Not sure if the exact mechanism is known. There have been quite a few studies on this, you are welcome to do a review of the data. It would be interesting to know more about this.
I raised this in
my first blogpost, and it is a subject that interests me greatly. (Probably not everything in that post is right, but I was fumbling my way towards finding a solution, and throwing out ideas for discussion and consideration.)
As I said in that blogpost, a paper describing how exertion can increase intestinal permeability can be read
here. And that was in athletes.
Interesting that the microbiome can affect susceptibility to influenza (EDIT - referring to
@Kati's linked paper). I have recently been in hospital, where they gave me an antiviral and an antibiotic. Probable consequence - liquid diarrhoea - a messed up gut, and now I have the first bad cold or flu I have had for many years.
I think
@alex3619 is right when he says that it is not (EDIT - usually?) bacteria that cross the gut epithelium. It commonly includes lipopolysaccharides (LPS), doesn't it?