Brief Answer:
Yeast is growing because acid reflux disturbs the normal ph of your mouth.

Detailed Answer:
Have gone through your details and i appreciate your concerns.
Initially i would like to say that your doctor is not treating you properly.
Why?
Please go through every line and try to understand that basic cause of your problem is reflux of acid from stomach to esophagus .Stomach is lined by a natural layer of mucosa membrane which is resistant to acid however mucosa in esophagus is easily destroyed by acid which regurgitates back from stomach.This cause severe irritation of esophagus leading to inflammation. the esophagus reacts to the repeated injury from the acidic fluid by changing the type of cells lining it from squamous (normal cells) to columnar (intestinal-type cells). This transformation, called metaplasia, is believed to be a protective response because the specialized columnar epithelium (epithelium means lining) in Barrett's esophagus is more resistant to injury from acid than the squamous epithelium.However in long term it increases risk of adenovarcinoma by 5%Inflammation in esophagus causes heart burn and sevee chest pain with acidic taste in mouth..
So as per the above explaination all the problems and symptoms are linked to each other.-

Now lets move to your treatment-
See as the name suggests ACID REFLUX should be treated in two phases-
1)Control production of acid-For which you are on PPI infact the most basic ppi in low doses.
2)To prevent the acid formed inside stomach to reflux back into esophagus-(This part of treatment is not covered by your doctor)-I would suggest you to add Levosulpiride. Itis a prokinetic drug and is very effective in controlling reflux of acid back into esophagus.A better way is to take it with Rabeprazole trials have shown that its very effective when combined with Rabeprazole.So you can switch over to Rabeprazole esomeprazoleze.

Please request your gastroenterologist to start you on PPI-antacids like Rabeprazole or Esomeprazole.Protonix will not help you much. Esomeprazole can be used in the dosage as high as 80 mg twice daily.Trials have shown that esomeprazole is superior to other PPI's in controlling reflux symptoms. Also, request him/her to add Domperidone 30mg or Levosulpiride(both are prokinetic)slow release once daily. This will slow down the reflux of acid back.Prokineic should be added in your regimen.

An antacid containing local anesthetic (Mucaine gel ) should be taken 2tsf thrice daily.

Acotiamide is another wonderful new drug and is very effective in controlling symptoms of GERD and esophagitis. In trials- Acotiamide, a gastrointestinal motility modulator, at a standard dose of 100mg thrice daily has significantly affected esophageal motor functions or gastroesophageal reflux in healthy adults.

All these drugs can be considered by your gastroenterologist to provide you with symptomatic relief in your problem.All these medicine can be used at a time also by your primary.
An initia aggressive approach is very important other wise things can become worse in near future.Acid reflux destroys normal ph of mouth hencevbacterias and yeast starts growing there also.

Please message this note to your gastro and ask him for an explainatin that why is he not following treatment as per protocol.Lets hear his explainations also.
As of now start medicines suggested by me you would see difference in 10 days.

Thanks!

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