Uploaded 9 test results in Claude. I am missing a bunch of good bacteria after way too many antibiotics. These were some of the ones that stood out to me:
Zero of these:
Bifidobacterium pseudocatenulatum
B. bifidum
Lactobacillus acidophilus
Lactobacillus plantarum
Oxalobacter formigenes
Phascolarctobacterium faecium
And zero of this organism: Methanobrevibacter smithii
Lactobacillus acidophilus is added intentionally to certain dairy products, it's not significantly present in the gut unless you're eating a lot of it. While there are other Lactobacillus species that are common (to be found at all) in the gut like L. gasseri, L. reuteri, and L. salivarius, their abundance is very low. A lot of them seem to come from food--breast milk in infants and fermented foods later in life. While they may not perfectly match dietary intake, they're generally a better indicator of your diet than the actual state of your gut, and it's telling that in other primates, none of these are observed at all in the wild, only when they're in captivity (and thus eating food that humans give them):
https://www.nature.com/articles/s41467-020-16438-8
Bifidobacteria, in contrast, ARE an integral part of the gut microbiome, particularly in infancy. Their abundance goes down with age but they generally don't disappear entirely. However, they're easy to supplement.
Oxalobacter is only found in some people. It's only if you're prone to oxalate kidney stones that it likely matters whether you have it or not, as really the only metabolic thing it can do is turn oxalate into formate. I don't have Oxalobacter and I DO have kidney stones, however recent testing showed that they're predominantly uric acid (and the bit of oxalate they contain is probably precipitated out BY the uric acid), thus even there the connection is tenuous. Uric acid, BTW, is degraded by a completely different set of gut bacteria that was the focus of a few high profile papers some years ago.
More importantly to me is the lack of biome diversity (5th percentile) enables Proteobacteria (Phylum) Rhodospirillales (Order) to overgrow. It is 23% of overall bacteria and the pain and inflammation are unbearable. Testing could not identify the genus or species. This bacteria comes from the soil or underwater and survives on oxygen (photosynthesis). I believe a quality FMT will cure this overgrowth much like increasing diversity quells C. Diff.
I going to test after the FMT to see if antibiotic caused low diversity can be improved. My guess is it can by its efficacy in treating C. Diff.
Edit: Adding a question: Curious if I should consider antibiotics before the FMT to reduce Proteobacteria or should the FMT be effective enough by itself? Opinions?
I believe the idea that Proteobacteria as a whole are inherently a problem is GREATLY exaggerated. There are certainly some you don't want too much of, like Klebsiella, and some that are outright pathogenic in any significant amounts (virulence factor-producing strains of H. pylori), but it doesn't seem like you have those, and something like Klebsiella rarely reaches anywhere near 20% even when it's present.
Rhodospirillales are in fact so under-represented in the gut (with the one exception of Acetobacter species in
insect guts) that having them at 23% seems to suggest a contaminated sample rather than an actual overgrowth. Having water- and/or soil bacteria reach over 20% of total abundance is what I would expect if you were to sequence a "blank" that doesn't actually have any stool in it.
