Was in the same boat even doing very low-carb, no cavities just gingivitis, tooth staining and bad breath. Hygienist said "you have bad bacteria in your mouth, no cure for that" as a microbiologist that got me thinking. Tried mouthwashes, Listerine, even the Crest one that turns your teeth brown!
Tried "oil pulling" -- still no joy. So I decided to fight fire with fire and try kefir. I also use an essential oil blend, WaterPik and sometimes brush with baking soda. Now I can probably go back to twice a year cleanings now all symptoms have disappeared