I also think that eliminating or at least reducing pathogenic bacteria and yeasts and fungi are really important. As you said, the problem is how to do it without digging the grave deeper. My husband did a round of Rifaximin, which is commonly prescribed to people who get traveler's diarrhea and is also widely used to treat SIBO; it is generally well tolerated and even though we are both wary of taking antibiotics, this seemed like the best way to deal with his worsening SIBO/IBS symptoms. It really wrecked his GI system and took a solid year to get back to a functional level.
We couldn't make sense of his reaction until recently he came across some information about a very important gut bacteria called E. Coli Nissle 1917 (the good E. Coli) which happens to get killed by Rifaximin. In people who have normal levels of this E. Coli, killing off some should eventually result in a repopulation, no problem. But in people who have significantly lower level of this E. Coli to begin with, killing off the few remaining bugs is disaster.
As a result of this experience, we are both really concerned about taking more antibiotics to get rid of pathogenic bacteria, because it's impossible to know which good ones are taken out with them, never to return again. I'm interested in knowing more about your experience with Flagyl, and whether you took other antibiotics or antifungals. Did you have any die-off symptoms? How long did you take it? In what ways did you repopulation afterward?
I haven't really seen anyone on this thread mentioning supplementing with E. Coli Nissile 1917 (found in the probiotic brand name Mutaflor, from Germany). This particular strain seems to be the C.B. of the E. Coli world, and is responsible for all sorts of things, like producing K2 and B12 among other things. We ordered it in the U.S. from a pharmacy in Canada. I highly recommend that folks on this thread at least look into it, if you haven't already.
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