I'm not overly optimistic about our prospects of being able to fully restore a healthy microbial community with diet & prebiotics only
I agree, we need better, more targeted probiotics, a next generation FMT, in addition to diet and prebiotics.
Still my experience over the past year or so combined with tracking by uBiome gives me some hope. I think my gut started out reasonably (vaginal birth, breast feeding), no childhood antibiotics, although my mother did have a mysterious waxing and waning illness which I strongly suspect might have been ME/CFS - so maybe not!
Certainly I never had any gut problems and was a healthy child. I took a lot of antibiotics in my 20s and 30s (for what I now believe was a chronic
Chlamydia pneumonii infection and likely the beginning of my ME/CFS) and again in my 40s and 50s (as in the post above).
From my first uBiome test it was clear that lack of diversity was a big problem. I simply didn't have many of the known important genera, or had them in tiny amounts, and the minor phyla were absent.
I tried various concentrated prebiotics but proved to be very sensitive to them, as well as to many probiotics (apart from VSL3) so I have mainly concentrated on diet and incorporating as many MACS as possible that way. (I do intend to revisit concentrated prebiotics at some point but have too many other things to deal with now - so it will be later).
With time the diversity has improved a bit (though still don't have any of the minor phyla) but the distribution of genera is normalising. Some genera which were absent have started to appear consistently and increase in number - eg
Bifidobacterium. Some changes have been quite astonishing - eg in
Faecalibacterium , the 2nd most numerous gut constituent on average and the most numerous Firmicutes (av 9.9%). From undetectable, it first appeared at fluctuating low levels but at the last test was 14.2% (things seem now to have gotten out of hand but I imagine with time will settle).
So change is possible. I still seem to be missing some major genera - eg Ruminococcus, but maybe it will just take longer for them to come back. If this doesn't ever come back then that would seem to be a good candidate for some future tailored probiotic treatment (which of course doesn't currently exist - but who knows what may result from the explosion of studies on our microbiome).
I have come to realise it will take a long time to get perspective on gut changes but I think it is worth the effort and so will continue with the uBiome tests (now monthly).