackgroundRoseburia intestinalis: A possible target for vascular calcification
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“Exercise can increase the concentration of short-chain fatty acids in feces and the ability of intestinal microflora to produce short-chain fatty acids (38).”
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“Allen et al [49] conducted endurance training on lean and obese adults for 6 weeks and observed the effects on their gut microbiota composition, functional ability, and metabolic output.”
Kim, Y.-I., Choi, W., Seo, M., Ka, S., & Park, J. (2025) · Physical Activity and Nutrition · doi:10.20463/pan.2025.0014 · Cited by 7
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Gut microbiome and prediabetes - a review
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Exercise and the gut microbiome: implications for supportive care in cancer
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“For example, Allen and colleagues [92] demonstrated that 6 weeks of aerobic exercise performed three times per week at a moderate intensity significantly modified a wide range of taxonomy for men and women with and without obesity, from relative phyla abundance through to genera abundance and SCFA…”
Zhu, L., Ming, Y., Wu, M., Zhang, X., Wang, X., Li, H., Lin, Z., Gao, F., & Zhu, Y. (2023) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202300673 · Cited by 7
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“As reported previously, physical exercise has been shown to affect the gut microbiome in humans (Allen et al., 2018; Dziewiecka et al., 2022).”
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BackgroundSynergistic effects of exercise and catalase overexpression on gut microbiome
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“A previous randomized controlled trial demonstrated that exercise training increases fecal SCFA concentrations and gut microbiome SCFAproducing capacity and influences BP by interacting with host SCFA receptors [45, 46].”
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“Physical activity has been shown to alter the composition and function of the gut microbiota (Allen et al., 2018).”
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“Although exercise affects the microbiota in both people and animals [17–19], it is unknown whether these metabolic alterations in gut bacteria are related to the development of AD.”
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Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications
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“The minority of studies that have implemented controlled feeding protocols (e.g., [8,70]) represent the gold standard but are logistically demanding, expensive, and may limit generalizability.”
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“As exercise increases the abundance of SCFA producing bacteria (Allen et al., 2018; Mailing et al., 2019), Blautia may be an exercise-responsive genus in groups that perform chronic exercise training as their increased abundance may be related to optimization of carbohydrate metabolism.”
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“There is increasing evidence showing that the gut microbiota may change under various conditions, including genetics, exercise, nutrition, obesity, injuries, and antibiotics [4–6].”
Microbiome Perturbations in Hidradenitis Suppurativa
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Association of leisure time physical activity with gut microbiota composition in early adulthood
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Interaction between Gut Microbiota and Dendritic Cells in Colorectal Cancer
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Background
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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