FMT, donor-matching, screening for specific microbes, and pre-treatment/eradication. "Killing things off" vs suppression & ecosystem restoration.

Michael Harrop

Active member
Jul 6, 2023
Someone wrote to me about this. It's always better to discuss publicly so others can learn and weigh in.

I have a strong suspicion which microbes are my problem based on test results and symptoms and I want to be sure that those microbes are not present in the donor stool.
See I do not think this is a valid approach. Current testing is way too limited, and I'll write more below.

Those are: desulfovibrio, desulfobacter, methanobacter, methanobrevibacter, blastocystis hominis, oscillibacter, cyanobacteria, helicobacter pylori.
This is absolutely not a valid notion (see link above). Much of what is listed are genera, and deciding good/bad at this level is erroneous. There are also other relevant pages, including the probiotic guide (discusses importance of strains), and H. Pylori has its own page. And I created a thread on Blastocystis.

Which donor would you recommend in that case (depending on the test results, see above)?
That's not a viable/valid notion.

it makes no sense for me to do an FMT from a donor who has these microbes and to add more of them to my gut if they might be my problem
The donor may have a non-pathogenic strain, or they may have other microbes that suppress problematic ones. In both cases, FMT from the donor would be beneficial.

With most microbes, it's rarely a case of "just eradicate it". Adding other microbes that suppress it, and restoring eubiosis, is typically the best option. You can't restore an ecosystem by continually killing things off. Ecologists are well aware of this. We've learned this the hard way with C. diff. And here is lots more supporting info with other conditions where the popular approach has been "kill it off":

There are plenty of people who test positive for pathogens but are asymptomatic, and the info above is probably a big reason why. However, I think other donor-quality criteria are still vital -- IE: things like stool type allow you to "see" the status of the person's gut microbiome. Someone who is asymptomatic, but has a bad stool type should be avoided.
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