For general information on the microbiome, and how it interacts with us and other animals, it's hard to do better than Ed Yong's
I Contain Multitudes
One of the points in the book is that instead of just viewing the immune system as a military defense system ready to destroy malicious microbial invaders, it might be more correct to see it as series of park rangers working to maintain a healthy microbiome ecosystem that works best for the host. As the exact same species of microbes can be beneficial in one context and harmful in another, it kind of makes sense.
And of course, antibiotics are overused nowadays as they kill huge swaths of bacteria that can be beneficial or just plain in the way of what can be nasty, resistant strains taking hold. Hospitals are kept so sterile that patients better recover from infections just by keeping some windows open.