Speciation and Phylogeny of Lactobacillus The lactobacillus, also called Döderlein's bacillus is a genus of facultative aerobic bacteria. There are several species such as Lactobacillus acidophillus and Lactobacillus reuteri. I have several questions, all linked, for the concern of speciation of bacteria species used for lactic fermentation by humans. * Are all species that are used for cheese and yoghurt fermentation part of the genus Lactobacillus? * Do all species used for cheese and yoghurt fermentation form a monophyletic clade? * Did the speciation of this clade occurr before or after the use of these bacteria by humans? * What was the ecological niche of the ancestor(s) before humans used them for cheese and yoghurt?

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._