Speciation and Phylogeny of Lactobacillus
generally, lactic acid bacteria (LAB) are the ones you should be looking at for milk-based fermentation products. although sometimes species like bifidobacterium are added, which is of a completely different phylum. also, for cheese production, or the Dutch variety I am familiar with anyway, you would need fungi as well. 

the lactobacillales order is not monophyletic, as you can see on the wiki page there are at least two different clades.

the wikipedia page 'Yogurt' speculates on the ecological niche of LAB: "Analysis of the L. delbrueckii subsp. bulgaricus genome indicates that the bacterium may have originated on the surface of a plant. Milk may have become spontaneously and unintentionally infected through contact with plants, or bacteria may have been transferred via the udder of domestic milk-producing animals." (source)

EDIT: the LAB are an order, they have been around for quite some time before the humans showed up.