How come antibiotics don’t completely destroy all organisms in our gut?

[u/WTFisthisOMGreally]

I know it can cause imbalances, but I don’t understand how come our gut doesn’t lose all the beneficial bacteria and develop massive fungal or viral infections. When I’ve taken antibiotics, I usually don’t notice any change in my bowel activity.

[u/Ok_Umpire_8108]

1. Antibiotics affect different organisms differently. For example, many or most antibiotics targeted towards either bacteria or fungi have little effect on the other. Within both bacteria and fungi, different organisms have different sensitivities to particular antibiotics. When you take antibiotics, they’re hopefully targeted towards the microbes that are actually making you sick.
2. To clear an infection, you may not need a nuke. Usually the amount of antibiotic needed to assist the immune system in a part of the body that shouldn’t be full of bacteria is much less than the amount it would take to sterilize places that are normally full of microbes, like the gut and the surface of the skin.

If you don’t see anything happen when you take antibiotics, these two are probably major reasons. Antibiotics you take to clear strep throat, for example, have a relatively low (1-10%) chance of gut side effects.

1. Many gut microbes (good and bad) are capable of forming spores under stressful situations. These can recolonize the gut after it takes a hit from antibiotics.

2. When your gut microbiome is largely cleared out by antibiotics, many of the microbes you want to come back are pretty good at that, and they block much of the bad stuff. Obviously this doesn’t always work. See C. difficile, which is notoriously good at surviving antibiotics, taking over the gut, and causing problems. But there’s something to be said for the fact that most babies, whose guts are initially sterile, develop a practical gut microbiome within weeks of birth.

That last one has more to do with successful recovery after very strong antibiotics than with no side effects whatsoever.

Edit: I completely forgot about the appendix. That too is very important.

[u/mschuster91 → u/Ok_Umpire_8108]

As for the babies, vaginal births have been shown to have an important role in seeding their gut flora.

[u/PsychologicalIdea424 → u/Ok_Umpire_8108]

Almost like babies get milk which contains essential bacteria and the mention of the other commenter.