From a livestrong article. I plan to pare it down to a simple list.
A number of microbes in the Lactobacillus family are considered to be probiotics. The University of Maryland Medical Center says that Lactobacillus acidophilus is the probiotic that consumers use most often. This friendly bacteria can live in the intestines, leaving less space for harmful bacteria to take over. Lactobacillus bacteria also digest food in the intestines, and the byproducts of this process make the intestinal environment less attractive to harmful bacteria. Lactobacillus acidophilus is present in enriched milk, yogurt, miso and tempeh, and also is available as a supplement in capsules at natural foods distributors. Probiotics such as Lactobacillus acidophilus are generating a lot of interest from health care researchers, and scientists at Stanford University School of Medicine have stated that gastric bypass patients who consume these friendly bacteria lose more weight than those who do not.
Bifidobacteria is a type of probiotic that is present in kefir, a fermented milk beverage first consumed in the Caucasus Mountains of Russia thousands of years ago. Acidic and slightly carbonated, kefir sometimes is used in soups, sauces and cakes. Consumption of products containing bifidobacteria helps to improve the microfloral population of the colon. This probiotic may be helpful in relieving the diarrhea and constipation experienced by those with irritable bowel syndrome. Dr. Peter Whorwell, of the University of Manchester, reported in the "American Journal of Gastroenterology" in July 2006 that after four weeks of taking Bifantis, a freeze-dried, encapsulated source of bifidobacteria, patients with irritable bowel syndrome showed significant alleviation of abdominal pain, bloating and bowel dysfunction.
Some streptococcal bacteria are associated with infectious diseases. Others are more closely related to delicious dairy products. Varieties of Streptococcus thermophilus, for example, are commonly found in yogurt, as well as cheddar, Emmental and Italian cheeses, while Streptococcus diacetilactis is found in sour cream, butter and buttermilk. The University of Maryland Medical Center notes that probiotics, such as Streptococcus thermophilus, may help prevent infections in the genital and urinary tracts, but notes that more research is needed to confirm the benefits of probiotics in alleviating these types of conditions.
Streptococcus diacetylactis. This is in a probiotic supplement powder called AviBios I got for free (donation to the wildlife center) it's intended for birds. The livestrong article says it's found in sour cream, butter and buttermilk. I haven't found any info on it's benefits.
A nice article listing various bacteria including those involved in sourdough http://kitchenscience.sci-toys.com/biology
It also lists antimicrobial activity of many herbs and spices. Such as garlic, onions, chamomile for e. coli.