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More Evidence to Support the Theory That GERD Is Caused by Bacterial Overgrowth


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Note: this is the third article in a series about heartburn and GERD. If you haven’t done so already, you’ll want to read Part I and Part II before reading this article.

Right after publishing yesterday’s article (The hidden causes of heartburn and GERD), I came across a new research (PDF) study hot off the presses that adds support to the theory that GERD is caused in part by bacterial overgrowth. Before moving on to my next planned article in the series, I want to take some time to review this study and discuss its implications.

Malekzadeh & Moghaddam performed a retrospective study to investigate the prevalence of GERD in patients with IBS and vice versa. The data comes from a very large number of patients (6,476). To my knowledge it’s the largest data set that has been reported about the overlap between GERD and IBS.

The authors found that 64% of IBS subjects studied also had GERD, whereas 34% of the GERD patients also had IBS. They also found that the prevalence of all functional symptoms (such as nausea, changes in bowel movement, headache, etc.) was higher in overlapping GERD and IBS subjects than the prevalence in GERD subjects without IBS or IBS subjects without GERD.

Implications of the Connection between GERD and IBS

What this correspondence suggests, of course, is exactly what I argued in the last article: that IBS and GERD may very well share a common etiology and underlying mechanism. From the conclusion:

This finding shows that in overlapping GERD and IBS, other functional abnormalities of the GI tract are also highly prevalent, suggesting a common underlying dysfunction.

The authors even speculate that the underlying cause may be an overgrowth of bacteria. Specifically, they mention H. pylori as a possible culprit. I think they’re on to something!

Assessing the role of H. pylori infection in GERD and IBS patients could be a target of future research, as in the present study the prevalence of H. pylori infection in GERD patients was found to be greater than in non- GERD patients.

The Role of H. Pylori in GERD

I believe that H. pylori infection plays a significant role in the pathogenesis of GERD and other digestive disorders.

H. pylori is the most common chronic bacterial pathogen in humans. Statistics indicate that more than 50% of the world population is infected. Infection rates increase with age. In general, the prevalence of infection raises 1% with every year of life. So we can expect that approximately 80% of 80 year-olds are infected with H. pylori.

Second, we know that H. pylori suppresses stomach acid secretion. In fact, this is how it survives in the hostile acidic environment of the stomach, which would ordinarily kill all bacteria. Treating an asymptomatic H. pylori infection with antibiotics increases stomach acidity and eradicating H. pylori with antibiotics improves nearly all patients suffering from hypochlorhydria.

Although it is commonly assumed that stomach acid production declines with age, recent studies suggest that the secretion of stomach acid doesn’t decrease with age and that the trend is actually to increase, especially in men.

However, this tendency for acid secretion to increase with age is completely nullified by the corresponding increase in H. pylori infection. Since the incidence of H. pylori infection increases with age, it follows that hypochlorhydria also increases with age.

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Acid Suppressing Drugs Increase Risk of H. Pylori Infection

Perhaps most importantly for those taking acid suppressing drugs, researchers now believe that the initial infection with H. pylori can only take place when the acidity level in the stomach is decreased (albeit on a temporary basis). In two human inoculation experiments, infection could not be established unless the pH of the stomach was raised by use of histamine agonists. (1, 2)

If low stomach acid is a prerequisite to H. pylori infection, we might expect acid suppressing drugs to worsen current H. pylori infections and increase rates of infection. That’s exactly what studies suggest. Prilosec and other acid suppressing drugs increase gastritis (inflammation of the stomach) and epithelial lesions in the corpus of the stomach in people infected with H. pylori.

A 1996 article published in the New England Journal of Medicine followed two groups of people who were being treated for reflux esophagitis for a period of five years. One group took Prilosec (20-40 mg/day) and the other underwent surgical repair of the LES. Among those who had documented H. pylori infections at the start of the study and who were treated with Prilosec, the rate of atrophic gastritis increased from 59 percent at the beginning of treatment to 81 percent by the end of the study. Among those who had no atrophic gastritis at the beginning of the study, 30 percent of those who took Prilosec later developed it. By contrast, just 4 percent of the surgically treated group developed atrophic gastritis.

Another Vicious Cycle You’d Be Smart to Avoid

The connection between low stomach acid, h. pylori and acid suppressing drugs kicks off another nasty vicious cycle, similar to the one we discussed in the previous article.

Low stomach acid >>> heartburn >>> acid suppressing drugs >>> H. pylori infection >>> further reduction of stomach acid >>> chronic heartburn & GERD

The increased risk of H. pylori infection caused by acid suppressing drugs is especially significant because H. pylori infection is associated with a small but significant increase in the risk of stomach cancer.

I’ll have more to say about this in the next article.

As I mentioned in the last article, fermentation of malabsorbed carbohydrates produces hydrogen gas in the intestines. Hydrogen gas is the preferred energy source for H. pylori. Elevated levels of hydrogen gas are also associated with other nasty bugs such as Salmonella, E. coli and Campylobacter jejuni, the leading cause of bacterial human diarrhea illnesses in the world.

Excessive fructose, certain types of fiber and starch, and particularly wheat increase hydrogen production, and thus increase the risk of infection by H. pylori and other pathogenic bacteria. If you’d like to avoid heartburn, GERD and the many other unpleasant symptoms associated with bacterial overgrowth, it follows that you should minimize your intake of sugars, starches and grains.

In the next article we’ll examine the many important roles of stomach acid and the significant risks of long term hypochlorhydria.

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Join the conversation

  1. Thanks Chris I’ll look into those. I’m going to give the mastic another week here, I didnt take it this morning and I’m so tired, cranky, bloated and my body aches 🙁 it’s been so great for my fatigue, I’m just going to try small meals and apple cider vinegar instead of the HCL right now.

  2. First of all I wanted to say thank you so much for your articles Chris, they’ve been so helpful for me in discovering what the heck is going on with my stomach.

    I’ve been having stomach issues for the past couple years, after too many unnecessary weeks on antibiotics. I used to feel food just sitting in my stomach for so long, it felt like it just wasn’t digesting. I started doing low carb, which gave me a uti. So I added in some carbs and started taking HCL w/ betaine. So helpful! My food started digesting, it helped my anxiety, depression and energy so much!

    My current dilemma is this now: I’ve started on mastic gum, 3 weeks now so far, and this past week I’ve noticed if I take even 1 capsule of HCL with my meals I get heartburn again 🙁 but if I don’t my food just sits in my stomach like it used to. Do you, or anyone else have any suggestions as to what to do now? My doctor suggested antibiotics, as I was diagnosed with h pylori through a stool test, but I definitely don’t want to go that route, antibiotics have already messed up my stomach so badly. I believe I have fructose malabsorption, I’m having a test here soon for that and sibo. I want to get rid of this h pylori, and the mastic gum seemed so helpful at first. . .

    It’s so frustrating because I feel my best on low carb, but that seems to give me uti symptoms each time I try it. I drink kefir, which helps a bit but not enough I guess. I have to add carbs in(like potatoes and rice), but then I start to get tired and depressed again.

    • H-PLR from Apex, Lauricidin and Interfase Plus (Klaire Labs) can all be helpful against H. pylori. They’re best taken under supervision, though. Some practitioners use manuka honey, and anecdotally it works for some, but there isn’t solid research on it yet.

  3. My doc told me that i have acute gastritis, GERD and H.pylori. He is saying GERD is due to incompetent Lower Esophageal Sphincter and that was most due to my stress, food habits and sedantry life style.
    Now, i would like to know, is there a way to strengthen the Lower Esophageal Sphincter?

  4. Chris,

    Why not wipe out all bacteria — bad and good – with antibiotics (larithromycin, amoxicillin, levofloxacin), then re-colonize with good?

    • Because antibiotics permanently alter the composition of the gut flora. It doesn’t come back in the same way. There are >1,000 species of organisms in the gut. Even the broadest spectrum probiotic only has about 15.

  5. Hi Chris,
    I do have to post that I did not have GERD…..not an ounce of it…….until I had HPylori TREATED by a heavy dose of antibiotics. I went in for a simple doc. appt b/c I was feeling tired……and had lose stool…..which led to a test for HPylori……positive result and heavy 2 week treatment of antibiotics that destroyed EVERYTHING in my gut……all bad and GOOD bacteria. I have yet to recover (4 years later) from that dose…….I was not longer after the antibiotic able to have coffee and eat / enjoy all of the things that cause or stress GERD symptoms………..
    Just wanted to share…… I now have gastroparesis…….take dexilant 30 mg per day on top of domperidome 4 times a day just to be able to eat again…………..everyone is different…….I guess that’s why I’m posting……

    • Angela,

      I have had a host of health problems, including acid reflux, but I am now finally getting better after five years of seeing different doctors and specialists at prestigious clinics who could do little to help me. I have been off of proton pump inhibitors now for 2 years. I highly HIGHLY recommend going to a good acupuncturist who also uses herbal therapy. Though I don’t know you, I wouldn’t be surprised if you need to detox and reintroduce good bacteria into your system. It sounds like your bady is seriously out of balance and an acupuncturist can help you get better. Look for an acupuncturist who has many years experience. If you need help with that, just reply to this message letting me know the area where you live ( city, town state) and I can research for you. I can even ask my acupuncturist, who is one of the best where I live. Please believe me when I say that you can get better from all of this, but unfortunately traditional, allopathic doctors can make problems worse with all the medications they dole out. Hang in there!

      • Thanks Nicole. I actually did go to an acupuncturist for a year and she was amazing! My insurance changed and no longer covered her. I now see a chiropractor who is AMAZING and has helped me immensely. I am able to eat many things that I once was not…….so weight is starting to come back on. I appreciate your comments. I have also been to a naturopath and have come off of wheat/gluten all together which has also helped immensely. I am on many vitamins that are helpful…….probiotics don’t agree with me but I’m able to tolerate other things that are beneficial…….vitamins b12, D3, magnesium, ferrous sulfate, multivitamins (all from whole foods/naturopath). They have been very helpful too ; )
        Thanks again!

      • Hello Nicole, would you be kind enough to let me know what good acupuncturist should I go visit who can guide me with herbal solution? I also have GERD issues due to this anti-biotics and my gut just seam to be so un-balanced. I am currently living in Hoffman Estates, IL, 60192, but can travel anywhere within Chicago area.


  6. But what do you do about silent reflux or laryngopharyngeal reflux? The culprits for those who have this are acid and pepsin. I follow a strict gluten, grain free, low glycemic diiet. I take probiotics, but still cannot handle any form of digestive enzyme, especially pepsin, or HCL. I even tried digestive bitters and lost my voice entirely for a week due to severely swollen vocal cords from silent reflux. And ironically, I have low stomach acid and enzymes in my gut. Maybe GERD is easier explained, but LPR is a mystery. Why is it that we can’t supplement with acid and enzymes when it’s the very thing our body needs? And many with LPR have normal LES and UES tightness, as I do. Does it have to do with vagus nerve malfunction, environmental pollution? Could it simply be a form of autoimmune disease? My ENT from UCLA humbly said, ” we don’t know a lot about LPR”.

  7. i am wondering if taking a product called carbgest would help, as this product is designed to digest carbohydrates

  8. I find a great deal of food for thought here and strongly support your contention that Big Pharma wants to sell us drugs to cure the symptom, not to cure the disease itself.
    However, I need you to explain this apparent contradiction: In the first article you write “Numerous studies have shown that stomach acid secretion declines with age.” while in the third article you write “Although it is commonly assumed that stomach acid production declines with age, recent studies suggest that the secretion of stomach acid doesn’t decrease with age and that the trend is actually to increase, especially in men”. A great deal seems to hang on this point.

    Which is it? Are the studies inconclusive?

  9. Hi Chris,

    I am wondering what can be done for a six month old breastfeeding infant with H. Pylori? She’s not eating much with her reflux. The doctors say not to worry because she is still gaining weight. She’s on probiotics, but I think she’s got a good case of some sort of bacteria. How can she be tested, and would you advise antibiotics or what treatment?

  10. Chris,

    The one ‘study’ you cite in support of your theory that PPIs worsen Pylori infections is contradicted by countless studies that contend exactly the opposite. It is, indeed, this bulk of scientific knowledge upon which the current cornerstones of H. Pylori treatment (Triple or Quadruple therapy, including a PPI and 2 or more antibiotics) are based. As these treatment regimines generally result in erradication rates of 80% or greater during front-line treatment, I’d be hesitant to argue the point if I were you. Long story short – the current mainstream approach to curing Pylori infections works, and works well. And the action of PPIs is an integral part of the treatment.

    Without going into details, you lack the understanding of how PPIs actually work in regards to killing H. Pylori. There are mechanisms of action that have little to do with the general pH of the stomach.

    I’d agree that reducing stomach acid concentrations in otherwise healthy individuals presents the risk of allowing overgrowth of ‘bad’ bacteria. But once a Pylori infection has taken hold, PPIs are a useful and important part of treatment.

    Telling people they aren’t – in direct contradiction to TONS of proof – is irresponsible.

  11. I just stumbled upon this site, and anyone’s help would be greatly appreciated. My six month old son has had severe reflux since he was about one month old. It is terrible, and he goes back and forth between the good days(spits up or vomits five times) to the bad days(what seems like vomiting every twenty minutes). He has always been breastfed. His pediatrician put him on Zantac, then prevacid, then Zantac with reglan(which I used twice out of desperation and then threw away) and is now on Prilosec. I breastfed him exclusively until he was 5 1/2 months, the entire time being told he would just grow out of it. He is now losing weight instead of just being able to maintain it- he now weighs 13.7 lbs. We had a fluoroscopy performed and that showed no obstructions and only mild reflux…he threw up four times after the test was done. He suffers from ear infections- a trip to the ENT suggested that he needed
    tubes and also referred us to a pediatric GI, but that appt is not until the end of the month.
    Until then, what should I be doing? The pediatrician said that maybe the reflux would get better when he started solid foods, but it hasn’t. What do you feed a six month old baby with severe acid reflux? Twice his sweet voice has sounded raspy(probably after having a particularly bad reflux day). I am terrified of what can happen if this is not helped.

    • Children that are plagued by GERD know better than to drink more milk (pain in their throat), hence the poor appetite. Just give as much milk as he/she will take until symptoms subside by aid of the ant-acids.

      The only thing that helped my son with the same symptoms and experience is as follows:
      * Burp the child until all the gas is out of his/her system, then burp the child again just to be sure.
      * Don’t put the child down to sleep immediately after a meal, even in the middle of the night. Keep them in an upright position (ie: lay on your chest) for at least 30mins before putting the child down to sleep, after properly de-gassed.
      * Lay the child down to sleep on his/her stomach, just like they did in the old days and despite all the studies on SIDS. If there are children dying of SIDS, it’s because of neglect. Parents should know when their child is choking on their own vomit. Parents should always check that their child is still breathing!..frequently!..even in the middle of the night!

      This is the secret to raising an infant with GERD..that and making sure the child doesn’t outgrow his/her dose of ant-acid. It’s what worked for me anyways.

  12. Becky- I hope you get this…….I was finally diagnosed with gastroparesis- and I KNOW I got it from the antibiotics I took for the Hpylori….it took almost 4 years of telling me I just had reflux….I did all the acid blockers- changed my diet- didn’t understand why some people who had reflux too could just take a pill and eat whatever they wanted- gastroparesis is when your stomach doesn’t digest properly- so the test to take for that is a Gastric emptying- (you eat radioactive eggs and lay still for 2-4 hours while they watch it digest……if you do have GP, then the food will not be completely out of your stomach when it should be- BUT, I like you don’t want to be on meds- so I’m working on coming off of them- but what you can do to try to see if it applies to you is to go on a low residue diet- basically – avoid all the reflux causing things, but also eliminate things that have husks, hulls, high fiber , high fat- no raw fruits, veggies, nuts, grains wheat, popcorn….etc etc…… you can eat yogurts without fruit- white bread, butters and oils are okay- eat things in moderation- small meals- try it for a few days and see if you start to notice that you feel better…….you could have what I do- and I hope I am saving you years of misery- I was just diagnosed 2 weeks ago- and am feeling better- now that I can identify with what is going on. Let me know if I can be of any help to you- my email is alerted if people leave messages in this forum. Good luck!

    • Thanks Angela! It’s so nice to hear from people who are having similar problems and finding good results.

      I hate taking drugs unless absolutely necessary, so I’m trying to take a natural approach for two weeks – probiotics, strong manuka honey and mastic gum, and avoiding yeast, caffeine, milk and sugars (kind of similar to your diet!) And then I’m going to ask my Doctor to test me for hpylori again.

      I hope that getting rid of hpylori naturally will stregnthen my intestine/stomach, and get rid of the acid reflux that’s giving me a phlegmy cough.

      I hope you continue to get better too – keep us updated! 🙂 Thanks again for your reply.

    • Angela, how is your acid reflux now? I am developing vocal issues… and have gone on strict diet but its not helping as much as i would hope. Im seeing a gastrowhatever on wednesday. if anything, what tests should i have done?

      Im am an extremely active person that works out and eats right regularly… so im really confused why im having the GERD/voice issues…

  13. Hello

    I had h. pylori which led to a bad stomach ulcer when I was 12 years old. I’m now 24 and I’m finding I have symptoms of acid reflux (excess mucus, throat clearing cough). I feel like they may be related, but my doctor has put me on Omeprazole PPIs for four weeks. I’m loathe to take drugs if there’s a natural remedy – I asked her about diet but she said the only advice she could give was less carbonated drinks and alcohol – but I don’t drink hardly at all.

    I need some advice from someone who really specialises in this and can help from a dietary POV. Can you help?

    I’d like to have a few definitive things to avoid and increase to make sure I’m doing the best for my body (without taking prescribed drugs!)


  14. Hi Cris

    I’ve read all your articles, and found that is very interesting, I’ve been suffering from gastro and laryngo reflux, like 3 months, already I went to ENT doctor, then a GI doctor, have an edoscopic but they don’t found anything, I had tried omeprazole 20 mg, 40mg 2 times a day, nexium , but nothing seems to take this nasty symptoms away, I feel desesperated, I had to quit job because it was extreme, I just feel relieve one o two days, then it come backs again, I even got a little dysphagia, and now I had problems to talk, I can feel my voice in my chest and back , like a speaker sensation, I don’t know something stranged, apart from that I had the same symptoms as ANGELIQUE, my mouth is burning, my ears I had like sinus, headache, a hot flare in the chest, abdomen that irradiated to my back, even my ribcage is painful as well as my spine.
    I don’t know if this is GERD or something else, any advice would be appreciate it. Thanks!!!

  15. I had H Pylori about 4 years ago (only symptoms were loose stool) and was treated with antibiotics . Since then I have never been the same. I developed severe acid reflux- have had 2 endoscopies- gastritis is the only thing they came up with and a hiatal hernia. I’ve tried chiropractic care and acupuncture……been on and off meds…….eat so bland and mild – so I’ve radically changed my diet- no coffee, caffeine, spicy, tomato, onion. etc..etc…… and had a recent flare up due to stress. Am now seeing a 3rd gi doc for her opinion.
    I don’t know what the spasms are that I get near my heart/stomach area (have had my heart checked and that’s okay)….. I get nausea, and lots of acid. Why is this happening? Is this forever? I get headaches when my refulx is bad. I’m on a 30 day treatment of dexilant right now. I’m meeting with a surgeon to consider repairing my hiatal hernia but not sure if that is the answer- I’m afraid if I have it, and the symptoms still exist- that I will have had it for nothing.
    Shouldn’t irradicating the hyplori fix the problems? I don’t get why it causes the reflux and I don’t get why I can’t eat a lot of basic things that other gerd patients can. I’ve lost 10 lbs in the last 4 weeks…….do you have any suggestions?????

  16. Hello,

    I stumbled upon this blog when someone told my mother that h. pylori might be the cause of my ever present reflux problems. I have been struggling with it for three years and have not gone in to actually get diagnosed because I was convinced that Acid Reflux was my problem. I have been doing online research throughout this time and trying to figure things out but frankly nothing seems to be working. I just don’t even know where to start or what tests I should have done or frankly what I should be doing anymore. I will give you am overview of what I have been dealing with. Any suggestions, guidance, (anything!) would be helpful. I honestly just feel lost and overwhelmed and not sure what steps I should really be taking.

    GERD/Acid Reflux Symptoms (or problems) and history
    • 2008: started noticing the feeling of a lump in my throat and constant phlegm and an increase in vocal problems. My vocal teacher and other peers suggested it might be acid reflux. So I started taking over the counter medication and tried to avoid foods that cause reflux. It helped for a while, however all symptoms did not go away. The symptoms grew to include the burning sensation, burping after
    I consumed anything, the bad taste in my mouth, irritation in my ears, sinus headaches, etc. It would continue to flare up especially right before and during my period.
    • 2010: I continued to have vocal problems and completely lost my voice on one occasion. It felt like it was a result of a respiratory bug and continued because of an increase in my reflux symptoms so I went to an ENT and discovered there was also some evidence of Vocal Nodules (small but significant enough). What frustrated me the most was that he would not even consider that Acid Reflux or
    GERD could be a factor in this issue. After they went away and I still had pain in my throat I convinced him to prescribe me prescription strength Prilosec. Again it provided minimal relief for a while but then things either leveled out or got worseagain. So I asked my aunt (who works in pharmacy) if I could try Nexium. I have been using that (now an off brand Dexilant) ever since.
    • 2011: Things got worse once again so now I added a Zantacs at night and I take Tums when I am really feeling it. I do my best to avoid foods I “shouldn’t” eat but there are so many lists out there that I have no idea what I should really be avoiding! The longer I deal with this the more things I seem to be taking off my list. I am not trying to eat low fat everything, avoiding spicy food, citrus, chocolate, anything with caffeine, tomatoes, yet none of this seems to help. No matter what I consume, good list or bad list, I at least burp after I eat it. At least once a day (usually after breakfast) I have something that resembles diarrhea. It feels like I do not go a day with out some sort of irritation no matter what I do! Now I am feeling weak and tired all the time because I am sure I am not getting the proper nutrition because I frankly do not know what to eat or how to eat like this when I am simply cooking for one. I am sure I don’t get enough fruits and vegetables simply because it is too expensive to be buying them only for them to get rotten because I cannot eat them fast enough by myself. I feel like the more I try to do to combat this and the longer I deal with this the worse it gets. I am starting to worry that I
    am going to permanently damage my voice (which is a big part of my life/career) and that if I don’t figure this out it could lead to more damaging and even fatal things like cancer.

    Where do I start? What should I be doing?

    • Have you seen my post below? I think I have the same as you (also a singer!) but in earlier stages. I’m trying a combination of manuka honey (15+), mastic gum and probiotics. I’ll let you know how I get on!

  17. HI Chris,

    I was wondering what you thought of the simple cure proposed by some, i.e. apple cider vinegar (preferably with the mother in it) 1 tsp per glass of water and 1/4 tsp of baking soda, taken 3 x /day on an empty stomach? I would value your opinion.

  18. Hi Chris
    I’ve been taking Prevacid for about 9-10 months on a daily basis (once per day).
    I read all this information on this article and I will definetely be trying the low carb diet. I’m just tired of feeling this way. Every since I got on the Prevacid I feel like my symptoms have increased and even though I lost weight from 158lbs to 145 i felt better, but still have to take the meds. I tried to skip 2 -3 days to try to weaned myself off of them but no success. My diet has been lots of carbs, fruits and some vegetables. I don’t eat many salads cause I feel that irritates my stomach, but perhaps I can eat something else to compensate. Where can I find a list of things that I can cook with that are low carb??? Please help!!!!! thank you so much in advance!!!!

  19. Hi Chris, wonderful reading thank you. I had a gastroscopy ,they found gastritis, and HP. I have been hesitant to take the anit biotics and have found a herbal formulas specifically for HP and gastritis. There was quite a lot of white blood cells around the stomach so i presume an infection is there. Thank fully i do not get reflux but i do get bloating, gas and found the GAPS diet helpful which is no grain or sugar but very high in fat. I do not follow it strictly but have found the no grain very beneficial. I would be interested for your opinion on GAPS.
    I have just started the herbal formula and will let you know how it goes. I don’t know if i am allowed to mention the brand so i wont.
    What is your opinion in taking the herbal remedy rather than the anti biotics.
    thank you for your thorough information