What kinds of bacteria live in water bottles?
In addition to the cracks providing a better place for bacteria to grow, all plastic bottles, when reused, are subjected to high levels of bacteria due to contact with hands and mouths. So your water bottle can potentially host a range of bacteria.
Your water bottle traps humidity inside and provides a perfect growing medium, especially near the threads of the mouthpiece and along/within cracks in the bottle which provide better bacteria accumulation.
Microorganisms that Grow

Overall, most sources I could find remained very vague (numerous News stories) or mentioned bacteria generally:

Staphylococcus and streptococcus species, [Source].

Norovirus [Source].

The seemingly most detailed studies I could find came from Watanabe et al. 2014 and Ohnishi et al. (2012) who examined microbial growth in numerous beverage types. However, I could only find their their abstracts online, which report:

microbial growth was detected in ~20% of poured samples, and in ~51% of drank samples.

225 bacterial strains, 27 mold strains, and 77 yeast strains were isolated

Bacteria: Streptococcus spp. (e.g., S. salivarius) and Staphylococcus spp. (e.g., S. aureus), made up the majority. Enterotoxin-producing S. aureus and Bacillus cereus were also isolated.

Molds: Cladosporium spp., Tramets spp., Bjerkandera spp., and Penicillium spp.






 [I Will hunt down these articles to get more details and will update accordingly when I find them...] 
Microorganisms in the Water

Based on a study found here, brand new bottles of water can have fungus spores (typically harmless), but opened bottles can show signs of greater diversity (e.g., fungi, skin Staphylococcus, and yeast.

Igbeneghu &amp; Lamikanra (2014) found Staphylococcus species (notably S aureus) and strains of Pseudomonas in bottled water available in Africa.

Your Livestrong article lists a number of non-human pathogens such as: Ralstonia Pickettii, Acidovorax Temperans, A. Delafieldii, Agrobacterium Rhizogenes, Burkholderia Glumae, and Bacillus Thermoglucosidasius.

Juvonen et al.'s  (2011) &quot;Microbiological spoilage and safety
risks in non-beer beverages&quot; provides a thorough list of organisms found worldwide in different bottled waters and other beverages.


Other Issues

According to Rose State microbiologist, Dr. Amy Hurst:


The plastic materials degrade into the water, so then you're drinking very small plastic molecules. [Source].


PET plastics tend to leach when exposed to realistic though extreme conditions, such as exposure to sunlight, heat and storage time. [See UF article]

Bisphenol-A (BPA) and phthalates present in the bottles can leach into the water and possibly cause harm to humans.

Rochester (2013) provides a good review of BPA effects in humans and other test organisms.

New research shows that BPA alternatives such as BPS aren't any safer either; in fact, in some cases they are considered more dangerous to humans. All bisphenols are capable of mimicking the body's sex hormones, says Robin Mesnage, research associate with King's College London.

Al-Saleh et al (2011) found that  76% of the bottled waters they tested in Saudi markets contained measurable amounts of phthalates.


So Reusable Plastic Bottles are Better Right?

Well, from a bacteria standpoint, this isn't necessarily true.  According to a small study  of 12 reusable bottles being used for a week:

Avg bacteria load: 300k CFUs (colony forming units). Ranged between 25 - 900k CFU/cm$^2$.

Notable types found: E.coli, salmonella, and various gram-positive cocci and gram negative rod bacteria.

They found that different bottle types harbored different amounts and kinds of bacteria.