I have noticed that when I got the pouch there was a gradual but constant reduction in the ability of my guts to digest various foods.  I didn't discover psyllium husk powder, which helped slow the transit time, until about 18 years in. Before that, the stool pretty much always had the chewed food look.  The slower transit gave my intestine a longer time to absorb nutrients and the food would come out generally more processed.  I added digestive enzymes and now the food is even less recognizable upon exiting my system.  I am still experimenting with those because there are so many, but using certain digestive enzymes has helped me gain more energy from my food and feel less bloated after eating.  It also reduces the look of chewed food in the stool.  I have never used antibiotics so I can't comment on that, but I do agree, when the guts are irritated, the chewed food look is more apparent, and the lack of processing seems to irritate the guts as well.

@Mark Y. posted:

I have had my pouch for 30 years. I have dealt with pouchitis off and on. More recently I have noticed when my pouch is good my stool is brown and consistent. When I have a flare my stool looks like chewed pieces of the food I ate that day. Flatly and Cipro are no longer effective

Has anyone else had this experience? If so how did you resolve it.

If Flagyl and Cipro no longer work then it’s probably time to try some new possibilities. Rifaximin is well worth a try, as long as you can get insurance to cover it. Other antibiotics that can work include Augmentin and a few others. Some folks also get help (mainly preventing/delaying bouts of pouchitis) from Visbiome or VSL #3, but those are also expensive if the doses are adequate.