Background: Time-restricted eating/feeding (TRE/TRF) and physical exercise are promising nonpharmacological strategies to improve gut microbiota composition, diversity, and functionality.
Aim: This review examines the independent and potential synergistic effects of TRE/TRF and various exercise modalities on gut microbiota, with a focus on underlying mechanisms and associated health outcomes.
Methods: A comprehensive literature search was conducted using databases such as PubMed, Scopus, and Web of Science for articles published between 2015 and 2024. Keywords included terms related to intermittent fasting, TRE, TRF, physical exercise, and gut microbiota. Eligible studies involved human or animal models and examined primary outcomes, including gut microbiota diversity, composition, and metabolic outcomes.
Results: The TRE/TRF has been shown to positively influence microbial diurnal rhythms, enhance microbial diversity, and increase beneficial bacteria such as Akkermansia muciniphila. Exercise, particularly aerobic and resistance training, enhances both α- and β-diversity, stimulates the proliferation of short-chain fatty acid producing and anti-inflammatory bacteria such as Bifidobacterium and Roseburia, and improves gut barrier integrity. However, findings from human studies remain heterogeneous and are influenced by intervention timing, participant characteristics, and dietary patterns. Limited evidence exists on the combined effects of TRE/TRF and exercise, but preliminary data suggest potential synergistic benefits, particularly in improving microbial diversity and metabolic outcomes.
Conclusion: The TRE/TRF and exercise represent promising, nonpharmacological strategies for enhancing gut microbiota and supporting metabolic health. While individual effects are supported by robust preclinical and clinical evidence, research on their combined impact remains scarce.
Graphical abstract:
The interaction between exercise modalities and time-restricted eating/feeding (TRE/TRF) on gut microbiota.
AngooraniPEjtahedH-SHasani-RanjbarS, et al. (2021) Gut microbiota modulation as a possible mediating mechanism for fasting-induced alleviation of metabolic complications: A systematic review. Nutrition & Metabolism18(1): 105.
2.
BaileyCPBoydPShams-WhiteMM, et al. (2024) Time-restricted eating in community-dwelling adults: Correlates of adherence and discontinuation in a cross-sectional online survey study. Journal of the Academy of Nutrition and Dietetics124(8): 1029–1040.
3.
BassJTakahashiJS (2010) Circadian integration of metabolism and energetics. Science330(6009): 1349–1354.
4.
BatitucciGAlmeidaOGDe MartinisECP, et al. (2024) Intermittent fasting and high-intensity interval training do not alter gut microbiota composition in adult women with obesity. American Journal of Physiology-Endocrinology and Metabolism327(3): E241–E257.
5.
BealsJWKayserBDSmithGI, et al. (2023) Dietary weight loss-induced improvements in metabolic function are enhanced by exercise in people with obesity and prediabetes. Nature Metabolism5(7): 1221–1235.
6.
Bonomini-GnutzmannRPlaza-DíazJJorquera-AguileraC, et al. (2022) Effect of intensity and duration of exercise on gut microbiota in humans: A systematic review. International Journal of Environmental Research and Public Health19(15): 9518.
7.
Camacho-CardenosaAClavero-JimenoAMartin-OlmedoJJ, et al. (2024) Time-restricted eating and supervised exercise for improving hepatic steatosis and cardiometabolic health in adults with obesity: Protocol for the TEMPUS randomised controlled trial. BMJ Open14(1): e078472.
8.
CampanielloDCorboMRSinigagliaM, et al. (2022) How diet and physical activity modulate gut microbiota: Evidence, and perspectives. Nutrients14(12): 2456.
9.
CataldiSBonavolontàVPoliL, et al. (2022) The relationship between physical activity, physical exercise, and human gut microbiota in healthy and unhealthy subjects: A systematic review. Biology11(3): 479.
10.
ChaixALinTLeHD, et al. (2019a) Time-restricted feeding prevents obesity and metabolic syndrome in mice lacking a circadian clock. Cell Metabolism29(2): 303–319.e4.
11.
Chaix A, Manoogian ENC, Melkani GC, et al. (2019b) Time-restricted eating to prevent and manage chronic metabolic diseases. Annual Review of Nutrition 39(1): 291–315.
12.
CheTYanCTianD, et al. (2021) Time-restricted feeding improves blood glucose and insulin sensitivity in overweight patients with type 2 diabetes: A randomised controlled trial. Nutrition & Metabolism18(1): 88.
13.
CroninOBartonWSkuseP, et al. (2018) A prospective metagenomic and metabolomic analysis of the impact of exercise and/or whey protein supplementation on the gut microbiome of sedentary adults. mSystems3(3): e00044–18. Gilbert JA (ed.).
14.
CullenJMAShahzadSDhillonJ (2023) A systematic review on the effects of exercise on gut microbial diversity, taxonomic composition, and microbial metabolites: Identifying research gaps and future directions. Frontiers in Physiology14: 1292673.
15.
De CaboRMattsonMP (2019) Effects of intermittent fasting on health, aging, and disease. New England Journal of Medicine381(26): 2541–2551. Longo DL (ed.).
16.
DhahbiWBrikiWHeisselA, et al. (2025) Physical activity to counter age-related cognitive decline: Benefits of aerobic, resistance, and combined training—A narrative review. Sports Medicine - Open11(1): 56.
17.
DmytrivTRStoreyKBLushchakVI (2024) Intestinal barrier permeability: The influence of gut microbiota, nutrition, and exercise. Frontiers in Physiology15: 1380713.
18.
Donati ZeppaSAmatoriSSistiD, et al. (2021) Nine weeks of high-intensity indoor cycling training induced changes in the microbiota composition in non-athlete healthy male college students. Journal of the International Society of Sports Nutrition18(1): 74.
19.
DupuitMRanceMMorelC, et al. (2022) Effect of concurrent training on body composition and gut Microbiota in postmenopausal women with overweight or obesity. Medicine & Science in Sports & Exercise54(3): 517–529.
20.
Eckel-MahanKSassone-CorsiP (2013) Metabolism and the circadian clock converge. Physiological Reviews93(1): 107–135.
21.
ErlandsonKMLiuJJohnsonR, et al. (2021) An exercise intervention alters stool microbiota and metabolites among older, sedentary adults. Therapeutic Advances in Infectious Disease8: 20499361211027067.
22.
EzenaborEHAdeyemiAAAdeyemiOS (2024) Gut microbiota and metabolic syndrome: Relationships and opportunities for new therapeutic strategies. Scientifica2024(1): 4222083. Dubey MK (ed.).
23.
FarhaniZGhouiliHDhahbiW, et al. (2025) Optimizing the number of players and training bout durations in soccer small-sided games: Effects on mood balance and technical performance. European Journal of Sport Science25(3): e12208.
24.
FengRYangWFengW, et al. (2024) Time-restricted feeding ameliorates non-alcoholic fatty liver disease through modulating hepatic nicotinamide metabolism via gut microbiota remodeling. Gut Microbes16(1): 2390164.
25.
FerrocinoIPellegriniMD’EusebioC, et al. (2022) The effects of time-restricted eating on metabolism and gut microbiota: A real-life study. Nutrients14(13): 2569.
26.
GabelKMarcellJCaresK, et al. (2020) Effect of time restricted feeding on the gut microbiome in adults with obesity: A pilot study. Nutrition and Health26(2): 79–85.
27.
GondaliaSCookeMKeenanS, et al. (2020) Gut microbiota Is linked to physical health improvements resulting from energy-restricted diet and exercise: A randomized controlled trial in healthy adults. In: First International Electronic Conference on Nutrients, Microbiota and Chronic Disease. Basel, Switzerland: MDPI, 8, 1–9.
28.
GrosickiGJDurkRPBagleyJR (2019) Rapid gut microbiome changes in a world-class ultramarathon runner. Physiological Reports7(24): 1–7.
29.
HernandezARKempKMBurkeSN, et al. (2022) Influence of aging, macronutrient composition and time-restricted feeding on the Fischer344 x brown Norway rat gut microbiota. Nutrients14(9): 1758.
30.
HuDYeYMaoY, et al. (2019) Time-restricted feeding during childhood has persistent effects on mice commensal microbiota. Annals of Translational Medicine7(20): 556–556.
31.
HuangCLiuDYangS, et al. (2024) Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome. iScience27(7): 110202.
32.
Humińska-LisowskaKMichałowska-SawczynMKosciolekT, et al. (2025) Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds. Scientific Reports15(1): 16061.
33.
JamshedHStegerFLBryanDR, et al. (2022) Effectiveness of early time-restricted eating for weight loss, fat loss, and cardiometabolic health in adults with obesity: A randomized clinical trial. JAMA Internal Medicine182(9): 953.
34.
JolletMNayKChopardA, et al. (2021) Does physical inactivity induce significant changes in human gut Microbiota? New answers using the dry immersion hypoactivity model. Nutrients13(11): 3865.
35.
KernTBlondMBHansenTH, et al. (2020) Structured exercise alters the gut microbiota in humans with overweight and obesity—A randomized controlled trial. International Journal of Obesity44(1): 125–135.
36.
KotarskyCJJohnsonNRMahoneySJ, et al. (2021) Time-restricted eating and concurrent exercise training reduces fat mass and increases lean mass in overweight and obese adults. Physiological Reports9(10): 1–17.
37.
LathakumariRHVajraveluLKSatheesanA, et al. (2024) Antibiotics and the gut microbiome: Understanding the impact on human health. Medicine in Microecology20: 100106.
38.
LeeECFragalaMSKavourasSA, et al. (2017) Biomarkers in sports and exercise: Tracking health, performance, and recovery in athletes. Journal of Strength and Conditioning Research31(10): 2920‐2937.
39.
LingZLiuXChengY, et al. (2022) Gut microbiota and aging. Critical Reviews in Food Science and Nutrition62(13): 3509‐3534.
40.
LiuDHuangYHuangC, et al. (2022) Calorie restriction with or without time-restricted eating in weight loss. New England Journal of Medicine386(16): 1495‐1504.
41.
LiuYYaoWNiY, et al. (2020) Gut microbiome fermentation determines the efficacy of exercise for diabetes prevention. Cell Metabolism31(1): 77‐91.e5.
42.
LongoVDPandaS (2016) Fasting, circadian rhythms, and time-restricted feeding in healthy lifespan. Cell Metabolism23(6): 1048‐1059.
43.
MahdiehMSMaryamJBitaB, et al. (2023) A pilot study on the relationship between Lactobacillus, Bifidibactrium counts and inflammatory factors following exercise training. Archives of Physiology and Biochemistry129(3): 778‐787.
44.
ManoogianENCChowLSTaubPR, et al. (2022) Time-restricted eating for the prevention and management of metabolic diseases. Endocrine Reviews43(2): 405‐436.
45.
ManoogianENCLaferrèreB (2023) Time-restricted eating: What we know and where the field is going. Obesity31(S1): 7‐8.
46.
Mengi ÇelikÖKöksalEAktürkM (2023) Time-restricted eating (16/8) and energy-restricted diet: Effects on diet quality, body composition and biochemical parameters in healthy overweight females. BMC Nutrition9(1): 97.
47.
MinLAblitipAWangR, et al. (2024) Effects of exercise on gut microbiota of adults: A systematic review and meta-analysis. Nutrients16(7): 1070.
48.
MokarramiACapacciATrioB, et al. (2024) Relationship between gut-microbiota and sport activity. Central European Journal of Sport Sciences and Medicine45: 25‐53.
49.
MokhtarzadeMMolanouri ShamsiMAbolhasaniM, et al. (2021) Home-based exercise training influences gut bacterial levels in multiple sclerosis. Complementary Therapies in Clinical Practice45: 101463.
50.
Molina-TorresGRodriguez-ArrastiaMRomanP, et al. (2019) Stress and the gut microbiota-brain axis. Behavioural Pharmacology30(2 and 3): 187‐200.
51.
MondaVVillanoIMessinaA, et al. (2017) Exercise modifies the gut microbiota with positive health effects. Oxidative Medicine and Cellular Longevity2017(1): 3831972. Morishita R (ed.).
52.
MoritaEYokoyamaHImaiD, et al. (2019) Aerobic exercise training with brisk walking increases intestinal Bacteroides in healthy elderly women. Nutrients11(4): 868.
53.
MotianiKKColladoMCEskelinenJ-J, et al. (2020) Exercise training modulates gut microbiota profile and improves endotoxemia. Medicine & Science in Sports & Exercise52(1): 94‐104.
54.
MuaddiMAMakeenAMGosadiIM, et al. (2024) Satisfaction paradoxes in health behaviors: Contrasting patterns across weight, physical activity and dietary habits. Nutrients16(14): 2246.
55.
O’NealMAGutierrezNRLaingKL, et al. (2023) Barriers to adherence in time-restricted eating clinical trials: An early preliminary review. Frontiers in Nutrition9: 1075744.
56.
PattersonRESearsDD (2017) Metabolic effects of intermittent fasting. Annual Review of Nutrition37(1): 371‐393.
57.
PhillipsNMareschalJSchwabN, et al. (2021) The effects of time-restricted eating versus standard dietary advice on weight, metabolic health and the consumption of processed food: A pragmatic randomised controlled trial in community-based adults. Nutrients13(3): 1042.
58.
PopaADNițăOGherasimA, et al. (2023) A scoping review of the relationship between intermittent fasting and the human gut Microbiota: Current knowledge and future directions. Nutrients15(9): 2095.
59.
PramonoAArdiariaMLimijadiEKS, et al. (2024) Intermittent fasting modulates human gut microbiota diversity in a phenotype-dependent manner: A systematic review. Bioscience of Microbiota, Food and Health43(3): 170‐182.
60.
PranotoARamadhanRNRejekiPS, et al. (2024) The role of long-term combination training in reducing and maintaining of body fat in obese young adult women. Retos: Nuevas Tendencias en Educación Física, Deporte y Recreación53: 139‐146.
61.
RatajczakMKrzywickaMSzulińskaM, et al. (2024) Effects of 12-week combined strength and endurance circuit training program on insulin sensitivity and retinol-binding protein 4 in women with insulin-resistance and overweight or mild obesity: A randomized controlled trial. Diabetes, Metabolic Syndrome and Obesity17: 93‐106.
62.
ResendeASLeiteGSFLancha JuniorAH (2021) Changes in the gut bacteria composition of healthy men with the same nutritional profile undergoing 10-week aerobic exercise training: A randomized controlled trial. Nutrients13(8): 2839.
63.
RettedalEACreeJMEAdamsSE, et al. (2020) Short-term high-intensity interval training exercise does not affect gut bacterial community diversity or composition of lean and overweight men. Experimental Physiology105(8): 1268‐1279.
64.
RibeiroFMRibeiroCFAGarciaACM, et al. (2019) Limited effects of low-to-moderate aerobic exercise on the gut Microbiota of mice subjected to a high-fat diet. Nutrients11(1): 149.
65.
Rodriguez-AyllonMPlaza-FloridoAMendez-GutierrezA, et al. (2023) The effects of a 20-week exercise program on blood-circulating biomarkers related to brain health in overweight or obese children: The ActiveBrains project. Journal of Sport and Health Science12(2): 175‐185.
66.
RustBMPickloMJYanL, et al. (2023) Time-Restricted feeding modifies the fecal lipidome and the gut microbiota. Nutrients15(7): 1562.
67.
SilvaJSCSeguroCSNavesMMV (2022) Gut microbiota and physical exercise in obesity and diabetes – A systematic review. Nutrition, Metabolism and Cardiovascular Diseases32(4): 863‐877.
68.
SlimaniMGhouiliHDhahbiW, et al. (2025) Position-specific biomarker responses to match vs. VAMEVAL test modalities in elite female soccer players: A comparative analysis study. Cogent Social Sciences11(1): 2447399.
69.
SoaresNLDorandVAMCavalcanteHC, et al. (2021) Does intermittent fasting associated with aerobic training influence parameters related to the gut-brain axis of Wistar rats?Journal of Affective Disorders293: 176‐185.
70.
SolimanGA (2022) Intermittent fasting and time-restricted eating role in dietary interventions and precision nutrition. Frontiers in Public Health10: 1017254.
71.
SouissiMAGouasmiaCDergaaI, et al. (2025) Impact of evening blue light exposure timing on sleep, motor, and cognitive performance in young athletes with intermediate chronotype. Biology of Sport42(3): 61‐68.
72.
ŚwiątkiewiczINuszkiewiczJWróblewskaJ, et al. (2024) Feasibility and cardiometabolic effects of time-restricted eating in patients with metabolic syndrome. Nutrients16(12): 1802.
73.
TaniguchiHTanisawaKSunX, et al. (2018) Effects of short-term endurance exercise on gut microbiota in elderly men. Physiological Reports6(23): e13935.
74.
ThursbyEJugeN (2017) Introduction to the human gut microbiota. Biochemical Journal474(11): 1823‐1836.
75.
TorquatiLGajanandTCoxER, et al. (2023) Effects of exercise intensity on gut microbiome composition and function in people with type 2 diabetes. European Journal of Sport Science23(4): 530‐541.
76.
TorresLLeeJLParkS, et al. (2022) Retention, fasting patterns, and weight loss with an intermittent fasting app: Large-scale, 52-week observational study. JMIR mHealth and UHealth10(10): e35896.
77.
UchidaMFujieSYanoH, et al. (2023) Aerobic exercise training-induced alteration of gut microbiota composition affects endurance capacity. The Journal of Physiology601(12): 2329‐2344.
78.
VaradyKAChowLS (2024) Optimizing the design of time-restricted eating human trials. Nature Metabolism6(8): 1423‐1425.
79.
VaradyKACienfuegosSEzpeletaM, et al. (2022) Clinical application of intermittent fasting for weight loss: Progress and future directions. Nature Reviews Endocrinology18(5): 309‐321.
80.
WangHLiQXuR, et al. (2023) Time-restricted feeding affects colonic nutrient substrates and modulates the diurnal fluctuation of microbiota in pigs. Frontiers in Microbiology14: 1162482.
81.
WangHXiaPLuZ, et al. (2021) Metabolome-microbiome responses of growing pigs induced by time-restricted feeding. Frontiers in Veterinary Science8: 1‐12.
82.
WangWWeiRPanQ, et al. (2022) Beneficial effect of time-restricted eating on blood pressure: A systematic meta-analysis and meta-regression analysis. Nutrition & Metabolism19(1): 77.
83.
WangWZhouHQiS, et al. (2024) The association between physical activities combined with dietary habits and cardiovascular risk factors. Heliyon10(7): e28845.
84.
WegierskaAECharitosIATopiS, et al. (2022) The connection between physical exercise and gut microbiota: Implications for competitive sports athletes. Sports Medicine52(10): 2355‐2369.
85.
WilkinsonMJManoogianENCZadourianA, et al. (2020) Ten-Hour time-restricted eating reduces weight, blood pressure, and atherogenic lipids in patients with metabolic syndrome. Cell Metabolism31(1): 92‐104.e5.
86.
WuKLuoQLiuY, et al. (2024) Causal relationship between gut microbiota and gastrointestinal diseases: A Mendelian randomization study. Journal of Translational Medicine22(1): 92.
87.
XiaJGuoWHuM, et al. (2023) Resynchronized rhythmic oscillations of gut microbiota drive time-restricted feeding induced nonalcoholic steatohepatitis alleviation. Gut Microbes15(1): 2221450.
88.
XieZSunYYeY, et al. (2022) Randomized controlled trial for time-restricted eating in healthy volunteers without obesity. Nature Communications13(1): 1003.
89.
YeYXuHXieZ, et al. (2020) Time-restricted feeding reduces the detrimental effects of a high-fat diet, possibly by modulating the circadian rhythm of hepatic lipid metabolism and gut microbiota. Frontiers in Nutrition7: 596285.
90.
ZebFOsailiTObaidR, et al. (2023) Gut microbiota and time-restricted feeding/eating: A targeted biomarker and approach in precision nutrition. Nutrients15(2): 259.
91.
ZebFWuXChenL, et al. (2020a) Effect of time-restricted feeding on metabolic risk and circadian rhythm associated with gut microbiome in healthy males. British Journal of Nutrition123(11): 1216‐1226.
92.
ZebFWuXChenL, et al. (2020b) Time-restricted feeding is associated with changes in human gut microbiota related to nutrient intake. Nutrition78: 110797.
93.
ZebFWuXFatimaS, et al. (2021) Time-restricted feeding regulates molecular mechanisms with involvement of circadian rhythm to prevent metabolic diseases. Nutrition89: 111244.
94.
ZhaoXZhangZHuB, et al. (2018) Response of gut microbiota to metabolite changes induced by endurance exercise. Frontiers in Microbiology9: 765.
95.
ZhaoYLiuYJiaL (2025) Gut microbial dysbiosis and inflammation: Impact on periodontal health. Journal of Periodontal Research60(1): 30‐43.
96.
ZhongFWenXYangM, et al. (2021) Effect of an 8-week exercise training on gut microbiota in physically inactive older women. International Journal of Sports Medicine42(07): 610‐623.
97.
ZhouXLinXYuJ, et al. (2024) Effects of DASH diet with or without time-restricted eating in the management of stage 1 primary hypertension: A randomized controlled trial. Nutrition Journal23(1): 65.
