The list of things that are sterile is shrinking as DNA sequencing methods become more sensitive and are able to pick up microbial signals in even the sparsest environments. A news article in the Times discusses research on the microbiome of the human womb and the fact that it is not actually as sterile as most doctors have assumed in the past. Researchers have detected microbes living in amniotic fluid, which was often thought of as a sterile liquid. It is hypothesized that microbes may be entering the womb through the mother’s mouth or vagina. There is still little known about this system and how microbes interact with it, but it’s clear that the mother’s health affects the baby in yet another way. Personally, I find it amazing and awesome every time sequencing technology is good enough to find microbes in a place that seemed sterile to us using past techniques. Hopefully this isn’t just a case of contamination!
There are most definitely microbes in the uterus, absent pregnancy. These are not kit or reagent contaminants and are distinct from the vaginal flora of the same person at the same time. They are spatially structured within the upper reproductive tract (as one would expect).