> What if a therapeutic bacteriophage (mutates and) attacks symbiotic gut bacteria?
We don't have only one species of bacteria in our gut, and even if it was possible to for it mutate to infect one kind of bacteria in out digestive system it's unlikely (like winning the lottery, a few dozens of times) the phage can can mutations to target all of them. In any case, damages to the human symbiotic bacteria already happens with antibiotics (which damage the entirety of the flora not just a single species).
Bacteriophages attack only one specific bacteria. Even in the unlikely case that it attacked our gut bacteria, it would be only one species, which would be a tiny minority of you guys bacteria.
it's the same issue with antibiotics what if they kill gut bacteria? The answer is they can and do [1]. My guess would be the changes are actually lower with the bacteriophages as they tend to be more specific in the bacteria they target [2] so if that did happen it probably wouldn't cause a widespread die off as much as kill off some specific ones.
Note that 10% of a human's weight and 90% of the cell count are those symbiotic gut bacteria.