In 2015, a research team at Harvard asked a group of Boston Marathon runners for an unusual favour: daily stool samples, starting a week before the race and ending a week after it. The analysis turned up one genus of bacteria, Veillonella, whose numbers jumped right after the marathon. When the team gave a strain of it to mice, the animals ran about 13% longer on a treadmill before exhaustion.

That study, published in Nature Medicine in 2019, made headlines around the world. It also started a wave of articles claiming that gut bacteria are the hidden secret of elite athletes. Some of those claims hold up. Others stretch mouse data into promises for humans.

This article looks at what the strongest evidence says today: meta-analyses, systematic reviews and position statements from sports nutrition societies. Where the data come from animals, I say so. Where an effect is small, I give the number. After 31 years treating athletes, I have learned that the gap between a good headline and a good recommendation can be wide.

 

What Is Different About an Athlete’s Gut?

Your large intestine hosts trillions of bacteria, along with fungi, viruses and other microbes. Together they ferment the fibre your own enzymes cannot digest. The main products of this fermentation are short-chain fatty acids (SCFAs): acetate, propionate and butyrate. Butyrate is the preferred fuel of the cells that line the colon. Propionate travels to the liver, where it can be used to make glucose. All three send signals to the immune system and help keep the gut wall tight.

The largest synthesis on physical activity and the microbiome so far is a 2024 systematic review and meta-analysis by Pérez-Prieto and colleagues in the Journal of Science and Medicine in Sport. It included 91 studies. Most of them found more SCFA-producing bacteria, such as Akkermansia, Faecalibacterium, Veillonella and Roseburia, in active people and after exercise programmes. Athletes also seemed to carry a richer microbial community than non-athletes. The authors were careful, though. The studies differed so much in design and lab methods that they could not draw firm conclusions (Pérez-Prieto et al., 2024).

A second 2024 meta-analysis, by Min and colleagues in Nutrients, looked only at controlled exercise trials in adults. Exercise raised the Shannon index, a standard measure of how varied the microbial community is. The effect, however, was tiny: a weighted mean difference of 0.05, right at the edge of statistical significance (p = 0.05). Women and older adults showed larger changes. Other diversity indices, such as Simpson and Chao1, did not change (Min et al., 2024).

So yes, training moves the microbiome. The shift is real but modest, and it builds over months, not days.

 

Does the Type of Sport Matter?

A 2024 meta-analysis from Sapienza University in Rome, led by Ghaffar, screened 1,318 studies and pooled the 10 that met its criteria. Both the type and the intensity of exercise changed the ratio between two major bacterial groups, Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) (Ghaffar et al., 2024). Endurance training and strength training seem to leave different fingerprints in the gut.

Here we need to separate training from food. A 2024 narrative review by Chen and colleagues in Nutrients points out that professional athletes eat more total energy, more protein and more fibre than the sedentary people they are usually compared with (Chen et al., 2024). Part of the “athlete microbiome” may simply be the “athlete diet”. Most cross-sectional studies cannot tell the two apart, because they record diet poorly or not at all.

 

Veillonella and Lactate: The Marathon Study Up Close

The study by Scheiman and colleagues deserves a closer look. It is the most quoted study in this field, and also the most misquoted.

The team collected stool samples from 15 marathon runners and 10 sedentary controls. Veillonella was the genus that changed the most from before to after the race. Runners seemed to carry more of it than sedentary people at baseline, but that difference was not statistically significant.

Veillonella has an unusual diet. It lives on lactate. During hard exercise, muscles release lactate into the blood. Using labelled lactate in mice, the researchers showed that lactate from the bloodstream crosses the gut wall and reaches the intestinal lumen. There, Veillonella converts it into propionate.

Then came the key experiments. Mice given Veillonella atypica isolated from one of the runners ran about 13% longer than mice given Lactobacillus bulgaricus, a bacterium that cannot use lactate. Mice that received propionate directly into the colon showed a similar gain. In a separate group of 87 ultramarathon runners and Olympic-trial rowers, the bacterial genes that process lactate became more active after exercise (Scheiman et al., 2019).

Figure 1. The lactate–propionate loop described by Scheiman et al. (2019). The performance effect was shown in mice, not yet in humans.

What this study does not show matters just as much. The 13% figure comes from mice on a treadmill, not from human runners in a race. Some articles report that runners with more Veillonella were “13% faster in time trials”. The paper does not say that. No human trial published so far has shown that taking Veillonella makes people faster.

The study remains excellent biology. It describes a plausible loop: exercise produces lactate, gut bacteria turn lactate into propionate, and propionate returns to the body as fuel. Whether that loop changes race times in people is still an open question.

 

How Diet Shapes the Athletic Gut

Training changes the microbiome slowly. Food changes it within days. For an athlete, the menu is probably the strongest lever available.

Hughes and Holscher, in a 2021 review in Advances in Nutrition, describe two directions of influence. Sports-focused diets, such as high protein intake or carbohydrate loading, affect gut bacteria. Gut-focused strategies, such as probiotics and prebiotics, may in turn affect performance (Hughes & Holscher, 2021). Most athletes think only about the second direction. The first one probably matters more.

 

Low-Carbohydrate, High-Fat Diets

The best data come from elite race walkers in Australia. In the study by Murtaza and colleagues, 21 male athletes followed one of three diets during three weeks of intensified training: high carbohydrate, periodised carbohydrate, or a ketogenic low-carbohydrate, high-fat diet. The ketogenic group showed more Bacteroides and Dorea and less Faecalibacterium, one of the main butyrate producers in the human gut (Murtaza et al., 2019). That same group lost exercise economy and did not improve its 10-km race time, while the two carbohydrate groups did.

Three weeks and 21 athletes make a small study. Still, the result fits what we know about gut ecology: bacteria that make butyrate need fermentable carbohydrate to work.

 

High Protein, Low Fibre

Strength athletes often eat a lot of protein and fewer plant foods. When large amounts of protein reach the colon and fibre is scarce, bacteria shift toward protein fermentation, which produces compounds such as ammonia and some phenols. The reviews by Hughes and Holscher and by Chen and colleagues both flag high-protein, low-fibre patterns as a concern for long-term gut health. Protein is not the problem. The missing fibre is.

 

Fibre, Plants and the Mediterranean Pattern

The European Food Safety Authority considers 25 grams of fibre per day adequate for normal bowel function in adults. Many athletes eat less, especially before races, when a low-fibre diet helps reduce bathroom stops. That short-term strategy makes sense. The problem starts when it becomes the everyday diet.

Different fibres feed different bacteria. Oats, beans, lentils, onions, whole grains, fruit and cooked-then-cooled potatoes each bring their own mix of fermentable material. Variety matters more than one large dose of a single fibre supplement. The Mediterranean pattern, rich in vegetables, legumes, olive oil and fish, fits these principles well; I covered it in more detail in the article on the Mediterranean diet and gut health.

 

When the Gut Struggles During Exercise

Ask any marathon runner or triathlete about stomach problems and you will hear stories: cramps, nausea, urgent stops, sometimes blood in the stool. Costa and colleagues gave this a name in a 2017 systematic review in Alimentary Pharmacology & Therapeutics: exercise-induced gastrointestinal syndrome (Costa et al., 2017).

During hard exercise, blood moves away from the gut toward the working muscles and the skin. The gut lining receives less oxygen. As intensity and duration rise, markers of intestinal damage, gut permeability and endotoxaemia (bacterial fragments in the blood) rise as well. Gastric emptying slows and absorption gets worse. Heat makes all of this worse, and so does running compared with cycling, probably because of the repeated impact. In the review, significant disturbances appeared above a threshold of roughly two hours at 60% of VO2max, whatever the athlete’s fitness level.

The same review brings good news: in healthy people these changes are reversible. The gut recovers after the effort.

This is where the microbiome and gut health meet. A leaky barrier lets bacterial products into the bloodstream, which triggers inflammation. The International Society of Sports Nutrition notes that some specific probiotic strains can improve gut barrier function in athletes during prolonged exercise in the heat (Jäger et al., 2019). “Some specific strains” is the key phrase, and I will come back to it.

 

Training the Gut

Sports dietitians now speak of “training the gut” in the same way coaches speak of training the legs. The stomach and intestine adapt to what they receive. An athlete who never eats during long sessions and then tries to take in 60 to 90 grams of carbohydrate per hour on race day is asking an untrained gut to do something new under stress. Repeating race-day fuelling in training helps the gut tolerate it. When you eat counts too, a topic covered in the article on nutrient timing in sports nutrition.

Measures with better support include training the gut by practising race-day fuelling during long sessions, following a hydration plan, using cooling strategies in hot weather, and asking your doctor before taking anti-inflammatory painkillers around long events.

 

Probiotics for Athletes: What the Trials Actually Show

 

Infections and Immunity

Athletes in heavy training catch more colds than people who train moderately. A 2021 meta-analysis of 14 randomised controlled trials by Łagowska and Bajerska in the Journal of Athletic Training tested whether probiotics help. Probiotics did not reduce the number of days of illness, nor the number or duration of respiratory infection episodes. They did lower the severity of symptoms (Łagowska & Bajerska, 2021).

In plain words: an athlete taking probiotics probably catches colds as often as before, but the colds may be milder. Claims of a 30% drop in infections, common online, are not supported by the pooled data.

 

Performance

The newest and largest analysis on performance is a 2026 Bayesian meta-analysis by Zhang and colleagues in Frontiers in Nutrition. It pooled 21 randomised trials with 685 healthy participants. Overall, probiotics produced a small-to-moderate improvement in performance, with a standardised mean difference (SMD) of 0.38. The clearest gains were in aerobic endurance (SMD 0.74). Strength, sprint speed and agility did not improve significantly (Zhang et al., 2026).

Figure 2. Effect of probiotics on performance in the Bayesian meta-analysis by Zhang et al. (2026). Blue bars do not cross zero; the grey bar does.

What does an SMD of 0.38 mean in practice? It means that, on average, the probiotic groups scored about a third of a standard deviation better than the placebo groups across different performance tests. For a recreational runner, that could be the difference between fading and holding pace in the last kilometres of a long run. For an elite athlete, whose results already sit at the edge of human capacity, the same shift may be harder to detect. An effect of this size is worth knowing about. It is not a reason to expect dramatic changes.

Three details from this study are useful in daily practice:

• Only the medium dose range, from 1 billion to 100 billion colony-forming units (CFU) per day, gave a reliable effect.
• Among single strains, only Lactobacillus plantarum showed a significant effect (SMD 0.82).
• Benefits were visible after about 30 days and were largest at around three months of use.

The authors rated the overall certainty of evidence as moderate, and lower for several subgroups, including athletes.

 

Who Seems to Benefit?

In the same analysis, the effect was significant both in trained athletes (SMD 0.38) and in non-athlete adults (SMD 0.46). The one trial in older adults was too small to conclude anything. Single-strain products (SMD 0.33) and multi-strain products (SMD 0.45) both worked, with a slight edge for the mixtures. Low doses and very high doses did not show a reliable effect, which suggests that more is not always better.

This pattern makes biological sense. A probiotic does not settle permanently in most people’s gut. Whether it has an effect depends on the bacteria already living there and on what the person eats. Two athletes taking the same capsule can respond in very different ways, and trials with 20 or 30 participants struggle to capture that variability.

A 2025 meta-analysis by Shirkoohi and colleagues in Physiological Reports (35 studies, 1,336 participants) found lower creatine kinase, a marker of muscle damage, and a VO2max gain of about 1.5 mL/kg/min with probiotics (Shirkoohi et al., 2025). Here too, the authors judged the certainty of evidence as low to very low.

Not every trial is positive. Several trials in runners and cyclists found no change in time to exhaustion or race time, even when gut symptoms improved during the race.

 

How to Read a Probiotic Label

The ISSN position stand makes a point that marketing tends to ignore: probiotic effects depend on the strain and the dose. The word “Lactobacillus” on a label tells you about as much as the word “dog” tells you about a specific dog’s temperament. A serious product lists genus, species and strain, for example Lactiplantibacillus plantarum TWK10, together with the number of live bacteria guaranteed at the end of shelf life, not at the time of manufacture. Overall, the ISSN describes the evidence for athletes as modest. For more on specific strains and recovery, see the article on probiotics and athletic recovery.

 

The Gut-Brain Link: Motivation to Move

One of the most surprising findings in this field comes from a 2022 study in Nature by Dohnalová and colleagues. In mice, gut bacteria produced endocannabinoid-related molecules that activated sensory nerves carrying the TRPV1 receptor. Those nerves raised dopamine levels in the ventral striatum, a reward area of the brain, during exercise. Mice with this pathway intact ran more. When the researchers depleted gut bacteria with antibiotics, blocked the receptors or cut the nerve signal, much of the running capacity disappeared (Dohnalová et al., 2022).

The authors suggest that part of the pleasure we feel during exercise may start in the gut. It is an elegant idea, and so far it is a mouse result. A 2024 narrative review by Xia and colleagues in the Open Access Journal of Sports Medicine discusses how this gut-brain axis might connect diet, mood and training (Xia et al., 2024). Human data on this pathway are still thin.

 

Practical Steps Supported by Current Evidence

Based on the reviews above, this is what I would tell an athlete today:

• Eat enough fibre most days, from many plant sources. Reduce it only in the 24 to 48 hours before a race if you tend to have gut trouble.
• Do not cut carbohydrates hard during heavy training blocks. The race-walker data suggest that both the microbiome and performance may suffer.
• Include fermented foods such as yogurt, kefir, sauerkraut or kimchi. Evidence for a direct performance effect is weak, but they are safe and add microbial variety. More on this in the article on fermented foods and gut health.
• If you try a probiotic, choose one with a named strain that has been tested in active people, take a dose between 1 and 100 billion CFU per day, and give it at least four weeks before judging.
• In hot conditions and long events, rehearse your race fuelling in training and follow a drinking plan.
• Do not take antibiotics you do not need. When a doctor prescribes them, complete the course.

Gut symptoms that do not go away, blood in the stool or unexplained weight loss need a medical visit, not a supplement. For probiotics in digestive disorders, see the article on probiotics for irritable bowel syndrome.

 

Where the Evidence Stops

A 2025 systematic scoping review of high-level athletes in Frontiers in Sports and Active Living reached a candid conclusion: we do not yet have a clear picture of how the microbiome and sport interact (Frontiers scoping review, 2025). Most studies are small, short and cross-sectional. They use different sequencing methods. Many do not control for diet. Much of the mechanistic work comes from mice.

The next step is clear enough. Researchers need larger trials that run for months, record what athletes eat, use the same performance tests and name the exact probiotic strain and dose. Until those trials exist, any strong promise about gut bacteria and medals runs ahead of the data.

Personalised microbiome tests sold to athletes go well beyond this evidence. A stool test can describe which bacteria are present today. It cannot yet tell you which training plan or supplement will make you faster.

What we can say is narrower and more useful. Regular training nudges the gut toward more SCFA producers. Fibre and adequate carbohydrate keep those bacteria fed. Hard endurance work in the heat stresses the gut barrier, and the gut recovers. Selected probiotic strains, at the right dose and for long enough, may give a modest boost to endurance and soften respiratory symptoms. For a wider view of how gut bacteria relate to inflammation across the lifespan, read the article on gut microbiota, inflammation and ageing.

 

References

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