Yellow can be fungal, bacterial, or reflux related. The fact that your throat is sore as well suggests it may be reflux, but it could also indicate an infection spreading to your throat.
I would just start treating it and try and reach your own differential diagnosis. Your Doctor doesn't seem too interested: Normal flora doesn't tell you much, as yeast is considered normal.
I would try a few more things in the mouth, such as:
1. Magnesium Ascorbate. It's non acidic Vitamin C. Let it sit in your mouth and drip down your throat. It will kill any yeasts or plaques.
2. Diluted Hydrogen Peroxide rinses.
3. Oil Pulling can help with various problems in the mouth, and makes the mouth feel really good. You can use Sesame, Sunflower, or Coconut Oil.
Then try treating the reflux. Betaine HCL and digestive enzymes would be my first choice. A gram of Vitamin C at the start of a meal helps as well. So does keeping the meal small and avoiding trigger foods.
Last resort would be antacids, or Proton Pump Inhibitors, which can cause more problems down the road. Avoid if possible. The problem is usually a lack of acid, not too much, and low acidity opens the door to pathogens.
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