In my opinion, gut microbiome stuff is massively overhyped.
Here's a study that tried fecal transplants to treat mental illness (and found no effect): https://pubmed.ncbi.nlm.nih.gov/41785480/
The pattern with this stuff is that, when a blinded study is carried out, there's usually no effect.
Can you link the data? I don't buy it.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11720530/ says there's a higher rate of AF in older, male althetes but a lower risk of stroke compared to similar aged, non-athletes.
At any rate, the data doesn't seem clear enough to claim that "distance running bad for you" or "any distance over 50K is bad for you".