This is an old question, but I just came across it. Obviously, there is a lot of research these days in relation to the human microbiome. Some even consider it as an organ. As you know a lot of stresses are associated with human spaceflight. To just name a few, confinement, workload, and exposure to the space environment (microgravity, radiation, increases CO2, etc). Therefore, few studies have been looking at these effects on the astronaut microbiome. It is still a new field but publications are slowly coming out. I would refer to the following two, one of which I was involved with. Additionally, we just submitted another one for peer review and should be out in a few weeks.

https://pubmed.ncbi.nlm.nih.gov/31289321/

https://pubmed.ncbi.nlm.nih.gov/32348348/

Finally a good set of papers just came out that provides a good summary of all effects on biological systems.

https://www.cell.com/c/the-biology-of-spaceflight