µBiome is vapid consumerism in my opinion. They don't contribute data to the research community (as far as I know).
The vast, vast majority of all bacteria are not culturable in a lab. That being said, we use rRNA/rDNA sequencing[1] to build phylogenies based off of BLAST E-values[2], or how likely it is two sequences evolved separately from each other. We have cultured and sequenced enough of the big three (and many of the top 100 gut microbes) that we can be statistically sure that they're related. We can't say for sure two different but closely related sequences are two different, closely related species but we can say they're related OTUs[3]
The vast, vast majority of all bacteria are not culturable in a lab. That being said, we use rRNA/rDNA sequencing[1] to build phylogenies based off of BLAST E-values[2], or how likely it is two sequences evolved separately from each other. We have cultured and sequenced enough of the big three (and many of the top 100 gut microbes) that we can be statistically sure that they're related. We can't say for sure two different but closely related sequences are two different, closely related species but we can say they're related OTUs[3]
[1] http://greengenes.lbl.gov/cgi-bin/nph-index.cgi
[2] http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYP...
[3] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609233/