you almost seem to have done your microbiome test with an other company.
Not another company, another combination of microbes.
There is not a universal ability or inability in the test to discriminate between organisms. It does very well with some, consistently detecting down to the species level: it does much less well with others. This is largely a property of the particular sequence in the DNA segment studied in the test - ie how similar or different it is from other sequences.
Since there is considerable variation in microbiome composition between individuals, there will be considerable differences between individuals in % loss of identification in the kind of analysis you are doing.
Also of course, since you seem to be trying to get estimates of overall loss of precision of identification, relative abundance is important. In your case, 1/10 of 65.12% (Firmicutes) makes more difference than 1/5 of 1.64% (Tenericutes) or even 1/4 of 20.16% (Bacteroidetes).
In the example I gave of my analysis, the contribution of
Clostridiales was even greater since this constituted almost my entire
Firmicutes count.
There was some loss in
Bacteroidetes, though not to the extent you see (presumably reflecting the presence of different members of the phyllum in my gut) and as with your analysis,
Proteobacteria, Acintobacteria, Lentisphaerae and
Verrucomicrobia had very little loss.
But beside that, how did your microbiome composition change over time?
My first gut test was done after taking a lot of antibiotics over a long time. Actually it was not as bad as I expected (there were no serious overgrowths of potentially harmful microbes) but there was a clear lack of diversity and virtual absence of a number of known beneficial species which on average are present in relatively high amounts.
I have concentrated on diet and consistent supply of a wide variety of concentrated prebiotics and have observed that, over time, diversity has increased and many beneficial species are returning. Star butyrate producers like
Faecalibacterium and
Roseburia established themselves fairly quickly and have remained consistently at good levels.
Others like
Bifidobacterium and
Akkermansia took longer (especially the latter) and Bifido in particular is still very up and down for no apparent reason.
One important genus,
Ruminococcus, has never appeared and I presume I have lost it completely. Of course there is great redundancy in the microbiome and many organisms can fulfill the same function, but this is one I would rather have than not have, unlike, for example,
Prevotella which I also don't have but don't care about.
So I am pleased with that aspect of things, but there are others that I am not sure how to interpret.
One noticeable aspect of the lack of diversity in my gut was the virtual absence of the minor phylla. While not much is known about the role of many of these organisms, it is thought their presence represents resilience, a store of possibilities to fill the gap if conditions suddenly change.
A couple have appeared (
Lentisphaerae and
Verrucomicrobia) but the rest remain stubbornly absent.
More worrying is the transitory overgrowth of a couple of members of
Proteobacteria, viz
Kluyvera and
Thallasospira. The first time this happened with
Kluyvera (present at 28% more than 8x average), I panicked. This is a member of the gamma
Proteobacteria which contains many notable pathogens and the organism is known to be a rare opportunistic pathogen.
I didn't have any particular symptoms so didn't think I had a serious infection but I was worried that this marked imbalance might eventually adversely affect gut function. Actually it resolved itself over a couple of months and I would have been none the wiser if I hadn't done tests at that time.
This has happened again with
Kluyvera and more recently with
Thallasospira, a member of the alpha
Proteobacteria about which little is known of its role in the gut. This took longer to resolve and again had no obvious ill effects.
I don't know what to make of this. I wasn't doing anything obviously different, I don't know if this sort of thing might happen frequently or whether it is unusual and is flagging a potential problem. If the latter I don't quite know what I can do differently to deal with it. So I continue to contemplate this and still do fairly regular tests to follow what is happening with these potentially problematic organisms.
Apart from that, I observe that my gut is fairly stable with the same grouping of organisms appearing in similar amounts most of time. There is a lot of variability at the lower levels but I think this just reflects the randomness of gut sampling.
