Regarding moldy food, it’s because you’re taking a gamble on what exactly the mold is. There’s many types of mold, and some can produce very toxic compounds. Eating the mold can poison yourself. Of course, if you know that it’s a safe mold, then you can eat it (that’s how cheese making works). But as with all things in microbiology, things tend to be complicated very quickly, and it can be pretty hard for amateurs and even professional microbiologists to accurately distinguish between safe and unsafe molds.

With regards to killing helpful bacteria, you are correct that one of their uses is that they help improve the efficiency of digestion. This is a very young and growing field (and also not entirely in my field of expertise), so many things I say might be outdated. The second most obvious downside to killing helpful bacteria is that they prevent actual harmful bacteria from growing out of control. There are several bacteria (in particular, C. dificile) where taking antibiotics actually makes the infection worse, since the antibiotics kills off the helpful bacteria that were helping to contain the infection.

Scientists also have found semi-recently that bacteria in your intestines have an incredible amount of control over you as a person. Your body even has a sort of hotline that connects from your intestines directly to your brain, called the vagus nerve, and the bacteria in your intestines use this to communicate with your brain. For instance, scientists have found that the type of bacteria in your gut can influence the onset and severity of autism symptoms. One current hypothesis for autism is that the body, during development, somehow messes up the composition of bacteria in your intestines, and that in turn messes up the development of the brain. I seem to recall reading papers that linked bacteria to other neurological diseases and disorders, but I don’t remember completely.

Another is that the bacteria are known to be linked to obesity. Scientists have found that if you give 2 people the exact same foods in the exact same amounts, one can develop obesity and one won’t. Whether someone develops obesity or not is highly predictable based on the composition of the bacteria in their intestines. As a matter of fact, scientists have even found that if you replace an obese person’s bacteria with bacteria taken from a healthy person, then the obese person will begin to lose weight, even if that person hasn’t changed anything else.

The bacteria in your intestines are also known to be in constant communication with your immune system. I believe the immune system uses the bacteria in your intestines to train when you’re young. But this back-and-forth extends well into adulthood. Scientists found that bacteria can control the development and activity of white blood cells. That, of course, leads to differences in things like fighting off infections and killing cancers.

The bacteria in your intestines are incredibly important, and we’re only just now beginning to understand what they do for us. That’s why I say that you have to weigh pros and cons. If you think you’d be fine without it, I recommend not taking antibiotics. But if the infection is severe, then it’s worth dealing with the downsides. Talk to your doctor if you’re unsure - he probably knows more about what situations are severe and which aren’t. But what you definitely don’t want to do (which I know many people tend to do) is to pressure the doctor into prescribing antibiotics. Antibiotics aren’t a wonder drug, and people shouldn’t be immediately jumping to antibiotics as a solution to their infections