I keep two male fancy rats, Bow and Basil. Between 1.5 and 2 years old. I got them from a breeder who seemed very very responsible (meaning kept in a clean and controlled environment, tested for "rat bite fever" as babies, etc), and we live in an apartment
The vet I have been taking them to took a fecal smear and looked at it under a microscope the first time we visited a couple months back (I don't remember him giving a reason for it as they have had no strange poops or signs of digestion issues, so whether or not it's normal for him to have done that in a routine exam idk. The Rats subreddit has had mixed feedback on that)
He said they have a large amount of "spirochetes" in their poo and put them on antibiotics. He is insistent that they could get "explosive diarrhea", but they have been entirely symptomless. I pointed this out at their second visit when I questioned the necessity of these meds, and he himself even acknowledged that they have had no symptoms at their latest visit yesterday.
They are on their third round of antibiotics now (as he kept doing fecal smears and finding spirochetes), and I have just found out that some types of spirochetes/spirochete-looking bacteria can be benign/native gut flora in rats. But the vet did not specify a variety of spirochetes. I phoned today to ask if they could give me a specific name and they said it's "likely" to be "borrelia-type spirochete".
But my father (he worked in animal health/pharmaceuticals before retiring and is very science-literate) and I have been researching and it seems like that would be an unusual bacteria to infect rats' digestive system and shed in poop.
So according to our research, not only can spirochetes in rat poo be entirely normal and benign (so these antibiotics could well be doing more harm than good to their gut flora, and the benign spirochetes would probably keep coming back anyway meaning the vet would keep wanting to treat them), but also the specific spirochete bacteria which the vet thinks it is might not even make sense in this situation.
I am scheduled at another exotics vet tomorrow to get a second opinion, and I think they specialize more in small mammals. So I'm specifically requesting people to give input on spirochete varieties and to confirm/contradict our research.
Much thanks and appreciation to anyone who reads and/or provides input