Most people are aware that the vagina has a natural population of various microorganisms, the same way the rest of our bodies do. (Random fact from your hostess the microbiology student: there are about 13 trillion cells in the human body, while there are about 14 trillion bacterial cells living on the skin alone, as a normal, healthy population. That doesn't include fungi. Fully 10% or something of dry body mass is bacteria-- that is what, 10-20 pounds of germs?)
Anyhow, the only bacterial species native to the vagina that I can name is Lactobacillus vaginalis. Other lactobacilli also inhabit the vagina. These are lactic-acid producing bacteria, and are largely responsible for the acidic pH in the vagina. Candida albicans is the yeast that causes yeast infections, but it can live peacefully in the vagina as well. My last pelvic exam indicated that there was Candida in me, and I have never had a yeast infection.
Among other things, the populations of these microbes provide competition to prevent other random pathogens from setting up home in the vagina. This is a very efficient way of staying free of harmful infections. Antibiotics and other factors can reduce the populations of friendly flora in the vagina, providing opportunities for particular microorganisms to reproduce and get out of balance. This is a common cause of yeast infections.
I've heard eating yogurt recommended to women fighting yeast infections. Presumably this is to help re-establish the normal bacterial populations (active yogurt contains both Lactobacillus and Acidophilus species). I don't really see how eating these bacteria would help them get to the vagina, but then by most logic they shouldn't even be able to get past stomach acid into the intestines, which they do.
I do know that various microorganisms can be spread from the bowel to the vagina, given the lovely moist crevice that joins the anus and the mouth of the vagina. This is apparently another way that yeast infections can be started (and a possible roundabout way for yogurt bacteria to finally get to the vagina? I hope not). When tampon manufacturers were first pushing their products in the US in the 30s, they claimed that pads promoted the transfer of yeast and other things between the anus and the vagina. I don't know how substantiated that is, but some gynecologists do recommend that patients prone to yeast infections stay away from brands of pads with plastic "topsheets" (ie: Always), which are more likely to get sweaty and wet. I do know that grooming habits are important: only wipe front to back, including when changing babies.
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