I was involved in this field some years ago now, in one of the first randomized trials that assessed gut microbiome changes as response to aerobic exercise (with a very small effect size). Back then i felt all the evidence for exercise changing the microbiome was quite weak.

At the time most of the evidence was observational or mice running on treadmills with very little actual randomised human evidence. The ones that were high-quality intervention studies with control groups showed very small effects. Additionally, they were always done for another primary outcome, so they never controlled for stuff like people who bike more every day will also eat more.

I think it is plausible that exercise will change the microbiome, from personal experience high-intensity running for instance will increase the transit time of feces, a major determinant of the microbiome. But i believe most of the studies are low-quality and overhyped, and a glance at this review seems to indicate that the field has not changed much.