When you need to resort to using 16s sequencing, the amount of bacteria you are detecting is extremely low, and with no guarantee that is living, and not dead. But that is besides the point. STDs are not spread via urine, not at all. Disease is not spread by urine.
I am seriously questioning, not stating fact, but since he said he would "rub up against the bottle", couldn't there be a sexual aspect to this and maybe spread as well. Talking maybe genital herpes or other diseases?