But it is still not clear exactly how exercise leads to changes in the community of microorganisms living in our guts, although there are several theories, says Woods.
“Lactate is produced when we exercise, and this could be serving as fuel for certain bacterial species,” he says. Another potential mechanism, he explains, could be through exercise-induced alterations in the immune system, especially the gut immune system, as our gut microbes are in direct contact with the gut’s immune cells.
Exercising also causes changes in blood flow to the gut, which could affect the cells lining the gut wall and in turn lead to microbial changes. Hormonal changes caused by exercise could also cause changes in gut bacteria. But none of these potential mechanisms “have been definitively tested”, says Woods.
Some elite athletes often suffer from exercise-induced stress due to the high-intensity training they do. As many as 20-60% of athletes suffer from stress due to overtraining and inadequate recovery, according to some estimates. But the bacteria in our guts could help control the release of hormones triggered by exercise-related stress, while also potentially helping to release molecules that improve mood. They can also help athletes with some of the gut problems they experience. Further research is however needed in this field.
But there is still much more we can learn about how our physical activity affects the creatures living inside our guts, such as how different types of exercise and its duration might alter the microbial community. It may also differ from individual to individual, based on their existing gut residents as well as BMI and other lifestyle factors, such as their diet, stress levels and sleep.
As scientists continue to tease out more of the secrets hidden within our gastrointestinal tracts, we may find new ways to improve our health through the bustling and diverse communities of organisms that call us their home.
If you liked this story, sign up for the weekly bbc.com features newsletter, called “The Essential List” – a handpicked selection of stories from BBC Future, Culture, Worklife, Travel and Reel delivered to your inbox every Friday.