From Quora: Do antibiotics weaken one's immune system? If yes, how?

This is a question that has a superficially simple answer - "No" - that has already been given by other respondents.  As best we know, antibiotics do not interact with the cells and molecules of the immune system, so there is no simple mechanism through which they could weaken the immune system.

However, consider this: many bacteria secrete molecules which modulate the activities of the immune system.  An example is Staphylococcus epidermidis, a skin commensal.  It secretes compounds that activate  toll-like receptors in keratinocytes (skin cells) which in turn stimulates the release of antimicrobial peptides.  These peptides suppress the growth of potentially pathogenic bacteria.  Another example: bacteria in the gut release polysaccharides which modulate the activity of CD4+ and CD8+ immune cells.  In both of these examples commensal bacteria are manipulating the immune response to suppress competitors.  If these competitors are also human pathogens, then the interaction is mutually beneficial.  Killing these bacteria with antibiotics might well weaken the immune system.

This sort of research is still in its infancy, and it is too early to say with any certainty what the effects of antibiotics on immune responses are.  But if we start thinking about the bacteria in and on our body as part of a tightly connected ecosystem, rather than as alien invaders, then the answer to your question becomes fairly obvious.  Although we really don't understand how, the likelihood that disrupting our bacterial ecosystems (which antibiotics most surely do) will also alter our immune systems is very, very high.