True enough the re-usability of plastic bottles is quite a problem even in the area I live. This is due to multiple factors; one of those factors is the symbiotic microorganisms that could be living in your mouth (from my lectures)
as well as any contaminant from anything you've eaten$^1$. That however isn't the only thing that could be contaminating your water bottle. The exposure to the air itself may contaminate. (that's why in microbiology we use a laminar flow cabinet or work close to a flame).
That's also why hospitals have air purification systems to avoid infections$^2$.
As a result, the amount of possible contaminants are too big to list. We could list those that I personally think would be more relevant to list -- these include our mouth natural flora since saliva is the most common contaminant of reusable bottles:
- Candida albicans;
- Streptococcus salivarius;
- Fusobacterium nucleatum;
List obtained from Almståhl et al.$^3$
Almost all of these microorganisms are associated with some sort of disease or another.
I didn't actually find any specific study on the reuse of water bottles so i apologize for not being capable of giving a more definitive reply.
Sorry if i have failed to answer your question in any way or have misinterpreted what was required, I hope my research was some help to you.
- (Mahvash Navazesh, DMD, Satish K.S. Kumar, MDSc1, Measuring salivary flow : Challenges and opportunities)
- (W.D. Griffithsa, A. Bennettb, S. Speightb, S. Parksb. Determining the performance of a commercial air purification system for reducing airborne contamination using model micro-organisms: a new test methodology.
- Almståhl A, Wikström M, Fagerberg-Mohlin B. Microflora in oral ecosystems and salivary secretion rates--A 3-year follow-up after radiation therapy to the head and neck region.