This is a single-celled green algae rather than bacteria, but it still fits the spirit of OP’s question as it’s an example of high concentrations of a microbe in rain; the rare but officially-recorded phenomenon of red rain or “blood rain” seems to very likely be the result of an unusual bloom of the microalgae Trentepohlia in storm clouds, or at least that seems most likely from studies of recent instances of the phenomenon in Southern India. Exactly why this occurs is not understood, although it has been recorded multiple times in the same geographic areas.

There are, of course, anecdotal reports of “blood rains” in various parts of the world going back to antiquity, which could conceivably be due to the same algae or a similar one, but since those instances generally fall more into the realm of folklore and mythology at a certain point, I’ll save speculation on them.

EDIT: since the above hypertext is just a news article, here’s an actual paper on the subject. Just wanted to make sure I had something truly scientific in here, since this a subject that got taken up by ufologists and conspiracy theorists when it was first being reported in the ‘00s, and there was all sorts of wild speculation about the cells in the rain being extraterrestrial in origin (with no real basis, of course), so I figured detailed published research on the Trentepohlia theory from a reputable journal was needed. Also, it seems that most likely it isn’t an algal bloom in storm clouds so much as the cells being swept up in storms from aquatic environments on the surface.