Another way to say it is that just as in eukaryotes, just because a gene is found in the genome of a microbe does not mean that associated protein will be expre

Another way to say it is that just as in eukaryotes, just because a gene is found in the genome of a microbe does not mean that associated protein will be expressed. The genes could be under tight regulation (e.g. epigenetic) and only get accessed in specific instances/people. Let's not forget, it's not in their best interest for microbes to kill you quickly, it's better to replicate and spread. You can do that as a pathogen, or you can do that as a friendly member of the microbiota. There are also mechanisms which "tame" the microbiota, such as the continuous secretion of mucus which is extremely diverse in its arrangement of sugars which continuously feeds the microbes but doesn't let any one metabolic strategy take over.