The hidden causes of heartburn and GERD

bread and other high carbohydrate foodsThis is the second article in a series on heartburn and GERD. If you haven’t read the first one, I’d suggest doing that first.

The idea that heartburn is caused by too much stomach acid is still popular in the media and the public. But as Daniel pointed out in the comments section of the last post, anyone familiar with the scientific literature could tell you that heartburn and GERD are not considered to be diseases of excess stomach acid.

Instead, the prevailing scientific theory is that GERD is caused by a dysfunction of the muscular valve (sphincter) that separates the lower end of the esophagus and the stomach. This is known as the lower esophageal valve, or LES.

The LES normally opens wide to permit swallowed food and liquids to pass easily into the stomach. Except for belching, this is the only time the LES should open.

If the LES is working properly, it doesn’t matter how much acid we have in our stomachs. It’s not going to make it back up into the esophagus. But if the LES is malfunctioning, as it is in GERD, acid from the stomach gets back into the esophagus and damages its delicate lining.

Here’s the key point. It doesn’t matter how much acid there is in the stomach. Even a small amount can cause serious damage. Unlike the stomach, the lining of the esophagus has no protection against acid.

We’ve been asking the wrong question

In a recent editorial published in the journal Gastroenterology, the author remarked:

Treating gastroesophageal reflux disease with profound acid inhibition will never be ideal because acid secretion is not the primary underlying defect.

I couldn’t agree more. For decades the medical establishment has been directing its attention at how to reduce stomach acid secretion in people suffering from heartburn and GERD, even though it’s well-known that these conditions are not caused by excess stomach acid.

Instead, the question researchers should have been asking is, “what is causing the LES to malfunction?” Since it is universally agreed upon that this is the underlying mechanism producing the symptoms of GERD, wouldn’t it make sense to focus our efforts here?

That’s exactly what we’re going to do in this article.

GERD is caused by increased intra-abdominal pressure

It is well accepted in the literature that GERD is caused by an increase in intra-abdominal pressure (IAP). Acid reflux occurs when pressure causes gastric distention (stomach bloating) that pushes the stomach contents, including acid, through the LES into the esophagus.

According to current thought, factors contributing to this include overeating, obesity, bending over after eating, lying down after eating, and consuming spicy or fatty foods.

For example, several studies have indicated an association between obesity and GERD, and this recent paper in Gastroenterology concluded that increased intra-abdominal pressure was the causative mechanism.

But while I agree that all of the currently accepted factors play a role, I do not think they are the primary causes of the increased IAP seen in GERD.

The two primary causes of increased intra-abdominal pressure

Instead, I believe the primary causes of IAP (and thus heartburn and GERD) are bacterial overgrowth and maldigestion of carbohydrates – both of which are caused at least in part by low stomach acid.

In a nutshell, the process looks like this:

diagram of what causes gerd

Let’s look at each step in turn.

Low stomach acid causes bacterial overgrowth

As I will explain in the next article, one of the chief roles of stomach acid is to inhibit bacterial overgrowth. At a pH of 3 or less (the normal pH of the stomach), most bacteria can’t survive for more than 15 minutes. But when stomach acid is insufficient and the pH of the stomach rises above 5, bacteria begin to thrive.

The gastrin knockout mouse, which is incapable of producing stomach acid, suffers from bacterial overgrowth – as well as inflammation, damage and precancerous polyps in its intestines. It is also well documented that acid-suppressing drugs promote bacterial overgrowth. Long-term use of Prilosec, one of the most potent acid suppressing drugs, reduces the secretion of hydrochloric acid (HCL) in the stomach to near zero. In one trial, 30 people with GERD were treated with a high dose of Prilosec (40g/day) for at least 3 months. 11 of the 30 Prilosec-treated people had developed significant bacterial overgrowth, compared with only one of the ten people in the control group.

Low stomach acid causes maldigestion of carbohydrates

Stomach acid (HCL) supports the digestion and absorption of carbohydrates by stimulating the release of pancreatic enzymes into the small intestine. If the pH of the stomach is too high (due to insufficient stomach acid), the pancreatic enzymes will not be secreted and the carbohydrates will not be broken down properly.

Bacterial overgrowth + maldigested carbohydrates = GAS!

Though microbes are able to metabolize proteins and even fats, their preferred energy source is carbohydrate. The fermentation of carbohydrates that haven’t been digested properly produces gas. The resulting gas increases intra-abdominal pressure, which is the driving force behind acid reflux and GERD.

When stomach acid is sufficient and carbohydrates are consumed in moderation, they are properly broken down into glucose and rapidly absorbed in the small intestine before they can be fermented by microbes. However, if stomach acid is insufficient and/or carbohydrates are consumed in excess, some of the carbs will escape absorption and become available for intestinal microbes to ferment.

A nasty vicious cycle: the role of hydrogen gas

Hydrogen (H2) is one of the gases produced by bacterial fermentation of carbohydrates. In fact, there have been explosions during intestinal surgery due to the high amounts of hydrogen gas production in the gut. This is significant because a recent landmark study demonstrated that pathogenic bacteria feed on hydrogen gas.

So, the more undigested carbohydrate you have in your gut, the more hydrogen gas bacteria will produce. The more hydrogen gas is produced, the more bacterial overgrowth will occur. And the more bacteria you have in your gut, the more gas will be produced by fermentation of undigested carbohydrate. This becomes a nasty vicious cycle.

There is significant evidence that the carbohydrates consumed in the “standard American diet” contribute to this phenomenon. Fructose is a particular problem. In one study researchers fed fructose to 15 normal adults. They found that more than half of the 15 adults showed evidence of fructose malabsorption after just 25g of fructose, and greater than two-thirds showed malabsorption after 50g of fructose. To put this in perspective, one 12 oz. can of Coca-Cola contains 30g of fructose.

One of the measures of malabsorption used in the study was a hydrogen breath test. Both the 25g and the 50g doses caused a large increase in H2, especially the 50g dose (a 5-fold increase). Bacterial fermentation of carbohydrate is the only source of hydrogen in the human body. This means that the hydrogen measured in the study indeed came from the undigested fructose in the gut.

Certain type of fiber and starch also promote hydrogen production. Almost all of the fiber and approximately 15-20% of the starch we consume escape absorption. The amount of gas that can be produced by undigested carbohydrates is almost hard to believe. According to Suarez and Levitt, just 30g of carbohydrate (equivalent to 1/2 of a small muffin) that escapes absorption in a day could produce more than 10,000 mL of hydrogen gas. That’s equivalent to ten large one-liter water bottles full of intestinal gas!

Finally, a recent study showed that ingestion of lactose (the carbohydrate found in milk) results in an increased number of transient lower esophageal sphincter relaxations (TSELRs), increased reflux episodes, higher esophageal acid exposures, and more severe GERD symptoms. Another study showed that oral administration of fructo-oligosaccharides (FOS) produces similar findings. Together these studies suggest that colonic fermentation of malabsorbed carbohydrates contributes to the pathogenesis of GERD.

Other supporting evidence

If gas produced by microbial fermentation of carbohydrates causes acid reflux, we might expect that reflux could be treated by either 1) reducing bacterial overgrowth or 2) reducing carbohydrate intake.

In fact, that’s exactly what we see. In a study by Pehl, administration of erythromycin (an antibiotic) significantly decreased esophageal reflux. In another study by Pennathur, erythromycin strengthened the defective lower esophageal sphincter in patients with acid reflux.

To my knowledge there have only been two small trials performed to test the effects of carbohydrate restriction on GERD. Both had positive results. A small case series showed a significant, almost immediate resolution of GERD symptoms in obese individuals initiating a very low-carb diet. A more recent study found that a very low-carb diet decreased distal esophagus acid exposure and improved the symptoms of GERD. Perhaps most importantly, the magnitude of the improvement was similar to what has been reported with treatment with proton-pump inhibitors (acid suppressing drugs).

Many researchers now believe that Irritable Bowel Syndrome (IBS) is caused by bacterial overgrowth in the small intestine (SIBO). A study performed at the GI Motility Center in Los Angeles in 2002 found that 71% of GERD patients tested positive for IBS – double the percentage seen in non-GERD patients being examined.

The high prevalence of IBS in GERD patients combined with the recognition that bacterial overgrowth causes IBS is yet another line of evidence suggesting that bacterial overgrowth is also a causative factor in GERD.

A unified theory

To summarize, GERD is caused by increased pressure in the stomach resulting in a malfunction of the lower esophageal sphincter (LES). The increase in pressure is caused by bacterial overgrowth and malabsorption of carbohydrates, both of which are precipitated by low stomach acid. Reducing bacteria loads and limiting carbohydrate intake have both been shown to greatly improve, and in some cases completely cure, acid reflux and GERD.

In the Part III of the series I discuss the connection between GERD and H. pylori, and further evidence supporting the theory that GERD is caused by bacterial overgrowth. Read on!

Related posts:

  1. More evidence to support the theory that GERD is caused by bacterial overgrowth A recent study confirms the link between GERD & IBS and speculates that the two...
  2. Audio interview on how to cure heartburn and GERD without drugs Joanne from Joanne Unleashed interviews me about the causes and natural cure for heartburn and...
  3. Get rid of heartburn and GERD forever in three simple steps Follow these three steps to get rid of heartburn and GERD once and for all...
  4. What Everybody Ought To Know (But Doesn’t) About Heartburn & GERD Contrary to popular belief, heartburn and GERD are caused by too little - not too...
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  1. Jeremy’s avatar

    Great article. I will wait for the followup.

  2. Kim’s avatar

    Well Chris, more interesting info. Some of this I was familiar with, but found the studies involving the use of antibiotics to treat the bacteria and resulting GERD symptoms especially strengthening the LES  intrigues me.

    Since I’m still in the early stages of overcoming this condition, could I possibly benefit from a course of antibiotics? And if so, is there an alterntive to erythromycin? It’s been years since I’ve taken any, but got horrible stomach pain when I did. I think it’s just a basic broad spectrum antibiotic, isn’t it?

    Secondly, I sensed that dairy was a problem for me due to the milk protein. In particular, it aggravated my asthma because it does cause production of mucous. However, I have recently discovered raw milk and seem to not  experience problems with it; either mucus production or reflux. I’m wondering as in the case of yogurt, if the naturally ocurring friendly bacteria in raw milk  pre-digests most of the lactose that feeds the bad bacteria in the gut.  In addition, perhaps those friendly bugs help keep some of the bad bugs in check that would produce the gas. Your thoughts?

  3. admin’s avatar

    Hi Kim,

    I’m not sure if I mentioned this, but I am planning a follow-up to this series on the connection between asthma and GERD.

    To answer your question, one of the reasons raw milk is superior to pasteurized milk is that it has lactase in it. Lactase is the enzyme we need to digest lactose, the sugar in milk. In non-dairy consuming societies, lactase production usually drops about 90% during the first four years of life (after weaning), although the exact drop over time varies widely.

    Pasteurization kills lactase. This is why so many people have trouble digesting pasteurized milk. But those same people can often digest raw milk without a problem, because it has lactase in it.

    The probiotics in yogurt (as well as kefir, sauerkraut, kombucha, kim chi and other fermented foods) can be helpful in re-establishing healthy gut flora.

    Before resorting to antibiotics, I would try a period of time with a grain-free, very low-carb diet (< 30g/day) combined with an increase in probiotic intake and HCL w/pepsin supplements. It's important to proceed slowly as you increase the probiotics, because moving too fast can cause gas, bloating and intestinal discomfort.

  4. admin’s avatar

    One more thing: there is evidence that raw milk can prevent asthma from developing in children. I haven’t seen any studies on whether it can actually treat or cure asthma, but it’s certainly possible.

  5. Daniel’s avatar

    Very good article.
    My acid reflux (very bad even at a young age) seemed to get worse during times in my life when (i) I weight lifted and (ii) drank a lot of beer.  Weight lifting can cause IAP as does the bloating from beer (and maybe some carb malabsorption too).
    I’ve considered going very low carb to avoid reflux but I think the other health costs weigh against it (but that’s another whole conversation).
    Thanks for your very thoughtful essay.

  6. Tim’s avatar

    Great article. I have a lot of questions  :)
    Except medicine, what can cause low stomach acid? I know there are people who had GERD but hadn’t taken any meds. Could it be low levels of minerals, proteins, fats? Or is it perhaps the bacterial overgrowth itself?
    How do one test for low stomach acid?
    I have a relative with GERD. The reflux happens when she drinks coffee. Do the bacteria like coffee? What other non-carb intense foods can cause reflux and why does this happen?

  7. tooearly’s avatar

    well written. I imagine that there is incredible variability in how each of our guts responds to different diets. Big protein meals for supper  have always made me sleep poorly.

  8. admin’s avatar


    Bacterial overgrowth can cause hypochlorhydria, especially h. pylori.  It’s estimated that more than 50% of people in the world are infected with h. pylori, so that’s probably the primary cause aside from PPI use.  Studies indicate that h. pylori infection increases with age and is the cause of higher rates of hypochlorhydria in the elderly.

    The medical test for low stomach acid is called the Heidelberg capsule test.  It’s a small plastic capsule with measuring equipment that is swallowed and monitored via radio.

    The “low-tech” way of testing stomach acid, which I’ll describe in the article on treatment, is to do an HCL challenge test.  You take a 200 mg capsule of HCL w/pepsin before a meal.  If you notice no burning, you increase to two capsules the next meal.  Proceed until you notice a mild burning sensation, then immediately reduce your dose to the number of capsules that preceded the burning or heat sensation.

    If one or two capsules causes burning, you either don’t have low stomach acid or your reflux is so severe that you won’t be able to take HCL until you get it under control.  NOTE: do not perform this test if you have an active ulcer or a history of ulcer.

    The bacteria don’t like coffee, but if she has milk and sugar in it they love that. Coffee is high in tannins, which can cause indigestion.

  9. admin’s avatar


    When stomach acid is insufficient, putrefaction of protein can cause gas and increased intra-adbominal pressure.  This could certainly affect your sleep.  It’s possible your stomach acid is low or borderline low, and you’re not able to digest large amounts of protein.

  10. Forty2’s avatar

    admin: gas and pressure, eh? I went off Aciphex today. I’ve been on a very low-carb/hi-fat/hi-protein diet, and have felt tremendous pressure all along the lower rib cage (upper colon?) especially on my right side for the past week or so, have been farting like a tuba quartet and haven’t taken a crap in a week. Maybe going off Aciphex will hopefully knock something loose.

  11. Chris Kresser’s avatar


    My guess is your stomach acid is extremely low from the Aciphex.  Try taking HCL w/pepsin capsules before meals.  You might also try slowly increasing your intake of fermented foods (yogurt, kefir, raw sauerkraut, kombucha, etc.) to address the bacterial overgrowth.  Constipation is almost always related to an insufficiency of healthy flora in the gut, which can also cause all of the other symptoms you describe.

  12. Mike’s avatar

    Awesome article, Chris, and excellent explanations and references!

  13. Forty2’s avatar

    Admin: I drink kombucha daily and some days I eat full-fat “Fage” yogurt as I did this morning right out of the container. There’s a jar of Bubbe’s fermented raw pickles  in the fridge I keep forgetting about.
    Do PPIs have a permanent effect? I’m loathe to try HCL supplements at this point. Psychologically, I suppose, but I don’t ever want to revisit the searing pain of reflux ever again.

  14. Chris Kresser’s avatar

    Thanks Mike!

  15. Chris Kresser’s avatar


    The effect is probably not permanent. However, there have been some reports that taking Prilosec can lead to achlorydia that can last more than two years after discontinuing the drugs. I completely understand your reluctance to try HCL. However, if it is low stomach acid that is causing your digestive problems, which seems likely, HCL could have a profound effect. Just make sure to take only 200 mg to start with, and do it before a meal. I’ve had several patients that have experienced remarkable results with HCL after years of heartburn and GERD.

  16. Forty2’s avatar

    OK, if the burn returns I’ll pick up some 200mg HCL/pepsin thingies. So far, so good, but it’s only been 24hrs since I took the last Aciphex. I *hate* taking any sort of medication so getting off the PPIs would be a big win.

  17. Tracee’s avatar

    We spent the last two years making dietary changes. The SCD seems to work great for us and now I’m looking into “fine tuning”. It’s funny/lucky, or however you want to put it, that your recent topics are covering things I have wanted to know more about, especially acupuncture and this. My son spent his first 8 mos of life on Zantec, so I have often wondered about this. I wonder if HCL could improve digestion. Is there a way to ask a doctor to check a small child for this?

     I really enjoy the information and your writing style is great, easy to understand. I really appreciate all of this. 

  18. Chris Kresser’s avatar

    Hi everyone,

    I’ve just published Part III of the series.  This was an unplanned article based on a study I just came across yesterday that provides further evidence that GERD is caused by bacterial overgrowth, and examines the connection between GERD and H. pylori.


  19. Sarah’s avatar

    Chris, I’m curious…
    What does spicy food have to do with it? Do you know why it is that people experience more GERD symptoms when eating spicy foods?
    Also curious about the FOS connection. Does that imply that FOS makes gas and heartburn worse?
    Thanks for taking the time to put together all this info. :)

  20. Chris Kresser’s avatar


    Spicy foods are often rated on surveys as among the worst culprits, but studies don’t actually support that notion. It’s difficult to isolate variables because nobody eats hot spices by themselves. They’re always eaten with food, and in many cases that food contains other ingredients like industrial vegetable oils and preservatives (i.e. kung pao chicken) that could irritate the stomach.

    In some cases I suppose the spices alone could irritate the gastric lining, especially if someone has an ulcer or chronic stress has inhibited prostaglandin production and their mucosal barrier is compromised. But in that case it’s not the spicy food that is the problem – it just exacerbates the underlying condition.

  21. Chris Kresser’s avatar

    Oops, forgot to answer your question about FOS.

    Yes, I think FOS will increase gas and heartburn in people with bacterial overgrowth.  However, the question is whether this effect is temporary, as the bacterial flora in the gut rebalance, or ongoing.  I don’t know the answer to that question.

  22. Chris Kresser’s avatar

    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.


  23. Donna Chang’s avatar

    Very nice article, Chris. That’s why drinking apple cider vinegar has been a popular home remedy for acid-reflux, for the reasons you explained. (2-3 teaspoon, with water if you feel it is too strong. It is good for blood stagnation type of chest pain too, even if it is not caused by heartburn)

  24. Dave’s avatar

    Great series! After taking prilosec for over a year, my wife persuaded me that after having been on a low-carb diet for about the last 6 months of that time, my problem may well be gone. It was! Have had maybe a half dozen instances since (all due to overeating just prior to bed, and involved an abnormaly large carb intake). I used to have that many instances a week!

  25. Chris Kresser’s avatar

    Smart wife! Aren’t you glad you listened to her? :)

  26. Chris Kresser’s avatar

    Final article in the series is up.

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

  27. Knittymama’s avatar

    How long does it usually take for some relief to start when using HCL and eating low-carb? My symptoms are a constant burning in my upper esophagus and throat. Will it take time for that to go away as my body heals, or should it go away as immediately?

  28. Chris Kresser’s avatar

    Everyone’s different. For some relief is relatively immediate, others it takes a bit of time. Either way, it’s worth it!

  29. Amanda Boyd’s avatar

    Hi Chris,
    I have been reading your very informative blog for a while, first found it through the podcast about fish oils.  I see you are yet another advocate of a low carb diet.  From everything i read here and everywhere it seems like all my problems (hypoglycemia, heartburn weight gain etc) should be cured by a low carb diet but in reality I didn’t experience any of these problems until after the first time I tried a low carb diet.  Every time I lower my carbs (am trying to lose 10lbs right now) I have gas, heartburn, hypoglycemia, mood swings, weight gain etc.  I think it is from the healthy fats in the fish and olive oil on the veggies so the obvious answer would be to switch back to higher carbs but I am fearful because of everything i read suggests the opposite.  I did go to the dr but they really seem to do more harm than good which is what brings me here.

  30. Chris Kresser’s avatar

    Amanda: problems with fat digestion are often caused by a sluggish gall bladder and/or low stomach acid. The fats in the fish and the olive oil wouldn’t be responsible for hypoglycemia, mood swings or weight gain. Try supplementing with ox bile and betaine HCL with pepsin right at the start of meals. That should help.

  31. Amanda Boyd’s avatar

    thank you!  will order some HCL for the heartburn and keep reading for the other stuff

  32. Brittany’s avatar

    Do you know much about gastroparesis? I saw that it could also present with my same symptoms, but I don’t know how common it is. I sometimes get heartburn, nausea(less frequently and not necessarily after eating),bloating and belching after a meal, and sometimes it comes or continues up until a few hours after I’ve ate! Are those symptoms still a normal case of indigestion/ low stomach acid? Everything started after I had a course of antibiotics with prednisone. First was the gastritis, which started out as major belching, then ended up burning badly, which I went on Prilosec for. I also have bowel troubles sometimes.  I’m worried of rushing into something and somehow making myself worse. In your opinion, should I be worried about another cause?

  33. Chris Kresser’s avatar


    Your symptoms are what they call “non-specific”, which means they could be caused by any number of things. Based on your history (i.e. they started after antibiotics & steroids), my guess is they’re due to intestinal dysbiosis. Both antiobiotics and steroids have a profound impact on the gut flora. Dysregulated gut flora can cause IBS, IBD, GERD and several other digestive conditions. The “three R” therapy I described in my GERD articles would still apply as a general strategy, but you may want to seek out help from someone familiar with treating GI problems with natural approaches. I use a stool or breath test for H. pylori. I’m not certain of the accuracy of the blood tests.

  34. Gwen Williams’s avatar

    In your summary – reduce bacteria AND limit carbs. Yes I live on fiber carbs for IBS/constipation prone and dairy for osteoporosis and recently have really started bloating and having gas. I’m a senior citizen who now has time to eat and I enjoy it and hate taking pills. I’ve always been convinced that what we eat makes us sick and what we eat will make us well. If it’s not carbs does that just leave meat?? And how do we reduce the bacteria? I take a lot of GAS X and every morning I take a Jarrodophilus with FOS capsule. I also test “allergic” to brewer’s yeast and baker’s yeast which none of the Dr.s I go to recognize. I need a Holistic, Geriatric Physican that specializes in diet. Thanks for your help.

  35. Chris Kresser’s avatar

    The natural human diet is high in saturated fats (65%), relatively low in carbs (20%) and moderate in protein (15%). So, yes, meat and traditional fats make up the bulk of calories, but by weight ends up being 60% plants (starchy tubers, fruits, berries & veggies) and 40% animal foods (fatty meats, seafood, eggs, healthy fats). You reduce the bacteria by reducing the carbohydrate content, and by consuming fermented foods.

  36. Sari’s avatar

    I have been diagnosed with GERD, and, through an endoscopy, was told that I have a small hiatal hernia. Isn’t that a structural issue that prevents the LES from functioning properly? Is there anyway, other than medication, that I can manage my reflux?

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