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Physical activity  has an effect on the composition of gut bacteria. The main result being an increased diversity of the gut microbiota diversity and changes in the ratio between certain major types of bacteria.

For example, in one study on humans it was show that individuals with higher levels of physical activity have significantly greater microbial diversity in their stool; specifically the Firmicutes to Bacteroidetes ratio was greater in professional male athletes compared to two control groups. Interestingly, exercise alone increased the ratio of Firmicutes to Bacteroidetes, independent of diet.