In a study with mice, mice that exercised had significantly higher amounts of a specific type of good gut bacteria than sedentary mice that were fed the same diet.
Studies on humans show that exercise increases gut bacteria richness and diversity.
Rats that exercised produced more butyrate than rats that did not. Butyrate is a short chain fatty acid, produced by the beneficial bacteria in the gut. Butyrate protects your gut lining, therefore it is better at keeping invaders while simultaneously giving your mitochondria their preferred food sources.
There is a strong connection between exercise and the microbiome. The more we exercise, the more butyrate is produced, which feeds our healthy gut bacteria and increases the health of our microbiome, which improves our overall health and longevity.