I suspect the MOMENT they start talking about gut bacteria (FOR REAL, and not just "eat healthy for your gut bugs", they start talking about Klebsiella causing Epilepsy, Desulfovibrio causing Parkinsons, big pharma stocks are absolutely going to tank and go to ZERO, maybe even criminal referrals by the DOJ if pharma companies hid research and buried cures.
It would be GREAT if more of the scientific community started talking about gut bacteria "for real" as you put it. But if the conclusions are what you are imagining (that specific species are "blamed" for diseases, as opposed to the
lack of certain species causing diseases), then the cure that will be pursued will almost certainly be more antibiotics. But not only do we not
want this, the problem there is that many people with these diseases will have taken antibiotics that kill these bacteria (fortuitously, for other reasons) and not gotten better, which will be a reason for everyone not already involved with these studies to be dismissive.
The issue seems to be, as you have likely already guessed, that "nature abhors a vacuum" and if you kill one thing, something else will fill its place, one that's in many cases worse than the original one you were trying to get rid of. And the only things widely available to "fill holes" are from one of two places on the bacterial tree of life--the Bacillaceae/Lactobacillaceae group within the Firmicutes and the genus Bifidobacterium within the Actinobacteria. If the hole you need to fill is from somewhere else on the bacterial tree, good luck getting something to fill it except from another human who already has it.
I suspect that a lot of the issue is the reliance on 16S stool tests, which miss many of the bacteria adhering to the mucosa (which are more directly interacting with the host anyway than those in the stool), and everything from the small intestine. I mean,
some scientists are
trying to "talk about gut bacteria for real", however they don't see anything except really broad trends where the specifics are very inconsistent. I even suspect that some of these broad trends might be misleading and/or misinterpreted--for instance the increase in Proteobacteria seen with antibiotics, which has been
interpreted to mean that "Proteobacteria are bad in general", whereas I suspect that this is rather a sign that some critical Proteobacteria have been
killed by the antibiotics (see the paper I posted earlier this year--https://forum.humanmicrobiome.info/threads/very-interesting-paper-about-metabolic-roles-in-the-gut-microbiome-aug.864/). But I don't see the studies getting any more consistent overall, which means that there is nothing other than "eat healthy for your gut microbes" that researchers can confidently
say with evidence.
It's not a cover-up, it's a field that's searching under the only lamppost they have because that's the only place they can see anything clearly, while the answer is likely somewhere else.