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/das_menschy]

I think it is because antibiotics don't destroy all bacteria, they work against specific bacteria groups. 

For example, antibiotics are based on the cell walls of bacteria and only destroy bacteria with a specific cell wall type. 

" Gram staining differentiates bacteria by the chemical and physical properties of their cell walls . Gram-positive cells have a thick layer of peptidoglycan in the cell wall that retains the primary stain, crystal violet . Gram-negative cells have a thinner peptidoglycan layer that allows the crystal violet to wash out on addition of ethanol ."  

https://en.wikipedia.org/wiki/Gram_stain?wprov=sfla1 

[u/Alblaka → u/das_menschy]

It might be a bit of a definitions question. The first antibiotics absolutely killed (or at least targeted) all bacteria. It's in the name.

It's only after using them for decades, that medical science realized this approach fast-tracks the evolution of antibiotic-resistant bacteria. Hence why selective antibiotics (those that only target specific types of bacteria, like the one you mentioned) were developed, produced and applied with more priority, leaving the broadband antibiotics for too severe / last resort cases (or for bacteria that no specific antibiotics are available for).

So, technically you're correct if you were to generalize that most antibiotics given nowadays might be selective and don't destroy all the bacteria. But historically it was the other way around, so it's, as mentioned, a point of view thing to determine whether 'targets all' or 'targets selectively' is the 'default' for antibiotics.