Libbbyt;
I would suggest that you be tested for helicobacter pylori. It is a very common bacterial infection that harms beneficial flora. I believe that there is a blood test for helicobacter pylori, but there is definitely another procedure that a gastrointerologist performs using an endoscope (anesthesia) down your nose/throat. If you choose not to be tested for helicobacter pylori, completely eliminate any form of sugar from your diet for 6-8 weeks, to test if the sugar is (partly?) the culprit. You should also increase your friendly flora by consuming fermented foods. If you can, try a good kefir product. Make sure the kefir is plain, because the flavored ones have added sugar. If you can't tolerate the sourness, try adding to a low sugar, high fiber cereal, or try other foods that help with beneficial flora; jerusalem artichokes, cruciferous vegetables (broccoli, cauliflower, kale, etc.), blueberries, souerkraut, beans, and others. Psyllium husks are said to be beneficial, but some people can't tolerate psyllium. Consult with your GP or a health food agent/manager. Also, please have your water checked. If you can, purchase a quality water filter/purifier that doesn't remove beneficial minerals. Also, have you had your blood/saliva/urine ph tested? You can purchase a ph test strip, but I'm not sure how accurate they are. You can also purchase a blood ph test kit, but I think that they can be expensive, and you probably will have to rely on lab for results. Of course, the best way is at your doctor's office. If it is discovered that you have helicobacter pylori, or even gastritis, then more than likely, your doctor will prescribe antibiotics. This is when you should absoultely consume foods which increase your beneficial flora, because many, if not all, antibiotics are believed to destroy all bacteria, which includes the beneficial gut flora. Some people highly recommend apple cider vinegar for acid reflux (other benefits also). I don't know if it works or not, but I do know that I've consumed it for a few months (diluted in water) and my system can't tolerate it.
Proton-pump inhibitors remove beneficial minerals, vitamins, which can cause a host of health problems. They were originally meant to be used short-term (2-6 weeks). I have a number of family members and friends who take these medicines, long-term, and every one of them are also taking additional supplements; vitamin B-12, (which rely's on an acidic gut environment) iron, and magnesium. They never took these supplements until they were on the proton-pump inhibitors. I would first change my diet (avoid as much sugar as possible, and increase beneficial flora containing foods), check to see what's in my water, and remove as much stress (sleep well, engage in things that reward your spirit/mind/body, and if you can, disengage from people who cause stress) from your life as possible. If these things don't help with your acid reflux, then I would take the proton-pump inhibitors.
Btw, are you a vegetarian/vegan?