How Bad Is Flagyl on your gut biome

It's not at all clear what microbiome is best for a J-pouch, so there may not be much reason to guard it quite so carefully. If your doc saw pouchitis it might be best to treat it, but you could choose to wait until symptoms appear. In my experience the symptoms sometimes came on so gradually that instead of noticing that I have a problem my life just slowly got worse and worse. I've been on Flagyl for years now, and I care a lot more about my quality of life (which is excellent) than about trying to protect the bacteria in my pouch.

Untreated inflammation in the pouch can cause some problems over time, so some docs treat pouchitis aggressively to prevent those problems.

Awesome cheers for the reply Scott.

Interestingly i see that a recent (2018) study shows that taking probiotics to recover from from antibiotic treatment could actually be counter intuitive... gah....theres never any clear answers is there..

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Basically the prevleance of a few strains of good bacteria that you have supplemented hinders the ability of other healthy strains to get a foothold.  People who didnt take prebitoics recovered normal gut flora in 3 weeks, people that supplemented with probitoics hadnt recovered within the 6 month trial!