True. But the thought was that every human would have a core microbime, at least in the gut. Even if there were variances between people, and within the same person over time. But it appears to be that there is no set of core species.
Actually, if you look at the Human Gut Microbiome Initiative, there are core set of species that seem to be very important. Bacteriodes thetaiotaomicron is a very big player in must everybody's gut.
The real thrust of the research is how the ratios between the different species is different for everyone. These ratios are measured by targeted 16s RNA reading (it's part of the mechanism that turns RNA into Amino acid chains, so essential to life). This data can infer species. But it has no real linkage to the actual function characteristics of a microbe, its just one gene.
But because of all the gene swapping (either by lateral transfer of phages moving random genes with their own replication mechanism) what is really going on in a particular cell may be quite different then previously catalogued members of that species.