The latest research points to there being not hundreds, but 1000's of strains of bacteria in our intestines (one report said 14,000). I'm leaning toward the idea that the reason probiotics aren't that helpful is b/c they only contain 8 or 10 or 14 strains, albeit in huge numbers of CFU's, but the bad guys really need dozens or hundreds of other strains surrounding them to keep them in check.
Yes, there are thousands of strains. This has actually been known for a long time. Back about 13 years ago I had read they identified about 4,000 strains. And it makes sense they have identified more since.
And yes, this is a bog problem with a lot of probiotic supplements. They only replace a small number of the thousands of strains of beneficial bacteria. This is why I prefer prebiotics for the long run to feed all the strains rather than just replacing a few. I addressed this in my Flora Garden write up: