With inaccuracy I meant that with only 44% of species identified there could be a whooping 56% of pretty nasty ones.
I don't understand where you are getting the 44% figure from, nor, in an earlier post, your claim that only 73% identification occurred at the genus level.
I think you are misunderstanding/misinterpreting your results.
The break-up of organisms is 100% accounted for down to the genus level for every uBiome test that I have looked at, and I have done quite a few.
You may need to follow this on the phylogenetic tree to pick up the groups that you appear to be missing.
Let me give an illustration. I just randomly picked one of my tests and looked at the counts attributed to the different taxa.
If we follow the different phyla through their subclassifications of class, order, family and genus, the counts add up perfectly. There is no loss of identification going from phylum down to genus - 100% of the counts are assigned for each phylum.
It is different at the species level because the short length of the DNA pieces don't always allow species identification.
BUT THIS VARIES FROM GENUS TO GENUS. ie, there is no blanket figure for % of species identified (your 43% figure).
As an example, in my randomly selected test, for the genus
Bacteroides, 76% of the genus counts were able to be attributed to different species, 100% for the genera
Phascolarctobacterium and
Victivallis, 52.5% for
Blautia, 21% for
Alistipes, 0% for
Clostridium.
However, if I understand you right, than all species already known to be pathogenic, like C. difficile, would have been identified. Or my 5,1% Clostridium with no species identified means, C. butyricum, C. boltae, C. botulinum, or C. clostridioforme definitely aren't there? Left out are only those not yet identified, and therefore not contained in databases?
No I don't mean that. My comment about lack of information referred to
Spirochetes.
There is plenty of information in databases about
Clostridium , though DNA sequencing technology has shown that the genus, and indeed much of the
Clostridiales, needs to be reclassified.The current uBiome technology used in the Explorer test can't discriminate between most
Clostridium species. That will not change until the technology changes.
I was really making a passing comment about the known gut members of the genus. A couple are known to be problems if they overgrow, but most are just part of the normal gut flora.
In other words, don't get overly concerned about potentially pathogenic species and definitely don't make the assumption that all the species not identified could be the nasty pathogenic ones. These are rare.