Elite athletes know the difference between training at full tilt before a competition and easing back in the off-season, their bodies feel it, and now it turns out their guts do too.
Researchers at Edith Cowan University studied national-level rowers, finding that high training loads were linked to higher short-chain fatty acids (SCFAs) and more frequent bowel movements.
The team published their findings in the Journal of the International Society of Sports Nutrition.
Training load matters for the microbiome in athletes
Gut microbes, or microbiomes, matter for athletes. They help with digesting food, moving things along the gut and may affect performance by helping absorb nutrients. Studies now show that athletes’ gut microbiomes differ from those of the general public. They often have higher levels of SCFAs, a wider range of microbes and shifts in the types of bacteria that are most common.
Short-chain fatty acids (SCFAs)
Short-chain fatty acids (SCFAs) are compounds produced when gut bacteria break down fiber. They support gut health, provide energy for intestinal cells and may influence metabolism and immune function.
Those differences likely come from both diet and fitness. Athletes eat differently; however, training metrics may also be tied to those microbiome changes. Earlier work has pointed to specific bacteria that process lactate and to faster gut transit times during intense workouts. However, most of those studies took a snapshot of athletes at one time, and there is limited research on what happens when the same athlete moves from a high-training phase to a rest phase. Until now, few studies had followed the same athletes across different phases of training.
The recent study compared rowing athletes during high-load and low-load training periods to see how their microbiomes, SCFAs, diets and gut habits change.
Study links training load to microbiome, diet quality and gut function
The team followed 23 national-level rowers at 2 different points in their training. One phase was before a major competition, when training was at its highest, and the other was in the off-season, when training load dropped sharply. Each athlete logged food intake for three days, provided stool samples and wore monitors to track exercise duration and intensity.
Training during the high-load period was 147% longer and 130% more intense than in the low-load phase.
“During low training load times, or periods of rest, athletes are often more relaxed about their diets, in this study we saw no change in total carbohydrate or fiber intake during period of rest, but we did observe a decline in the diet quality of food eaten. This decline was related to increases in processed fast foods, decreases in fresh fruit and vegetables and a moderate increase in alcohol intake.
These changes did impact the composition of the gut microbiome,” said lead author Ms. Bronwen Charlesson, doctoral candidate at Edith Cowan University.
Gut function also changed between phases. Bowel movements were more frequent during the high-load phase, while nearly half of athletes (47%) in the low-load phase couldn’t provide a stool sample within 24 hours, compared to 8% during heavy training.
“Another observation made during the research was the significant slowing of gut transit times in athletes during low training loads. That slowing of transit time during the low training load appears to also be impacting the gut microbiome for an athlete,” Charlesson said.
Microbiome samples confirmed these shifts. SCFAs such as propionate and butyrate were higher during high training and bacterial diversity was lower. The ratio of Firmicutes to Bacteroidota dropped, and overall microbiome types remained stable, except for one athlete.
Bacterial diversity was slightly higher during the low-training phase, even though beneficial fatty acid levels were lower.
Implications of microbiome changes for athlete health and performance
The changes seen in the study weren’t random; when athletes trained hard, they produced more SCFAs – compounds linked to gut health and metabolism. Since the gut may play a role in processing lactate during high-intensity exercise, these shifts could matter for performance – linking training physiology with microbiome activity in a way that hasn’t been fully explored.
However, the sample was small, and some athletes dropped out during the low-training phase. Diets also were not strictly controlled, which makes it harder to separate the effects of training from food. Other factors, such as stress, sleep or hormonal cycles weren’t tracked, and they may also shape the microbiome.
“Future studies that assess the composition of microbiome and metabolic pathway activity would be beneficial to deepen insights into the relationship between training load, transit time, diet quality and the composition of gut microbiome in highly trained athletes,” said the team.
Understanding those links may eventually help tailor diet or training strategies to maintain gut health and performance through different phases of training.
Reference: Charlesson B, Jones J, Abbiss C, et al. Training load influences gut microbiome of highly trained rowing athletes. J Int Soc Sports Nutrit. 2025;22(1):2507952. doi: 10.1080/15502783.2025.2507952
This article is a rework of a press release issued by Edith Cowan University. Material has been edited for length and content.