Not neceserally: they still are in skin contact with the parents, and babies put EVERYTHING into their mouth, giving ample opportunities for microbes to start living in their guts.

Microbes are everywhere and our body has multiple "built-in" systems which help the good microbes to profalite. The gut microbiome is an ecosystem on its own, constantly changing and growing as our habits, environment, stress level, eating habits (and so much more) change while our immune system works hard to keep them in check and make sure they don't do anything which they shouldn't do.