I'm going to say this as delicately as possible, but some encounters with my wife "transferred" stuff from her to me. My GP did run a vaginal flora test out of curiosity a couple years ago (I think?), but all I remember is that he said it was "perfectly normal." So I assume that worked.
I've seen those studies on post-op vaginal flora, and they suffer from the same issue as most studies on trans people - there simply weren't a large number of people being studied. That doesn't mean the studies are *wrong,* necessarily, but it does mean that generalizing to the larger population is less likely to be accurate than when a substantial and representative sample size was achieved.
(Incidentally, the studies also tended to find that trans women who had penetrative sex had a much higher percentage of fecal bacteria in the vagina, which makes sense given the nearness of the structures. So if the study data IS generalizable, a) it may be partly a question of whether other bacteria are arriving to overwhelm a more limited population of "good" bacteria and b) trans women who do not have penetrative sex may be more likely to have cis-normal flora [this could, ahem, explain my results]. At the very least, this implies some suggestions: perhaps careful washing of *all* the relevant parts, including the anus, before and after sex and/or using the supplements shortly thereafter, for one thing.)