There's no known reason to avoid treating non-pouch infections with appropriate antibiotics. There's no evidence that (for example) they can cause pouchitis. They'll have about the same safety profile as they do for folks with colons. 

Anything that disturbs the gut flora can cause all kinds of gastrointestinal distress.

During my time with the ileostomy, I took antibiotics without a second thought and I dont ever recall my gut flora being disturbed, unless it was contain within the part of my gut which was removed.

Currently, I've been taking antibiotics for 5 days and with no adverse effect, I have maybe another 5 days of pills to take to complete the course.

Over here in France, they automatically give a script for Brewer's yeast along with each script for antibiotics...I didn't get it back in the 80's but now the science backs up the idea of putting the good flora back once the bad have been irradicated...

You can take probiotics as well if you feel runny or bubbly or gassy once you finish...a 5-7 day run should not destroy your pouch but eating some yogurt daily wouldn't hurt either.

Sharon

My opinion is that antibiotics are as safe or problematic for us as they are for the general public. If you need them, take them. Just be alert for side effects. Don’t ask for antibiotics if they aren’t appropriate (such as viral infections).

Jan

No viral infection.

I've completed the antibiotic course now and no adverse effects.

Prior to my ileostomy and J pouch I tried the probiotics yogurt type drinks and the set yogurts and they made me ill, caused urgency and diarrhoea,

Took a while to realise what was the cause, each time, I thought it was the start of an UC flare up; that was some years ago, never tried em since, but thanks for the suggestion.