I've been doing a ton of research on probiotics and the human microbiome lately, and the more I've learned, the more convinced I've become that the nearly universal dominance of lactobacillus strains in probiotics is 90% marketing, 10% evidence.
It makes sense from a historical perspective, as lactobacillus strains have been used for centuries to make cheese and other cultured foods. But if you look at the research on the actual role of lactobacillus in the body, the results are shocking. As the latest study from the Human Microbiome Project shows (http://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Nature_HMP_061312.pdf), lactobacillus only dominates the vagina (Figure 3b, above link). Bacteroides dominates the colon.
I think this is worth pointing out because when people take probiotics, they think they are repopulating their GI tract with the good bacteria that naturally reside there. But the latest evidence shows that lactobacillus really has a very small presence in the GI tract, and competitive inhibition will always keep it in that small population.
I have a feeling that in the future probiotics will diverge greatly from the dominance of Lactobaccillus and Bifidobacterium and include Bacteroides and other genera much more frequently. There is one probiotic called Prescript-Assist that does include Bacteroides, it's the one I'm currently using.
I'm not discouraging anyone from taking Lactobacillus probiotics if they're feeling a benefit, just pointing out that the Science seems to be moving in another direction.