Sickness caused by bacteria doesn't happen as soon as one bad bacteria (bacterium?) enters your body, a certain critical mass is usually required. This is very similar to the concept of "viral load" where a certain amount of viral genetic material needs to be exchanged before the viral infection can take hold.

The "beneficial bacteria" on your skin and in your gut make it harder for bad bacteria to take root in many different ways, one of them simply being they provide competition, "crowding out the bad guys".

Another way is that many, many, many types of antibiotics were originally discovered as metabolites produced by bacteria and fungi (examples include penicillin, streptomycin, chloramphenicol, and tetracycline).

And for completeness sake, milk kefir contains many Lactobacillus species that are also a natural part of the mammal microbiome (which makes sense when you think about it; Lactobacillus are named for consuming lactose, an ingredient of mammal milk).