Is it true that taking a proton pump inhibitor for acid reflux can cause bad breath by allowing bacteria / fungi to accumulate?

Possibly: There is still a lot of research being done, but some studies have found a correlation between halitosis and gerd medications, specifically proton pump inhibitors. Again, so far, the links are suggested, but not fully proven. Either way, bacteria are thought to be the root cause. Brush and floss regularly, use a tongue scraper, and ask your dentist about specific products to reduce halitosis.