I took Protonix for about 10 years. about 2 years ago, it stopped working. I didn't do anything about it at first, just kept taking it and feeling miserable. When it got to the point where I could only sip tepid water because swallowing anything else hurt and created heartburn, I went to a GI. From the time I first got diagnosed with GERD up to this point I had not kept in touch with the GI who initially diagnosed me. When I moved to a new town and found a new primary physician, he just kept refilling my prescription for Protonix. When I asked him to suggest a local GI, he did and that GI is the one I've been working with for about a year and a half.
An endoscopy was done by this new physician and showed no Barretts, but serious damage inside the esophagus. He started talking about my being a good candidate for surgery - this was my introduction to the fundoplication procedure and the one that is done endoscopically. The GI wanted to put me on Nexium but I stated I had tried it before and it didn't agree with me - it gave me severe cramps and made me feel sick. While discussing digestive issues, I mentioned being lactose intolerant. The GI said sometimes an overgrowth of bacteria can cause a person to not be able to tolerate Nexium and also show signs of lactose intollerance. So he ordered a test - it's a breath test where you blow into a bag to get a baseline of the gasses you exhale, then drink a nasty drink, then breath into separate bags every 15 minutes for 3 hours to collect your exhaled breath. If you have an overgrowth of bacteria, it will show up in your exhalation. Low and behold I was off the chart with bacterial overgrowth. He prescribed an antibiotic. Two weeks later, I was enjoying a glass of milk like I hadn't been able to in years. Then I went on Nexium with no problems. And yes, the overgrowth was due to bacteria that is supposed to be killed by stomach acid getting into the intestines and running rampant in an environment that they weren't supposed to get to in the first place.
I do believe in probiotics, however, I use them in conjuction with antibiotics. The antibiotic will get rid of the overgrowth - as well as the good stuff. So I take probiotics along with the antibiotic to ensure when everything gets "nuked" I'm replenishing the good before the bad can take hold.
I spoke to both my GI and surgeon about the less invasive endoscopic procedure through the esophagus that someone posted about on this forum. Because it's a newer procedure, I was uncomfortable with it. The research I did found that it was not permanent and had to keep being redone after a couple of years. I wanted a chance for long-term relief.
I also tried the naturopath route several years ago, but my reflux was too bad to be controlled naturally plus the hiatal hernia contributed to my misery. I do see a naturopath physician regularly as well as a regular MD. I find they compliment each other quite nicely.
Hope this answered your question.