Effects of Exercise Training on Gut Microbiota Diversity: Energy Benefits of Short-Chain Fatty Acids

Preface: A Scientific Bridge from the Lab to Taiwan’s Roads

The human gut is home to trillions of microorganisms whose combined genetic material far exceeds that of our own genome, constituting a “second genome” that influences metabolism, immunity, and mood. Over the past decade, the intersection of exercise science and microbiology has revealed that exercise does more than reshape muscles and cardiorespiratory function—it also remodels the gut ecosystem. Athletes harbor more diverse microbiota, richer in short-chain fatty acid (SCFA)-producing species, and SCFAs (acetate, propionate, butyrate) serve both as an energy source for colonocytes and as signaling molecules that regulate systemic inflammation and metabolism. This article provides a cross-disciplinary analysis along the pathway of “exercise → microbial diversity → SCFA → energy and immune benefits.”

The Microbial Fingerprint of Elite Athletes

Barton, Clarke, and colleagues (Gut, 2014/2018 series) analyzed Irish professional rugby players against controls and found that athletes exhibited significantly higher α-diversity of the gut microbiota, an increased relative abundance of Akkermansia muciniphila (associated with metabolic health and intestinal mucosal barrier integrity), enhanced SCFA-related metabolic pathways, and higher fecal SCFA concentrations. Although athletes also consumed more protein, exercise remained an independent contributing factor after statistical adjustment. This illustrates that “diversity equals resilience”: a richer microbiota is better able to maintain homeostasis in response to dietary changes, travel, and antibiotic challenges, and is linked to superior metabolic and immune performance.

The Multifaceted Benefits of Short-Chain Fatty Acids

SCFAs are produced by the microbiota through fermentation of dietary fiber. Butyrate is the preferred energy substrate for colonic epithelial cells (supplying approximately 70% of their energy), maintains intestinal barrier integrity, suppresses pro-inflammatory pathways (NF-κB), and induces regulatory T cells (Tregs) to sustain immune tolerance. Propionate and acetate enter the circulation to participate in hepatic gluconeogenesis and peripheral energy metabolism, and even influence appetite and satiety via the gut-brain axis. For endurance athletes, healthy SCFA production helps reduce the exercise-induced increase in intestinal permeability (“leaky gut”) and the risk of endotoxemia during prolonged exertion, indirectly supporting long-distance performance and post-race recovery.

The Surprising Discovery of Veillonella and Lactate Metabolism

Scheiman et al. (2019, published in Nature Medicine) analyzed Boston Marathon runners and found that the relative abundance of Veillonella atypica increased after the race. This bacterium uses lactate as its sole carbon source, metabolizing the lactate produced during exercise into propionate. When this bacterium was transplanted into mice, their time to exhaustion on a treadmill increased by approximately 13%. This provides causal evidence that “the microbiota directly participates in athletic performance,” opening avenues for probiotic-based approaches to enhance endurance. Although translation to humans requires further validation, it is already sufficient to overturn the outdated notion that “gut bacteria only handle digestion.”

Prebiotics, Probiotics, and Postbiotics: Clarifying Concepts and Practical Applications

When discussing gut health, one often hears about probiotics, prebiotics, and postbiotics—three distinct entities. Probiotics are live beneficial bacteria (e.g., lactic acid bacteria in yogurt and fermented foods); prebiotics are dietary fibers that feed beneficial bacteria (e.g., inulin, resistant starch); and postbiotics are the beneficial metabolites produced by microbial fermentation (e.g., SCFAs) themselves. For athletes, the key is not to aggressively supplement with a single probiotic product, but rather to feed one’s existing microbiota through diverse fibers (prebiotics), allowing them to continuously produce SCFAs (postbiotics). Research shows that “diversity” of fiber intake is more effective at enhancing microbial diversity and SCFA production than single supplements. Dietary strategies should prioritize diverse whole foods—colorful vegetables and fruits, whole grains, legumes, and fermented foods—rather than relying on expensive probiotic capsules, whose strain- and dose-dependent benefits vary by individual and are often overstated.

Exercise-Induced Gastrointestinal Syndrome: The Gut Challenge of Long-Distance Exercise

Prolonged high-intensity exercise can induce “exercise-induced gastrointestinal syndrome”: blood flow is redistributed from the gut to muscles and skin, causing intestinal ischemia; elevated core temperature and mechanical vibration further compromise the intestinal barrier, leading to increased permeability, endotoxin leakage, and symptoms such as nausea, abdominal pain, and diarrhea. Costa et al. (2017) provided a systematic review detailing this mechanism. A healthy, diverse microbiota and an intact intestinal barrier help reduce the severity of such problems. Countermeasures include “gut training” in the weeks before a race (gradually adapting to in-race nutrition), active hydration during exercise to reduce intestinal ischemia, avoiding hyperosmolar or unfamiliar nutrition products, and building long-term gut resilience through a high-fiber diet. Understanding this mechanism helps long-distance athletes prevent late-race gastrointestinal collapse from a “microbiota–barrier” perspective.

Causal Challenges and Individual Variability in Microbiota Research

Gut microbiota research is exciting, but one must also recognize its scientific challenges. Most human studies are “associational”—the fact that athletes’ microbiota differ from those of sedentary individuals does not mean the microbiota “cause” performance differences (training and diet may jointly contribute). Animal transplantation experiments (e.g., Veillonella) provide causal evidence, but translation to humans is a stretch. Furthermore, individual variability in the microbiota is enormous; the same diet or exercise regimen can elicit different microbial responses in different people, limiting the efficacy of “one-size-fits-all” microbiota recommendations. Therefore, a rational attitude toward microbiota and exercise is: mechanisms and associations support the broad direction that “regular exercise and a high-fiber diet benefit the microbiota,” but do not expect a single probiotic product to work miracles, nor treat the microbiota as a universal explanation for performance. Cultivating a healthy microbiota over the long term through a diverse diet and regular exercise is the most robust personalized strategy.

A Cross-Disciplinary Perspective: The New Horizons Microbiology Opens for Exercise Science

Research on exercise and the gut microbiota represents a brand-new horizon that microbiology has opened for exercise science. It overturns the old notion that “the body consists solely of human cells”—we are “superorganisms” coexisting with trillions of microbes, and these microbial communities profoundly influence metabolism, immunity, inflammation, and even mood and performance. This cross-disciplinary integration extends the boundaries of exercise physiology from human cells to the symbiotic microbial ecosystem. From a metabolic standpoint, SCFAs provide energy and anti-inflammatory effects; from an immunological standpoint, the microbiota trains the immune system; from a gut-brain axis standpoint, the microbiota influences fatigue and mood; from a performance standpoint, specific species (such as Veillonella) may even directly enhance endurance. These connections illustrate that an athlete’s health and performance depend not only on their own physiology but also on the state of their microbial partners. This has given rise to the new field of “exercise microbiomics” and new strategies for supporting performance through diet-based microbiota care. Understanding this perspective allows us to view exercise and health through a more holistic, ecological lens—caring for the microbial ecosystem within us is caring for the foundation of metabolism, immunity, and performance.

From Research to the Training Ground: An Action Framework for Microbiota Care

Caring for an athlete’s gut microbiota can follow the “Diversify–Ferment–Adapt–Protect” framework. Diversify: consume a diverse range of dietary fibers daily (colorful vegetables and fruits, whole grains, legumes, and resistant starches such as sweet potatoes and taro), pursuing diversity of fiber sources rather than a single one, to support a rich microbiota and SCFA production. Ferment: incorporate Taiwan’s local fermented foods (kimchi, miso, fermented tofu, natural yogurt) as sources of live bacteria and postbiotics. Adapt: gradually increase fiber intake in the weeks before a race to allow the microbiota to adapt, avoiding sudden high-fiber intake on race day that could cause bloating; engage in “gut training” by progressively adapting to high-concentration carbohydrate nutrition during long training sessions to improve in-race tolerance. Protect: avoid unnecessary antibiotic use (to preserve microbial diversity), actively hydrate during exercise to reduce intestinal ischemia, and carefully test nutrition products to avoid gastrointestinal distress. For the common late-race gastrointestinal issues in Taiwan’s long-distance events (round-island rides, ultramarathons), this framework can systematically build gut resilience before the event. The core principle is: cultivate a healthy microbiota long-term through a diverse whole-food diet, rather than relying on expensive probiotic capsules—feeding one’s own microbiota is more aligned with the logic of symbiosis than supplementing with foreign bacteria.

Local Applications in Taiwan: Climate, Events, and Cultural Context

Taiwan’s dietary culture is quite friendly to the gut microbiota: resistant starches such as sweet potatoes, taro, and brown rice, as well as fermented foods like kimchi, miso, fermented tofu, and yogurt, are excellent substrates for SCFA-producing species. We recommend that cyclists and runners adopt a three-pronged approach: “high-fiber diverse vegetables and fruits + moderate fermented foods + regular aerobic exercise.” Gastrointestinal discomfort is common in Taiwan’s long-distance rides (round-island, Wuling), and is related to intestinal ischemia and increased permeability during prolonged exercise; strengthening fiber intake in the weeks before a race to build SCFA-producing capacity, and carefully testing nutrition products during the event to avoid gastrointestinal burden, are strategies worth adopting.

Taiwan’s ultra-long-distance events, such as round-island rides and ultramarathons, are popular, and exercise-induced gastrointestinal problems are a common race-ending threat. Combining the microbiota care and gut training recommendations in this article, athletes can systematically strengthen gut resilience in the weeks before an event and repeatedly rehearse in-race nutrition strategies during training, turning the gut from a race weakness into a manageable component.

Frequently Asked Questions and Myth-Busting

Myth 1: Taking probiotic capsules will improve your microbiota? Benefits vary by strain, dose, and individual, and are often overstated. Research shows that diverse dietary fiber (prebiotics) is generally more effective at enhancing microbial diversity and SCFA production than single probiotic supplements.

Myth 2: Athletes have better microbiota because they take supplements? It primarily stems from regular exercise and overall dietary patterns, not specific supplements. After statistically adjusting for diet, exercise remains an independent contributing factor.

Myth 3: The more fiber, the better? It should be progressive. A sudden large increase in fiber (especially before a race) can cause bloating and diarrhea; the microbiota needs time to adapt, and consistent long-term intake is the key.

How to Read Exercise Science Research: Developing Evidence Literacy

This article cites research from four international top-tier journals (such as Journal of Applied Physiology, Medicine & Science in Sports & Exercise, Sports Medicine, Nature, and Cell series), but as a reader, cultivating “evidence literacy” will help you absorb this knowledge more rationally rather than accepting it wholesale. First, distinguish study types: randomized controlled trials (RCTs) have the strongest causal inference, observational studies (cohort, cross-sectional) can only show associations rather than causation, and animal and cellular studies reveal mechanisms but require caution when translating to humans. Second, pay attention to samples and contexts: results from small samples or specific populations (e.g., elite athletes or specific age groups) may not apply to you; studies predominantly based on European and American populations also warrant consideration regarding applicability to Taiwanese populations. Third, emphasize effect size rather than merely “statistical significance”: statistical significance does not equal a practically meaningful benefit; ask “is this difference important in real training or health terms?” Fourth, be wary of over-extrapolation and commercialization: preliminary findings from a single study are often exaggerated into “miracle” products or methods; wait for replication and systematic reviews. Fifth, judge based on the “consistency” of mechanistic, associational, and interventional evidence, rather than rejecting everything because of one study’s flaws or accepting everything because of one striking result. Sixth, understand that “individual variability” is the norm in exercise science: the same intervention elicits different responses in different people due to genetics, training background, lifestyle, and environment; research presents group averages, so when applying to yourself, be sure to observe your own actual responses and adjust accordingly. Seventh, prioritize the “fundamentals”: sleep, nutrition, regular training, and recovery—these have overwhelming evidence support and clear benefits, and are always worth investing in before any novel supplements, equipment, or methods—many seemingly sophisticated interventions have marginal benefits far smaller than getting the basics right. Exercise science is a constantly evolving field; maintaining an open yet critical attitude, updating your understanding as evidence evolves, while respecting individual variability and valuing fundamentals, is the way to truly translate cutting-edge research from international journals into training and health decisions that are useful, safe, and sustainable for yourself—rather than blindly following trends or deferring to a single authority.

Key Takeaways

Synthesizing the cross-disciplinary research and mechanistic analyses above, the core points can be distilled as follows: Consume diverse vegetables, fruits, and whole grains daily, pursuing fiber “diversity” rather than a single source. Incorporate Taiwan’s local fermented foods (kimchi, miso, natural yogurt) as sources of live bacteria and postbiotics. Gradually increase fiber intake in the weeks before a race to allow the microbiota to adapt, avoiding sudden high-fiber intake on race day that could cause bloating. Regular aerobic exercise itself is a prebiotic behavior; the exercise–diet synergy is most effective. Use antibiotics judiciously, avoiding unnecessary use to preserve microbial diversity. Behind these points lies the convergence of multiple fields—sleep science, immunology, genomics, neuroscience, microbiology, endocrinology, and data science—which together convey a core message: the benefits and adaptations of exercise are the integrated result of multiple body systems working in coordination, not something captured by any single factor. Understanding this cross-disciplinary integrative perspective helps us move beyond fragmented “treat-the-symptom” thinking and view training, recovery, and health more comprehensively. Incorporating these principles into daily training and life, and dynamically adjusting based on individual circumstances, actual responses, and professional advice, is how to translate cutting-edge findings from top international journals into practices that are truly feasible, safe, and sustainable in Taiwan’s climate, events, and lifestyle context. The value of exercise science ultimately lies in helping every athlete—elite or amateur, young or old—enjoy sport more intelligently, more healthily, and more joyfully, and achieve physical and mental growth through it.

Practical Recommendations for Taiwanese Athletes

1. Consume diverse vegetables, fruits, and whole grains daily, pursuing fiber “diversity” rather than a single source.
2. Incorporate Taiwan’s local fermented foods (kimchi, miso, natural yogurt) as sources of live bacteria and postbiotics.
3. Gradually increase fiber intake in the weeks before a race to allow the microbiota to adapt, avoiding sudden high-fiber intake on race day that could cause bloating.
4. Regular aerobic exercise itself is a prebiotic behavior; the exercise–diet synergy is most effective.
5. Use antibiotics judiciously, avoiding unnecessary use to preserve microbial diversity.

Research Citations and Further Reading

• Barton, W., et al. (2018). The microbiome of professional athletes differs from that of more sedentary subjects. Gut, 67(4), 625–633.
• Clarke, S. F., et al. (2014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63(12), 1913–1920.
• Scheiman, J., et al. (2019). Meta-omics analysis of elite athletes identifies a performance-enhancing microbe. Nature Medicine, 25, 1104–1109.
• Mohr, A. E., et al. (2020). The athletic gut microbiota. JISSN, 17, 24.

This article is a translation of exercise science knowledge; individual physiological responses vary. For any training or intervention adjustments, please consult professional coaches and sports medicine physicians, and proceed gradually according to your personal health status.

Related Reading

• Gut Microbiota and Endurance Performance: How the Microbiome Affects Energy, Inflammation, and Recovery
• The Association Between Gut Microbiota Composition and Endurance Performance: A Study on Energy Supply from Short-Chain Fatty Acids
• Gut Microbiota and Endurance Performance: Your Gut Bacteria May Be Stealing Your Power
• Microbiome Research in Cycling: The Effects of Endurance Training on Gut Microbiota