More evidence to support the theory that GERD is caused by bacterial overgrowth

April 2, 2010 in GERD, Myths & Truths | 35 comments

picture of H. pyloriNote: 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.

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.

{ 35 comments… read them below or add one }

Mark April 2, 2010 at 5:57 pm

Is there a simple test for H. pylori infection?
Would it make sense to test for and, if present, treat for this infection in the absence of Heartburn/GERD symptoms in order to prevent any esophagial damage that may occur before the onset of symptoms?


Chris Kresser April 2, 2010 at 6:03 pm

There are several methods of testing for H. pylori. Your doctor will be able to order it for you.

If it were me, and I tested positive but didn’t have symptoms, I would probably go on a very low carb diet and try to starve it out before I did the antibiotics. Second choice would be an antibiotic herbal formula, but you’d have to find a qualified herbalist to prescribe that.


Richard Nikoley April 2, 2010 at 6:00 pm

I found this particularly interesting.
“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.”
Anecdotal, but my dad should have bought stock in Rolaids when I was a kid. He was always chewing them. I can remember times when he’d get heartburn at night and said he went through a whole roll and still couldn’t shake it. (All four of his sons “inherited” awful heartburn, all were on PPIs and I believe one of my brothers still might be.)
Then dad found PPIs and to him, it was a miracle. Fast forward to a couple of years ago when he went LC paleo (grain & sugar free). He was able to stop the PPIs cold turkey and claims to have not had on e single episode of heartburn. He just turned 72.
I’m wondering if simply taking 200mg of HCI per hour for a few days, perhaps more and then decreasing to every 2, 3, etc., might simply serve to quickly eradicate H. Pylori, essentially setting up a beneficial circle as the bacteria die off and more natural stomach acid is produced, and so on.
I can’t even begin to tell you what a great and informative series this is, Chris.


Chris Kresser April 2, 2010 at 6:14 pm

Hi Richard,

Your father’s story is indeed interesting. What a testament to the therapeutic power of a low-carb diet for heartburn and GERD!

Although H. pylori can only take hold when stomach acid is low, I’m not sure that HCL would be therapeutic once the H. pylori infection is established. H. pylori avoids the strongly acidic environment of the lumen by migrating below the mucous layer in contact with the epithelium. In this way it protects itself from acid output once it becomes normalized.

However, as I said in my reply to Mark, a very low carb diet should be effective in at least reducing bacterial loads, since hydrogen gas produced by carbohydrate fermentation is the major food source of H. pylori. H. pylori is notoriously difficult to eradicate, but if you completely remove its food source that should certainly be a step in the right direction. You could also combine HCL supplementation (to ensure an environment inhospitable to recolonization) and mastic gum with the very low carb diet. There is mixed research on mastic, but some studies suggest it has significant therapeutic benefits. If you can find a licensed Chinese herbalist in your area, that would also be a good choice. There are several effective antimicrobial herbs in the Chinese pharmacopia.

Good luck Richard! Keep us posted.


Musings of a Housewife April 2, 2010 at 6:52 pm

I’m a long time follower of your blog, but I’m not sure I’ve ever commented.  These articles are tremendously interesting to me, as I have suffered from a variety of gastrointestinal ailments for the past four years.  I was on Nexium for 2 or 3 years, and I finally went off it and managed my symptoms with low-carb, smaller portions, and apples, lol.  Apples really helped.  Now I’m virtually symptom free, unless I backslide into my carboholic ways.  I also have horrid gas pains from time to time, and have had IBS since I was a child.  It all makes sense now.  THANK YOU for bringing these issues to light.  I am so frustrated with the medical community on this issue, it just makes me livid.  I’ll be linking to this series tomorrow from my blog.  Can’t wait to read the next one.


Chris Kresser April 2, 2010 at 7:01 pm

I completely understand your frustration. I have Crohn’s disease myself and the medical establishment is completely clueless about how to treat it. I’ve been able to almost completely eliminate any G.I. symptoms by following a low/specific carbohydrate diet, properly preparing (soaking/sprouting) grains when I do eat them (rarely), re-establishing healthy gut flora through consumption of fermented foods (yogurt, kefir, sauerkraut, kombucha, etc) and managing stress. Thanks in advance for the link!


Forty2 April 3, 2010 at 6:49 am

I picked up H. Pylori in 1999 when I lived in China. It is rampant in China. A course of antibiotics treated it, but symptoms returned a couple years later which is when I was put on Nexium. i had to switch to Aciphex last year because my so-called medical insurance no longer covered it, even though Aciphex is more expensive. This makes no sense to me, but then I am not a Big Pharma/Med executive raking in the bonuses so what do I know.
Anyway it has been a few days since I have stopped the Aciphex and aside from a mild twinge here and there I feel fine. I suppose it’ll take awhile for my stomach acid levels to recover.


Tim April 3, 2010 at 2:15 pm

I did some reading after you wrote your first two articles about gerd. Many seem to believe that it’s really bad to have helicobacter pylori in your body at all. But as you write, it should be fine as long as you have enough stomach acid. Nora Gedgaudas writes this:  ”We do need some H pylori, however. It plays a complex role in the regulation of leptin, so fully eradicating it is not the answer. Managing excess overgrowth, with certain nutrients and restoring normal hydrochloric acid levels, is the better alternative.”. According to her, having some H pylori is even beneficial. Have you heard of this? So if this is true, would a H pylori test do any good? Or can the test show if the pylori is in excess and if it actually caused an infection?
So why do one get low stomach acid in the first place that allows for bacteria/yeast overgrowth and maldigestion of foods? Nora writes that too much sugars and starches and an inadequate intake of protein is an extremely common cause of low stomach acid. She also mentions some other causes of low stomach acid: low thyroid function, B1 C zinc deficiences, excess alcohol and chronic stress.


Chris Kresser April 4, 2010 at 11:18 am


Is that quote from Nora’s book?

I’m not convinced that H. pylori is beneficial, but most would agree that there is always a balance of pathogenic and beneficial bacteria in the gut. In health, the beneficial bacteria keep the pathogenic in check. In disease, the pathogenic bacteria have gotten out of control. This happens not only in GERD, and not only with digestive diseases, but with many other conditions including obesity.

I agree with Nora that controlling the overgrowth is probably a better choice unless you have an ulcer or serious digestive condition. I also agree that low stomach acid can be caused by a high-carb, high sugar diet (which in turn increases bacterial overgrowth, which inhibits stomach acid production). And chronic stress is surely a factor. I may write a post about this, because it deserves attention.


Tim April 4, 2010 at 3:22 pm

Yes, that’s from Nora’s book.

Some further googling gave me some more interesting info. says “Increasing microbiological and epidemiologic evidence indicates that H. pylori was once more common, perhaps nearly universal in humans, than it is in our postmodern society”. That article is ten years old, though.

Interesting study:

So I guess it’s just fine to have some H pylori as long as you got normal stomach acid levels.


Chris Kresser April 4, 2010 at 3:48 pm

Thanks for that link, Tim.  Interesting paper.

Yes, I agree that H. pylori is probably not worth going after with drugs in asymptomatic or mildly symptomatic individuals.  A low-carb diet and ensuring sufficient stomach acid is a better choice in most cases.


Desdemona April 5, 2010 at 8:55 am

I wonder how this all ties in with pregnancy.  Anyone who’s know a pregnant woman or two knows that stomach acid is a big complaint.  I took my share of tums when I was pregnant a few years ago.  I was on a SAD diet at the time though.  Plenty of carbs.

It is a common thought that immunity goes down with pregnancy.   I seemed to get sick a lot easier then.  I am guessing that might also be a factor in the raised amount of reflex in pregnancy?


Chris Kresser April 5, 2010 at 9:01 am

Both obesity and pregnancy increase intra-abdominal pressure, which causes the LES to dysfunction. That’s why there’s a higher incidence of GERD in both of these populations.


Tim April 5, 2010 at 1:31 pm

Chris, do you know exactly how lots of carbs and low protein cause low stomach acid?
I would be very interested in knowing my stomach acid levels. Maybe I should try some HCL pills and see how many I need until I get that burning feeling.


Chris Kresser April 5, 2010 at 3:01 pm


The theory is as I explained it in the second article:

Malabsorbed carbs > bacterial overgrowth > stomach acid suppression

We know that H. pylori suppresses stomach acid, and it’s certainly possible that other bacteria do as well.

Protein stimulates the secretion of HCL. If you eat a very low protein diet, stomach acid will likely decline. I’ve seen this happens with vegetarians.


Beth C April 6, 2010 at 11:58 am

Thanks so much for your website.  I’m a long time GERD & IBS sufferer who is in the process of learning how to take care of myself.   It really is a self discovery process when one comes to the realization that we are on our own – health wise.    I’m trying to live low carb, no sugar & no industrial oils with a two steps forward – one step back  dance that I guess is progress.  I feel better than before and that’s good.
Can you explain the properties of how HCL operates in our bodies when used as a supplement and why taking it before a meal is advised as opposed to during or after a meal?  Also, could taking it after a meal (as in when I forget until the meal is starting to let me know something is wrong) be helpful although perhaps not optimal?
Beth C


Chris Kresser April 6, 2010 at 1:19 pm


HCL is hydrochloric acid, which our stomach secretes to digest protein and assist in nutrient absorption (vitamins and minerals). It also indirectly helps with digestion of carbs and fat by stimulating the release of pancreatic enzymes and bile into the small intestine. Taking it before a meal ensures that there’s enough HCL in the stomach to properly digest the food eaten at that meal. It is possible to take after a meal, but some people experience burning that way if they aren’t digesting the food properly and they burp, brining the most recently swallowed material (HCL in this case) up into the esophagus.


Tim April 6, 2010 at 2:46 pm

But what comes first, the low stomach acid or the malabsorbed carbs? Can carbs be malabsorbed even when stomach acid is normal? I guess one possible reason could be overeating which could lead to some non-digested carbs getting through…


Chris Kresser April 6, 2010 at 5:39 pm

I don’t think it’s a straight, linear, causal relationship. There are other factors that can decrease stomach acid, including (perhaps most significantly in today’s world) chronic stress. Carbohydrate malabsorption can be caused by any number of conditions, including gluten intolerance, which is significantly undiagnosed. In that case consumption of gluten blunts the intestinal villi, which in turn inhibits digestion. In the end, it doesn’t matter so much exactly what order the steps of dysfunction took, because the treatment is the same: reduce carbs, increase stomach acid, manage stress, eat fermented, probiotic foods and use bitters and other botanicals if needed.


Beth C April 7, 2010 at 8:23 am

Hello again,
Is there an optimal time to take HCL prior to a meal?  15 min?  30?  1 hour?
My not so controlled trial is that up to 15 minutes prior doesn’t do too much.   It seems like 30 minutes to an hour is more useful.  Does the acid production rise and stay within the stomach that long?   And is there any harm in taking HCL and then not eating?


Deanna April 7, 2010 at 8:57 am

I’m a 47 yr old female, diagnosed with GERD–prescribed and taken Prilosec, then Nexium, for the last 13+ yrs. Switched to a mostly real food diet about 5 yrs ago. Recently stepped-up the diet a bit with inclusion of only pastured raw milk, eggs, meat and no (except for the special occasion) processed food of any kind, white sugar or white flour. Eat plenty of homemade yogurt and drink raw kombucha. Recently stopped taking my purple pill to see if I can fix what’s obviously been broken in my gut for years. Been taking ACV/honey/b soda 3x a day for 3 days now. Symptoms better than expected and certainly manageable, but still have heartburn flair-ups.

Two questions: 1) Am I beyond fixing? and 2) Will your next (or any future) article in this series address the specifics of what we can try/do to remedy GERD?

I’ve read all three articles in your series so far, plus a couple others that mention GERD. Thanks for the information and the help.


Chris Kresser April 7, 2010 at 9:10 am

I don’t think you’re beyond fixing. The next article will discuss the importance of stomach acid in health, and the danger of acid suppressing drugs (which you’ve already experienced). The article following that one will contain my recommendations for treatment. Stay tuned!


Jesse April 7, 2010 at 9:24 am

Interesting articles. I don’t really know anything about GERD, so this is as good a starting point as any for finding out about it.
Just for fun, sorta, here’s an article about some research that implies that H. pylori might protect against tuberculosis. I suspect your readers won’t worry about that too much though, in the face of a real problem.
My father-in-law has heartburn, so that he can’t eat too late in the evening or he won’t be able to lie down for a while, but when he eats low-fat high-carb vegan food he doesn’t get it. What’s with that?


Chris Kresser April 7, 2010 at 2:32 pm


There is anthropological evidence suggesting that humans in the past were universally colonized by H. pylori, and there are also studies (like the one you linked to) indicating possible benefits to H. pylori colonization. That is why I don’t generally recommend aggressive treatment of H. pylori with drugs, unless someone is suffering from a severe ulcer, which has dangerous potential complications.

On the other hand, studies do consistently show that H. pylori colonization moderately increases the risk of gastric cancer.

It’s well known that we have a combination of both “good” and “bad” bacteria in our guts. This isn’t a problem as long as the good keep the bad in check, which is normally the case. But factors such as stress, antibiotic use, overconsumption of simple sugars, etc. can tip the balance in favor of opportunistic pathogenic bacteria.

My guess is that H. pylori isn’t a problem unless it proliferates to an unhealthy concentration. In most cases carbohydrate restriction, HCL, and probiotics should be enough to restore balance.

I’m not sure why your father-in-law has that experience. Each person is different. But it’s possible he has trouble digesting protein due to low stomach acid, so when he eats fruit and vegetables he feels better.


Jesse April 7, 2010 at 3:27 pm

Yeah, maybe most people are colonized by H. pylori because it has some benefit in some situations that outweighs its negative effects.  I agree that trying to wipe it out now isn’t a good idea though.
It probably is the healthiness of the vegan food that helps my FIL. His alternative would be something unhealthy like fast food probably.


Chris Kresser April 10, 2010 at 4:05 pm

Hi folks,

The next installment in the series is up: How your acid stopping drug is making you sick (Part A).  Part B will be published on Monday or Tuesday.



Chris Kresser April 16, 2010 at 10:41 am

Final article in the series is up.

Also, the entire series as well as recommendations for books and offsite articles can be found here.


Kora May 27, 2010 at 7:31 pm

As a gerd sufferer, I can’t believe that no one has stated the obvious problem for many of us with a low-carb diet:  HOW TO KEEP THE WEIGHT ON.    I am too thin, and tried to do the low-carb and no wheat together for a week.  Didn’t notice a big change but part of my problem was that when I don’t eat enough, I get bad nighttime heartburn.  Any suggestions?


Chris Kresser May 27, 2010 at 7:43 pm

Most people don’t eat enough fat on a low-carb diet. When you remove the carbs, you have to increase fat intake commensurately. My diet is approximately 60% calories from fat, to give you an idea. The thing to be aware of is that there’s a transition phase you’re just going to have to get through. When the body is used to burning carbs for energy, and you switch over to burning mainly fat, it takes a while to make that shift. L-carnatine can be helpful during that period, because it promotes fatty acid metabolism. You can also have a couple spoons of extra-virgin coconut oil when you get hungry. Coconut oil is an MCT (medium-chain triglyceride) and is rapidly absorbed, which makes it a great source of quick energy. Once you get accustomed to the low-carb diet, you’ll find that you have a very even level of energy throughout the day and don’t have the swings of hunger you have on a high-carb, lower fat diet. It can be a difficult transition, but the end result is well worth it!


Oscar Picazo April 11, 2011 at 10:17 am

Hi Chris, I have been diagnosed H. Pylorii through the breath test, and I am in treatment (antibiotics for 7 days and omeprazole for 6 weeks).

Following all the reasoning behind, I do not understand why using a proton pump inhibitor for the treatment, it seems like going against the effect of lowering pH in the stomach to keep H. Pylorii away!.

What do you think about that?


Chris Kresser April 11, 2011 at 1:20 pm

PPIs do not lower pH, they increase it. Increased pH = decreased acidity. One of the purposes of stomach acid is to kill bacteria like H. Pylori. H. Pylori has a survival mechanism where it suppresses stomach acid. So PPIs are a bad idea with H. Pylori.


Oscar Picazo April 14, 2011 at 9:28 am

Thank you very much for your reply Chris, yes, that’s what I meant, using PPI goes against lowering pH = increase acidity, therefore it seems a bad idea to use them when treating H. Pylori with antibiotics… I have found most treatments take PPI the same time as antibiotics, they do not extend PPI 5 additional weeks! I will ask my doc…

By the way, just three days on treatment and I really can notice the change, not only in gastroesophagic disturbance, but also on energe levels, I do not feel tired anymore. H. Pylori looks to be a nasty guest, I am being treated to find out if platetelet count increases, as it has been observed this effect on some people, although it is not known yet the mechanism by which the bacteria affectes trombocyte levels (a self-immune response is suspect)


Brittany August 29, 2010 at 4:29 pm

About a month or so after the start of my stomach problems, I was tested for H. pylori through a blood test. Would that be an accurate enough test to assume my levels are at least in a reasonable range?


Chris Kresser April 11, 2011 at 1:21 pm

No. Stool and breath tests are the only accurate tests.


Soraiya Edressi June 21, 2011 at 11:45 am

Hey Chris, for the past three years I have been in and out of specialists offices for abdominal pain which is radiaing to my back. I have been on many many meds., and two months ago a very high shot especialist put me on pantoprazole, after many upper GI test, and diagnosed me with GRED. Because of the hursh side effects of this med, I have started to research for alternative solutions and I have found your WEB. I have read your articles and followed your recommandations. I feel 80% better in a week. Thank you for exposing the scames of drug dealer doctors in USA.


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