tl;dr: Long-term harm that might happen to kill off whatever's harming you in the process, but don't count on it.
Long version: It depends on specific antibiotic- generally, they wipe a portion of the strains completely, suppress most of the rest, and give anything resistant the opportunity to grow out of control, a state which persists for weeks to months during which you're extra susceptible to external pathogens, food poisoning, etc. A healthy microbiome is resilient, and sadly if you don't have one, FMT is the only way to do it.
Long version: It depends on specific antibiotic- generally, they wipe a portion of the strains completely, suppress most of the rest, and give anything resistant the opportunity to grow out of control, a state which persists for weeks to months during which you're extra susceptible to external pathogens, food poisoning, etc. A healthy microbiome is resilient, and sadly if you don't have one, FMT is the only way to do it.