@Aubry Very sorry for your plight. Don't lose hope. While fecal transplants may be helpful, they're not the Holy Grail.
It takes persistence and a well thought out plan to fix the microbiome. There is no perfect microbiome, and no perfect regimen, but much you can do to improve things.
I'm celiac, and had lengthy ciprofloxacin treatment, then chemotherapy, and then oral rifampin and azithromycin and am currently on a triple antibiotic IV protocol to kill chlamydia pneumoniae. If anyone's gut should be a mess, mine should. Mine isn't perfect, but under continual surveillance my doctors find mine is far better than expected.
Strategies that have helped:
- A high fiber, low carb organic diet, with lots of varied nonstarchy vegetables, no grains, and very little fruit. Certain foods can encourage or discourage growth of certain bacterial strains
- Glutamine, if needed, for the intestinal lining
- A DNA stool test every 3-4 months for mid-course corrections, including bacteria, fungi, parasites, and viruses
- Probiotics, rotated every couple of months of high potency (50-350 billion, not 2 billion) matches to the gaps in my microbiome. Its impossible to get them all at once, but starting with lacto/bifido & moving to more exotic strains
- Prebiotics - in my doctor's words when the expensive probiotics is taken weren't showing up on tests "They have nothing to stick to!" I've been on Seeking Health ProBio Immune GOS product and Thorne FiberMend, but there are others like inulin. You need to match them to the bacteria you want to cultivate.
- Bad actors - candida, parasites, bad bacteria. Find them and get rid of them. If you don't have anything good, its an opportunity for bad to proliferate. Bad bacteria can crowd out or kill good ones, so you need to figure out how to crowd them out.
- Cfsremission.com has some interesting ideas for cultivating certain strains. I don't think it'll cure ME/CFS as he proposed, but he has some good hints of what to try in more exotic situations
- Watch stomach acid and pancreatic enzymes - take them if you need them to make food easier to digest
- Be aware of nutrient deficiencies. Various good bacteria extract different nutrients and convert them to usable forms, so if you don't have the right strains, you'll be nutrient deficient. Transdermal, sublingual, and/or IV nutrients can help.
Its a project, and in my experience, doesn't happen overnight. The stuff you read about the gut rebounding after a week is nonsense. Its more like 12-24 months of a wise, concerted effort, especially if yours is in bad shape to begin with.
Best wishes...