The biggest issue inside water bottles of any kind (metal or plastic) is the buildup of biofilm — that is when bacteria establish protective colonies inside your bottle. The closest parallel is plaque on teeth.

Biofilms are impervious to most chemicals, and so it is important to scrub bottles clean regularly, depending on ambient temperature. The one best way to remove biofilm is scrubbing the inside of the bottle with a brush (not unlike the need for physical brushing and flossing of teeth). The warmer the water temperature the more rapidly “bottle plaque” can buildup.

Species of bacteria is irrelevant if you keep the bottle clean, as they will not have time to attach themselves in a biofilm. For bottles with built-in straws, use a narrow fitted-wire brush.