Only if you wreck your gut flora enough that you’re also at a high risk of dying from diarrhoea-induced dehydration, or other opportunistic infections. It would have to be very, very bad.

In addition to that, there is the stomach-acid which acts a barrier.

If you’re worried about the effects of antibiotics on your gut biota, you can take probiotics during the course.

But don’t be worried about eating honey, any more than you’d be worried about wearing boots that are too heavy to swim in while it’s raining.

If your doc martens are a drowning risk just because there’s rain, several other very noticeable things have gone exceptionally wrong.