There is some evidence pointing out to the fact that bacteria might be not a genetic continuum but evolved in genetic and ecological discernible populations (read Caro-Quintero 2012, Environmental Microbiology 14(2), 347–355).

Also, I have been looking into metagenomic data and some abundant bacterial groups and found this phenomena. 

Would be curious to know what other people are finding.

Thanks Sarah. What about if we restrict the question to genus or family? Especially for the cultivable and “popular” ones, i.e., the ones where many species are identified, e.g., Staphylococcus, Streptococcus, Enterobacteria, etc..?

I am tempted to say we do not have enough representative genomes of the "popular" bacteria to assess the question. The way we obtain those genomes is very biased and might not appropriately represent what happens in nature.