Abstract
he gut microbiota plays a fundamental role in human physiology by influencing metabolism, immunity, and neuroendocrine communication. Growing evidence suggests that physical exercise modulates gut microbial composition; however, study findings re- main inconsistent due to variations in design, training type, and population characteristics. This review summarizes current research on how different forms, intensities, and frequen- cies of exercise shape the gut microbiota and discusses their implications for athlete health and performance. Moderate and sustained physical activity generally promotes higher microbial diversity, increases short-chain fatty acid (SCFA)-producing bacteria, and en- hances gut barrier integrity. Endurance training, particularly long-term, is most consistently associated with beneficial microbial shifts, including increases inPrevotella,Akkermansia, andFaecalibacterium. In contrast, excessive or high-intensity endurance exercise was shown to cause dysbiosis, inflammation, and greater intestinal permeability. Resistance training appears to induce milder changes but was shown to improve mucin synthesis and butyrate production, especially in older adults. Exercise frequency also plays a role, with regular daily training enriching metabolic pathways linked to gut and systemic health. Overall, the impact of exercise on the gut microbiota depends on the type, intensity, and duration of activity. Balanced, moderate exercise combined with a healthy diet emerges as the most effective strategy to enhance microbial diversity,
production, especially in older adults. Exercise frequency also plays a role, with regular daily training enriching metabolic pathways linked to gut and systemic health. Overall, the impact of exercise on the gut microbiota depends on the type, intensity, and duration of activity. Balanced, moderate exercise combined with a healthy diet emerges as the most effective strategy to enhance microbial diversity, reduce inflammation, and support overall performance and well-being in athletes. Keywords:athletes; exercise intensity; exercise physiology; gastrointestinal health; gut microbiota; physical activity 1. Introduction The gut microbiota, a diverse and dynamic microbial ecosystem within the human gastrointestinal tract, plays a central role in host physiology. It supports essential functions such as immune regulation, digestion, nutrient metabolism, and bidirectional signaling along the gut–brain axis [1,2]. Through the production of metabolites including short chain fatty acids, bile acid derivatives, and neurotransmitter precursors, the gut microbiota influences gastrointestinal function as well as systemic metabolic and neuroendocrine Gastrointest. Disord.2026,8, 1 https://doi.org/10.3390/gidisord8010001
Gastrointest. Disord.2026,8, 1 2 of 23 balance. Its composition and activity are strongly shaped by environmental and lifestyle factors, most notably diet, antibiotic exposure, stress, and physical activity [3]. Although diet has long been considered the primary determinant of microbial diver- sity and metabolic potential, recent evidence shows that physical activity also exerts a meaningful regulatory effect on the gut microbiota. Exercise produces systemic physio- logical changes that alter the gastrointestinal environment [4–6], including modifications in body temperature, splanchnic blood flow, immune and hormonal signaling, and in- testinal motility. These shifts can influence the intestinal milieu and, consequently, the microbial communities that inhabit it. The concept of the exercise gut microbiota axis has emerged from these observations, highlighting the potential for exercise induced alter- ations in microbial composition and function to shape host metabolism, inflammation, and overall health [7–9]. Regular and moderate physical activity is associated with increased microbial diversity, greater abundance of short chain fatty acid producing taxa, and enhanced intestinal barrier integrity. These adaptations may contribute to improved metabolic efficiency, reduced inflammation, and greater neuroendocrine resilience. However, the relationship between exercise and the gut microbiota is complex and not always beneficial [10]. Excessive or very intense training can lead to increased intestinal permeability, microbial imbalance, and systemic inflammatory responses, effects frequently reported in endurance athletes, especially when combined with insufficient recovery or suboptimal nutrition [11–13]. Despite growing interest in this field, current findings remain inconsistent. Research varies widely in methodological design, microbial sequencing approaches, intervention duration and intensity, and participant characteristics such as diet and fitness level. Some studies report strong positive associations between physical activity and microbial diversity, while others observe minimal or short-lived changes, particularly in resistance based or brief interventions [14,15]. Many available studies rely on small or highly specific cohorts, which further limits generalizability [15,16]. The absence of standardized protocols for microbiota sampling and data interpretation also complicates comparison between studies and the development of firm conclusions [13,17]. These limitations highlight the need for an integrated and critical synthesis of existing evidence. Understanding how different exercise modalities influence the gut microbiota has important implications
on small or highly specific cohorts, which further limits generalizability [15,16]. The absence of standardized protocols for microbiota sampling and data interpretation also complicates comparison between studies and the development of firm conclusions [13,17]. These limitations highlight the need for an integrated and critical synthesis of existing evidence. Understanding how different exercise modalities influence the gut microbiota has important implications for both the general population and athletes, as physical activ- ity represents a promising non pharmacological strategy to support gastrointestinal and systemic health. The intersection of exercise physiology and microbiome science also offers new opportunities for personalized approaches to nutrition, recovery, and the prevention of metabolic and inflammatory disorders. This review summarizes current knowledge on how different types, intensities, and frequencies of physical activity influence gut microbiota composition and function. It outlines the physiological, metabolic, immune, and neuroendocrine mechanisms that may drive these changes, compares the effects of endurance and resistance training, and de- scribes both the beneficial and potentially harmful impacts of exercise on the gut ecosystem. The aim is to clarify key concepts, address inconsistencies in the literature, and highlight priorities for future research on the relationship between exercise and the gut microbiota. 2. Basics of the Gut Microbiota The microbiota refers to the microorganisms that inhabit a defined environment; in this context, the focus is on the human gut [18]. The gut microbiota is composed of bacteria, archaea, viruses, and eukaryotes. Among these groups, bacteria are the most abundant due to the favorable conditions for their growth. The dominant bacterial communities in the human gut are traditionally classified into seven major phyla: Firmicutes (Bacillota), Bac- https://doi.org/10.3390/gidisord8010001
Gastrointest. Disord.2026,8, 1 3 of 23 teroidetes (Bacteroidota), Fusobacteria (Fusobacteriota), Actinobacteria (Actinomycetota), Proteobacteria (Pseudomonadota), Verrucomicrobia (Verrucomicrobiota) and Cyanobac- teria (Cyanobacteriota) [19]. Among these, Bacteroidetes (Bacteroidota) and Firmicutes (Bacillota) together comprise more than 90% of the total bacterial population in the hu- man gut [20]. In addition to traditional taxonomic classification, the gut microbiota can also be described in terms of enterotypes. Enterotypes were proposed as a way to sum- marize the main characteristics of the human gut microbiota and to group individuals based on patterns in interindividual variation in microbial community composition [21–23]. Three enterotypes have been described. Enterotype 1 is dominated byBacteroidesand is commonly associated with a Western type diet rich in saturated fats and animal proteins. Enterotype 2 is dominated byPrevotella and is linked to a plant-based diet high in fiber and complex carbohydrates.Prevotella species are capable of producing vitamin B1 (thiamine) and participate in the degradation of mucin glycoproteins. Enterotype 3 is dominated byRuminococcus, one of the most frequently observed enterotypes in the human gut. This community type is associated with heme metabolism and the ability to degrade mucins [21–23] (Figure). However, several studies argue that this three enterotype model oversimplifies the human gut ecosystem. Rather than belonging to discrete and fixed groups, most individuals appear to fall along a continuum between these community types [24]. Figure 1.Human Gut Microbiota: Distribution Across Microbial Groups and Enterotypes. From a metabolic perspective, the gut microbiota participates in carbohydrate, lipid, protein and amino acid metabolism, as well as vitamin synthesis. Carbohydrates that escape digestion in the small intestine are fermented by gut microbes. Fermentation is a major energy source for the microbiota and produces short chain fatty acids [25]. Short chain fatty acids supply up to 10% of human caloric needs and contribute to gut barrier maintenance, immune modulation and neuroprotective functions. They also influence epigenetic regulation, immune pathways and central nervous system plasticity [26,27]. In lipid metabolism, the microbiota supports digestion by upregulating colipase, a protein required for fat breakdown, and participates in the regulation of fat storage by mod- https://doi.org/10.3390/gidisord8010001
needs and contribute to gut barrier maintenance, immune modulation and neuroprotective functions. They also influence epigenetic regulation, immune pathways and central nervous system plasticity [26,27]. In lipid metabolism, the microbiota supports digestion by upregulating colipase, a protein required for fat breakdown, and participates in the regulation of fat storage by mod- https://doi.org/10.3390/gidisord8010001
Gastrointest. Disord.2026,8, 1 4 of 23 ulating lipoprotein lipase activity [28]. In protein and amino acid metabolism, microbial proteinases and peptidases assist in digestion [29]. In addition to digesting carbohydrates, lipids and proteins, the microbiota contributes to the synthesis of vitamin K and several B vitamins, conversion of primary to secondary bile acids, and oxalate degradation [30,31]. The immunologic functions of the microbiota include several key roles. Microbial colonization after birth contributes to the development of gut associated lymphoid tissue. Microbes can induce pro-inflammatory or anti inflammatory responses. Activation of TLR MyD88 signaling increases the production of Th17 cells, which promote inflamma- tion [32–34]. Conversely, some organisms, such asClostridiumclusters andBacteroides fragilis, stimulate regulatory T cells that suppress inflammation. The gut microbiota also promotes IgA production by B cells and supports neutrophil priming, enhancing immune readiness [35–37]. The microbiota also contributes to structural integrity of the gut. Butyrate, a major microbial metabolite, increases the production of tight junction proteins and strengthens the intestinal barrier. It also stimulates goblet cells to produce mucin [38,39]. Certain bacteria then degrade mucin for nutrients, which in turn stimulates its regeneration [40]. Butyrate further promotes intestinal stem cell division and the renewal of epithelial cells. Microbiota also protect against pathogens by competing for nutrients and space, and some bacteria produce natural antimicrobial compounds [41,42]. The neurological functions of the microbiota include the production or modulation of neurotransmitters such as serotonin and dopamine. Microbes help maintain the integrity of the blood–brain barrier through regulation of tight junctions. Microbial metabolites can influence afferent nerve activity by binding to receptors on nerve endings and altering signal transmission [19,43–45]. Numerous factors influence gut microbiota composition. Lifestyle factors, especially diet, play a major role. Diets high in fat reduce microbial diversity and promote metabolic dysfunction, whereas fiber rich diets support beneficial microbial communities and reduce inflammation [46]. Enterotypes are strongly associated with dietary habits [47], and rapid microbiota shifts can occur following dietary changes [48]. Other lifestyle factors, such as stress, smoking, sleep patterns and physical activity, also influence microbiota composition. Physical activity, the focus of this review, alters the microbiota
and promote metabolic dysfunction, whereas fiber rich diets support beneficial microbial communities and reduce inflammation [46]. Enterotypes are strongly associated with dietary habits [47], and rapid microbiota shifts can occur following dietary changes [48]. Other lifestyle factors, such as stress, smoking, sleep patterns and physical activity, also influence microbiota composition. Physical activity, the focus of this review, alters the microbiota depending on exercise type and intensity, and this will be discussed in later sections [49–52]. Beyond lifestyle, host related factors strongly influence gut microbiota development. Mode of delivery is important; infants born vaginally are exposed to maternal microbiota that support immune development, while infants delivered by cesarean section acquire different microbial communities. Some studies associate cesarean birth with increased risk of obesity and diabetes, although findings remain inconsistent [53]. Breastfeeding exposes infants to bacteria present in maternal milk, which support early microbial development. Some evidence suggests that mothers who deliver by cesarean section have reduced micro- bial diversity in breast milk [54,55]. Chronic conditions such as inflammatory bowel disease and irritable bowel syndrome are associated with reduced microbial diversity [56], and medications, especially antibiotics, further diminish microbial richness [57,58]. Genetics also shapes the microbiota; monozygotic twins share more similar microbiota than dizygotic twins [59,60]. Sociodemographic factors, including geographic location, socioeconomic status and household environment, also contribute to microbial variation [61]. 3. Potential Mechanisms Exercise can influence the gut microbiota through multiple mechanisms, which can be broadly categorized into physiological changes, metabolic effects, and the actions of myokines. Physiological mechanisms include alterations in gut motility and blood flow, https://doi.org/10.3390/gidisord8010001
Gastrointest. Disord.2026,8, 1 5 of 23 which can impact microbial composition. Metabolic effects involve shifts in nutrient avail- ability and energy metabolism that create a favorable environment for certain microbial species. Myokines (bioactive molecules released by muscles during exercise) can further modulate gut microbiota composition and function, linking skeletal muscle activity directly to microbial health. Moreover, long-term exercise can positively influence several host factors that in turn affect gut microbiota. Regular physical activity has been shown to enhance immune function, improve sleep quality, regulate appetite and dietary habits, and reduce the risk of infections and medication use. These exercise-associated improve- ments may create a more favorable gut environment, supporting microbial diversity and metabolic health [62–68]. 3.1. Physiological Mechanisms Linking Exercise to Gut Microbiota Exercise can influence gut microbiota through several physiological mechanisms. One major factor is gut motility (transit time). Multiple studies indicate that exercise tends to increase gut motility, leading to more rapid passage of food through the colon. This can stimulate the release of gastrointestinal hormones, which may alter colonic pH and, in turn, affect microbial composition [62,63]. Visceral blood flow is another critical factor. During exercise, blood is preferentially redirected to active muscles, reducing perfusion to visceral organs. This transient hypoper- fusion can induce epithelial hypoxia and increase intestinal permeability. Upon restoration of blood flow, reactive oxygen species (ROS) may be generated, potentially damaging intestinal epithelial cells and further increasing permeability. Epithelial hypoxia can also trigger autophagy and reduce Toll-like receptor 4 (TLR4) expression, which may alter the gut microbiota composition and affect microbial functions related to lipid, nucleotide, and amino acid metabolism [64–66]. Finally, hyperthermia and dehydration associated with exercise can impact gut micro- biota. Exercise-induced increases in gut temperature may disrupt tight junction protein expression, leading to higher intestinal permeability. This, combined with fluid loss, con- tributes to dehydration. Elevated permeability and dehydration have both been linked to dysbiosis, impaired pathogen clearance, and reduced Th17 cell function and differentia- tion [65,67,68]. From a physiological perspective, exercise can modulate gut microbiota by increasing gut motility, altering visceral blood flow, and inducing hyperthermia and dehy- dration, all
leading to higher intestinal permeability. This, combined with fluid loss, con- tributes to dehydration. Elevated permeability and dehydration have both been linked to dysbiosis, impaired pathogen clearance, and reduced Th17 cell function and differentia- tion [65,67,68]. From a physiological perspective, exercise can modulate gut microbiota by increasing gut motility, altering visceral blood flow, and inducing hyperthermia and dehy- dration, all of which create a dynamic environment that influences microbial composition and function. 3.2. Metabolism-Related Mechanisms Linking Exercise to Gut Microbiota Exercise can influence the gut microbiota through metabolic mechanisms, with several metabolites acting as key mediators. One well-studied example is the interaction between lactate andVeillonellaspecies. During exercise, skeletal muscles produce lactate, which enters the bloodstream and can reach the gut lumen.Veillonellaspecies utilize lactate and convert it into short-chain fatty acids (SCFAs), mainly acetate and propionate [69,70]. These SCFAs serve as an energy source for colonocytes, regulate immune responses, and support gut barrier function, showing how exercise-induced metabolites directly shape microbial activity. In addition to lactate, exercise can influence other metabolite pathways, including bile acid metabolism. Physical activity can alter the abundance of bile-acid-metabolizing bacteria, such asClostridiumandBacteroides, many of which produce bile salt hydrolase (BSH), an enzyme that deconjugates bile acids and shapes the intestinal bile acid pool. Changes in BSH activity modulate FXR and TGR5 signaling, affecting lipid metabolism and energy homeostasis. For example, recent work has shown that inhibiting microbial https://doi.org/10.3390/gidisord8010001
Gastrointest. Disord.2026,8, 1 6 of 23 BSH increases conjugated bile acids, suppresses intestinal FXR signaling, and improves lipid metabolism in high-fat diet–induced obesity [68,69]. Exercise may also modulate tryp- tophan metabolism, supporting the production of microbial-derived indoles that regulate gut immune homeostasis and epithelial integrity [68–70]. Overall, these examples illustrate that exercise provides substrates and environmental signals that selectively enhance the growth and metabolic activity of certain gut microbes. Through these metabolic interactions, exercise contributes to shaping microbial composi- tion, functional output, and ultimately host physiology. 3.3. Myokine-Mediated Mechanisms Linking Exercise to Gut Microbiota In addition to physiological and metabolic effects, exercise can modulate the gut microbiota through myokines, which are bioactive molecules released by contracting muscles. There are hundreds of myokines with diverse functions, and some have been shown to influence the gut microbiota directly or indirectly [71]. Interleukin-6 (IL-6), which increases during exercise, can affect gut microbiota by stim- ulating glucagon-like peptide 1 (GLP-1) secretion and elevating levels of anti-inflammatory cytokines such as IL-10 and IL-1 receptor antagonist (IL-1ra). GLP-1 enhances glucose tolerance and may contribute to intestinal mucosal repair in conditions such as inflamma- tory bowel disease. Increases in IL-10 and IL-1ra are associated with reduced intestinal inflammation, which can favor a healthier microbial environment [72]. Irisin is another exercise-induced myokine that typically peaks up to 60 min after physical activity. Several studies have suggested that irisin may ameliorate dysbiosis- related conditions and exert anti-inflammatory effects in ulcerative colitis. It has also been reported to directly influence gut microbial composition by selectively increasing or decreasing the abundance of specific bacterial taxa. Moreover, mice lacking irisin display alterations in gut microbiota and exhibit anxiety- and depression-like behaviors, supporting the possibility of a gut–brain–muscle axis. However, irisin remains a highly controversial molecule. Questions persist regarding the specificity of commonly used antibodies, the reliability of circulating irisin measurements, and whether it is produced at physiologically meaningful levels in humans. Consequently, although emerging data suggest potential roles for irisin in gut homeostasis and host–microbe interactions, these findings should be interpreted cautiously until more rigorous and standardized measurement methods are established [73,74].
highly controversial molecule. Questions persist regarding the specificity of commonly used antibodies, the reliability of circulating irisin measurements, and whether it is produced at physiologically meaningful levels in humans. Consequently, although emerging data suggest potential roles for irisin in gut homeostasis and host–microbe interactions, these findings should be interpreted cautiously until more rigorous and standardized measurement methods are established [73,74]. Interleukin-15 (IL-15), which can be elevated for several hours following exercise, has anti-diabetic and immunomodulatory effects that may indirectly shape gut microbial composition by reducing inflammation and supporting host metabolic homeostasis [75]. Therefore, myokines produced by skeletal muscles can influence the gut micro- biota through multiple pathways: directly, by modifying microbial composition or pro- moting intestinal mucosal repair, and indirectly, by enhancing immune function and reducing inflammation. 4. Observed Patterns for Aerobic and Anaerobic Exercise Exercise influences gut microbiota in distinct ways depending on the type of activity. Aerobic exercise, such as running or cycling, generally promotes microbial diversity and beneficial metabolite production, while anaerobic (resistance) exercise induces subtler changes but may enhance pathways like mucin and butyrate synthesis. In this section, we summarize the observed patterns for aerobic and anaerobic exercise. https://doi.org/10.3390/gidisord8010001
Description
This review summarizes how exercise affects gut microbiota and implications for athlete health.