Most athletes think in terms of VO₂max, training zones and recovery gadgets. Fewer think about what is happening in their intestine when they eat, move and recover – and how this “invisible” system decides whether training pays off or leaves them chronically tired.
In a detailed German-language article for sportaerztezeitung, physician Dr. Henning Sartor describes the Darm–Sport-Achse – the gut–exercise axis. He shows how the microbiome and its metabolites influence inflammation, mitochondrial function and ultimately strength, endurance and motivation to move.
This post condenses his core ideas into a practical overview for athletes and active people.
From “silent intoxication” to “silent inflammation”
For years, chronic low-grade inflammation has been recognised as a driver of many long-term diseases and a brake on performance. Sartor argues that behind this silent inflammation often lies a more fundamental problem: silent intoxication – a continuous, low-level toxin load originating in the gut.
When digestion is incomplete and the intestinal environment shifts in an unfavourable direction, certain bacteria produce metabolites that burden the body instead of supporting it. These substances can damage mitochondria, the cellular power plants that fuel muscles and the nervous system. The result can be fatigue, loss of power, slower recovery and eventually neurological symptoms if the situation persists.
Why stool pH matters for athletes
One of the central points in Sartor’s article is the pH of the stool – essentially the acid–alkaline balance inside the intestinal lumen.
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A slightly acidic environment (around pH 6)
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typically linked to sufficient lactic acid and short-chain fatty acids (SCFAs) from fermentation of fibre and resistant starch.
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A more alkaline environment (pH >7)
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very common in Western lifestyles, often reflects a dominance of protein putrefaction and the production of so-called putrefactive toxins.
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In an alkaline milieu, proteolytic bacteria break down undigested protein into compounds such as ammonia, TMAO, phenols and indoles, many of which are toxic in a dose-dependent manner and can be carcinogenic.
Several of these metabolites impair mitochondrial function, including in heart and brain tissue, with direct consequences for endurance, cognition and coordination – all crucial for sport.
Acid-forming “good flora” vs. toxin-forming bacteria
The article highlights a kind of internal competition: Actinobacteria and other acid-forming microbes on one side, Proteobacteria and other proteolytic species on the other.
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Acid-forming bacteria thrive on carbohydrates and prebiotic fibres from vegetables, herbs and grains. They produce lactate and butyrate, helping to keep the environment mildly acidic and protecting the gut wall.
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Proteolytic bacteria prefer a more alkaline milieu and undigested proteins. In that setting, they generate putrefaction toxins that suppress the protective flora and promote inflammation.
Certain butyrate-producing bacteria such as Faecalibacterium prausnitzii are associated with anti-inflammatory effects in the gut and may protect against inflammatory bowel disease and colorectal cancer. Reduced levels of these species are linked to chronic inflammation and poorer gut integrity.
For athletes, this means that microbiome composition is not just a longevity topic – it directly influences how well muscles can perform and recover.
Slow transit, constipation and reduced performance
Another aspect Sartor discusses is slow transit constipation, which is widespread in Western populations due to low fibre intake.
When stool moves slowly and becomes hard and infrequent, toxins have more time to build up and interact with the gut wall. Over time this weakens the intestinal mucosa and its mitochondria, something Austrian physician F.X. Mayr already described as the problem of the “weak small intestine” in athletes and non-athletes alike.
Physical activity supports intestinal motility mechanically, but research also shows deeper effects: exercise influences blood flow to the gut, the release of muscle-derived signalling molecules (myokines) and the absorptive capacity of intestinal cells.
In other words, movement shapes the gut – and the gut shapes how far movement can take you.
Practical implications for training and nutrition
Taken together, the gut–exercise axis suggests a few clear priorities for anyone who cares about performance:
1. Optimise digestion, not just macros.
Eating slowly, chewing thoroughly and avoiding oversized, protein-heavy meals helps prevent undigested residues reaching the colon, where they would otherwise be turned into ammonia and other toxins.
2. Favour an acidic stool milieu.
A diet rich in resistant starches, fermentable fibres and fermented foods supports acid-forming flora and SCFA production, helping to move stool pH towards the protective range around 6.
3. Support regular bowel movements.
Daily, soft bowel movements indicate that transit time is reasonable and toxins are not accumulating unnecessarily. Fibre, hydration and regular movement all contribute.
4. Respect the brain–gut–motivation loop.
Emerging research suggests that gut-derived signals can even influence motivation to exercise via gut–brain pathways. A disturbed gut environment may therefore not only limit physical capacity, but also the drive to train in the first place.
The Upgraders® perspective
In his conclusion, Dr. Sartor describes a structured approach to correcting putrefactive dyspepsia and restoring a healthy intestinal milieu, referring to it as the Upgraders® Method – a combination of gentle dietary measures, bowel cleansing and targeted support of the acid-forming flora. The aim is simple: reduce toxic load from the gut, normalise stool pH and rebuild a microbiome that supports both health and performance.
For athletes, therapists and coaches, this gut-first perspective reframes performance as more than training volume and periodisation. Long-term strength, speed and resilience depend on what happens in the intestine – every single day.
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Source and further reading
This article is based on and inspired by the German-language piece “Darm-Sport-Achse – Gesundheit und Performance beginnt im Darm” by Dr. med. Henning Sartor, published in sportaerztezeitung. It summarises and adapts the scientific content for readers who prefer an English overview.
