Digestive Health, Stomach Acid & Enzyme Formulas -- Natural Health Newsletter

Date: 03/12/2007    Written by: Jon Barron

Stomach Acid & Digestion

Something must be going on with stomach acid. We've received over 50 emails in the last 30 days on stomach acid. Yes, we get 10,000 emails a month, but getting 50 on one topic is highly unusual. The questions on stomach acid were of all kinds mind you, but surprisingly, not one on what I would consider the most important issue: low stomach acid.

Anyway, in this newsletter, we'll cover all aspects:

  • Stomach acid and digestion
  • Too much stomach acid
  • Too little stomach acid
  • Stomach acid and proteolytic enzymes
  • Stomach acid and probiotics

Stomach acid and digestion

Before we can even talk about stomach acid, we need to spend a little time talking about how it fits in the digestive process. Most people believe that when you eat a meal it drops into a pool of stomach acid, where it's broken down, then goes into the small intestine to have nutrients taken out, and then into the colon to be passed out of the body -- if you're lucky. Not quite.

What nature intended is that you eat enzyme rich foods and chew your food properly. If you did that, the food would enter the stomach laced with digestive enzymes. These enzymes would then "predigest" your food for about an hour -- actually breaking down as much as 75% of your meal.

Only after this period of "pre-digestion" are hydrochloric acid and pepsin introduced. The acid inactivates all of the food-based enzymes, but begins its own function of breaking down what is left of the meal in combination with the acid energized enzyme pepsin. Eventually, this nutrient-rich food concentrate moves on into the small intestine. Once this concentrate enters the small intestine, the acid is neutralized and the pancreas reintroduces digestive enzymes to the process. As digestion is completed, nutrients are passed through the intestinal wall and into the bloodstream.

That's what nature intended. Unfortunately, most of us don't live our lives as nature intended!

Processing and cooking destroy enzymes in food. (Any sustained heat of approximately 1180 - 1290 F destroys virtually all enzymes.) This means that, for most of us, the food entering our stomach is severely enzyme deficient. The food then sits there for an hour, like a heavy lump, with very little pre-digestion taking place. This forces the body to produce large amounts of stomach acid in an attempt to overcompensate. In addition to failing in this attempt (much of the meal still enters the small intestine largely undigested), there are two major consequences.

  1. Too much stomach acid.
  2. Too little stomach acid.

Too much stomach acid

This is obvious. In an attempt to overcompensate for lack of enzymes in the food, the stomach produces an inordinate amount of stomach acid to compensate, leading to acid indigestion. Taking antacids or purple pills doesn't actually solve the problem; it merely eliminates one of the symptoms. Ultimately, though, it passes even more quantities of poorly digested food into the intestinal tract where it leads to gas, bloating, bad digestion, chronic digestive disorders, in addition to blowing out your pancreas, which tries to compensate by producing huge amounts of digestive enzymes for use in the small intestine. All of this is exacerbated by foods and beverages such as alcohol (especially beer), high sugar foods, and caffeinated foods (coffee and tea, etc.) that can actually double acid production.

Phi-Zymes from Baseline Nutritionals

The simple solution for most people with excess stomach acid is to supplement with digestive enzymes which can digest up to 70% of the meal in the pre-acid phase, thus eliminating the need for large amounts of stomach acid and also taking tremendous stress off the digestive system and the pancreas.

One other factor which may be contributing to the problem is a hiatal hernia, in which part of the stomach can protrude through the diaphragm into the chest cavity allowing food and stomach acid to back up into the esophagus. Combine a hiatal hernia with excess stomach acid and you have the potential for great distress. The standard treatment for severe hiatal hernias is laparoscopic surgery -- with mixed results. Fortunately, there are chiropractic alternatives that can be quite effective.

In either case, dietary changes and supplemental digestive enzymes are likely to produce significant results, without creating problems further down the digestive tract.

Drinking 2-4 ounces of organic, stabilized, aloe vera juice every day can also help soothe irritated tissue in the esophagus and help balance out digestive juices in the stomach.

Too little stomach acid

Follow the logic here for just a moment.

If you spend years forcing your body to massively overproduce stomach acid to compensate for the lack of enzymes in your diet, what do you think the long-term consequences might be in terms of your ability to produce stomach acid?


Eventually, your body's capacity to produce stomach acid begins to fade, with a concomitant loss in your body's ability to sufficiently process food in the stomach. The health consequences can be profound. Low production of stomach acid is quite common and becomes more prevalent with age. By age forty, 40% of the population is affected, and by age sixty, 50%. A person over age 40 who visits a doctor's office has about a 90% probability of having low stomach acid. Consequences can include:

  • Poor digestion. Not only is there insufficient stomach acid to break down food, there is insufficient acidity to optimize the digestive enzyme pepsin, which requires a pH of around 2.0. This results in partial digestion of food, leading to gas, bloating, belching, diarrhea/constipation, autoimmune disorders, skin diseases, rheumatoid arthritis, and a host of intestinal disorders such as Crohn's and IBS.
  • It is estimated that 80% of people with food allergies suffer from some degree of low acid production in the stomach.
  • Many vitamins and minerals require proper stomach acid in order to be properly absorbed, including: calcium, iron, vitamin B12, and folic acid. Vitamin B12 in particular requires sufficient stomach acid for proper utilization. Without that acid, severe B12 deficiency can result. (Note: ionic delivery systems can bypass this problem.)
  • With low acidity and the presence of undigested food, harmful bacteria are more likely to colonize the stomach and interfere with digestion. Normal levels of stomach acid help to keep the digestive system free of harmful bacteria and parasites.

It's worth noting that symptoms of low acidity include:

  • Bloating, belching, and flatulence immediately after meals.
  • Indigestion, diarrhea, or constipation.
  • Heartburn.

Is it just me, or doesn't this list sound very similar to the symptoms associated with too much stomach acid? In fact, up to 95% of people who think they are suffering from too much stomach acid are actually suffering from the exact opposite condition. The use of antacids and purple pills then become exactly the wrong treatment to use since they exacerbate the underlying condition while temporarily masking the symptoms.


  • Supplementing with digestive enzymes to reduce the need for stomach acid -- giving the body a chance to rest and recover its ability to produce sufficient stomach acid.
  • Mix one teaspoon of apple cider vinegar with water and a little honey and drink this with each meal. You may gradually increase the vinegar up to 3-4 tablespoons in water if needed.
  • Supplementing with betaine hydrochloride (HCL) tablets can also help, but anything beyond minimal doses as found in most health food store supplements should only be administered under the supervision of a health practitioner to avoid damage to the stomach lining.

Stomach acid and proteolytic enzymes

As I mentioned at the top of the newsletter, we received a number of questions on stomach acid in the last 30 days. Most of them had nothing to do with high or low stomach acid, but rather with the effect of stomach acid on supplements. In fact, the bulk of the questions we received were concerned with how stomach acid affects proteolytic enzymes, and they all pretty much ran along the following lines.

Since enzymes are made from proteins and proteolytic enzyme formulas are taken orally:

  • How do they survive the digestion of proteins that takes place in the stomach? Wouldn't they be broken down by stomach acid into amino acids?
  • If they do make it through the stomach, since they are so large, wouldn't they be unable to pass through the intestinal wall?

Surviving the stomach

Not all proteins (enzymes are proteins) are broken down by stomach acid. Rather than get technical, let me just point out pepsin. Pepsin is an enzyme secreted by the stomach to aid in digesting the proteins in your food. Not only is it NOT broken down by stomach acid, its optimum pH environment is about 2.0 (very, very acidic). Bottom line:

  • Although some enzymes such as serapeptase are destroyed by stomach acid, most are not -- just temporarily rendered inactive. (Note: that's one of the reasons I do not use serapeptase in my own proteolytic enzyme formulation.)
  • Different enzymes function differently in different pH environments, which is why I formulated my proteolytic enzyme formula, pHi-Zymes, to function in a wide range of pH's.

Passing through the intestinal wall - absorption

Enzyme absorption absolutely occurs and manifests through two main avenues:

  • Pinocytosis
  • Peristalsis

Pinocytosis. Enzyme molecules are bound to, and encapsulated, by other substances such as water. Since they are encapsulated, the intestinal wall cannot recognize them as enzymes and thinks they are "water," thus readily passing them through the intestinal wall. Once the enzymes are in the bloodstream they attach to lymphocytes and travel easily throughout the vascular and lymphatic systems.

Peristalsis not only forces food (and enzymes) down through the intestinal tract, it also forces transit through the intestinal wall.

Stomach acid and probiotics

The questions related to probiotics are essentially the same as those for proteolytic enzymes: aren't they broken down and destroyed by stomach acid -- thus requiring special, acid-proof capsules? And the answer, for most probiotics, is absolutely not. (I think this is primarily a marketing pitch for companies selling probiotics in enteric coated capsules, but the logic is flawed.)

The reason we're supposed to take probiotic supplements is to replace the probiotics that we used to get in a wide range of unprocessed fermented foods such as homemade yogurt, sauerkraut, buttermilk, pickled foods, kimchi, real soy sauce, raw vinegar, tempeh, etc. -- foods that are no longer a significant part of our diet. But think about this for a moment. These foods are not enteric coated. How could these foods provide probiotic value if the beneficial bacteria were destroyed by stomach acid? The simple truth is that beneficial bacteria, for the most part, easily survive stomach acid. Also, if you take your probiotic supplements with water on an empty stomach (as we've already discussed), they encounter almost no stomach acid anyway.


The bottom line here is that most people are very confused about the role stomach acid plays in health. Most people:

  • Think they have too much, when in fact they have too little.
  • Treat the symptom and suppress stomach acid production, ultimately leading to long-term health problems.
  • Ultimately lose the capacity to produce sufficient stomach acid as a result of dietary abuse and continual use of medications to suppress the body's ability to produce it.

Don't get into that trap.

  • Use digestive enzymes with all your meals.
  • Drink aloe vera juice.
  • Use probiotic supplements with confidence.
  • Use proteolytic enzyme supplements with confidence.
  • And, if needed, use apple cider vinegar or betaine hydrochloride supplements to make up for stomach acid insufficiency.

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    Submitted by Audrey on
    April 5, 2012 - 8:31am

    Thank you for the reply - yes I've read through the very informative newsletters - that's what prompted my email since no specifics were mentioned like: can the stomach lining actually heal as gastritis is different to an ulcer.

    Submitted by Guest on
    July 21, 2012 - 7:25pm

    This is a fantastic article! I've been suffering with belching after eating and stomach discomfort for a few months now. I still don't know my issue exactly. I've been to a GI specialist a few months ago, who performed an endoscopy and found minor acid reflux. He prescribed me with a month of omeprazole (what a shock). I took it for three weeks, and couldn't tolerate the pain anymore. I began researching my issue and read about low stomach acid, overgrowth of bacteria, and other issues that I thought I may have. I started taking a probiotic supplement, digestive enzyme (Now Super Enzyme), and HCL with pepsin. I believe I've had some success with these, but I still find that I burp minutes after eating most meals. I decided to see a wholistic doctor two weeks ago, as I've heard they find the root cause of the proper and treat the issue rather than the system. While I've only been one time ($225 for first session since insurance doesn't cover) , she told me to continue to take a digestive enzyme with every meal, as well as some lemon juice in the morning with honey and perform heel drops (apparently these may help with positioning the stomach or something?), and continue to take HCL as needed. I stopped at whole foods tonight with my wife and picked up some organic aloe vera juice and I will try taking that. I was just wondering if anyone could provide me with some thoughts or tips on how to treat my issue. I would really appreciate the help! I've turned into a hypochondriac over this digestive problem, and I just want to know what it is or what I can do to get better. Thank you again!

    Submitted by Dawn on
    May 23, 2012 - 8:07am

    Can you take Bragg's apple cider vinegar and probiotics? I normally take my probiotics in the morning on an empty stomach and a half an hour later I drink 2 tablespoons of ACV in an 8 oz glass of water. I just want to make sure that the ACV is not cancelling the probiotics. About an hour or so later, I take a digestive enzyme tablet before eating breakfast.

    Submitted by BaselineFoundation on
    May 23, 2012 - 2:50pm

    Hi Dawn,

    Surprisingly, raw, natural apple-cider-vinegar such as Bragg’s actually a good source of beneficial probiotics in its own right. It is made by crushing fresh, organically grown apples and allowing them to mature in wooden barrels. This boosts the natural fermentation qualities of the crushed apples, which differs from the refined and distilled vinegars found in supermarkets. When the vinegar is mature, it contains a dark, cloudy, web-like bacterial foam called mother, which becomes visible when the rich brownish liquid is held to the light. The mother is essentially a beneficial bacterial foam.

    So no, taking Bragg’s will not kill beneficial bacteria. That said, you may not want to actually take your probiotics at the same time as the Bragg’s. If possible, the best time to take probiotics is before bed on an empty stomach. That allows them to quickly pass into the intestinal tract without encountering significant stomach acid and start establishing themselves in your gut before you consume anything else in the morning.

    Submitted by Dawn on
    May 24, 2012 - 4:50pm

    Thank you for the quick response! The information provided has been helpful and I will follow the suggested routine in regards to when to take ACV and probiotics.

    Submitted by Sam on
    May 29, 2012 - 6:50pm

    I recommend a naturopathy doctor for people with long standing issues. Regular physicians will NOT tell you about any home remedies, they are TRAINED to PRESCRIBE medicine, many of which they will not tell you about the side effects (sometimes harsh).

    I am a 24 year old healthy female who went on vacation and came back with an upset stomach (consistent diarrhea) and went to my doctor and he prescribed me Nizatidine (H2 Blocker- reduces stomach acid). About a week in, I had horrible nausea, headaches, anxiety, dizziness, and some disorientation. It was ridiculous! I told him this and he prescribed me omeprazole, which I did not end up taking. I did some research into how dependent people become on this and HELLO i DID NOT HAVE HEARTBURN OR ANY SYMPTOMS OF GERD. I ended up seeing a naturopathy doctor who gave me some great probiotics. Seems to have really improved my system, though I am experiencing acid rebound (google it). My doctor made a small stomach issue into an almost 3 month recovery process that has been hell. NATUROPATHY! Try it!

    Submitted by Barbara on
    October 2, 2012 - 5:04pm

    MY QUESTION:(background info. follows) I took the Heidleberg test to determine if my HCL levels were normal, high or low. Unfortunately, the test showed "pyloric valve insufficiency", which resulted in sometimes the HCL was too high and sometimes too low during the testing process, which took one hour or more. So my question is: should I take ACV with meals or not? I read so many good things about ACV, but don't want to contribute to too much HCL if that's what my stomach produces intermittently, but what about the times when the HCL is too low? I'd appreciate any reply. Thanks so much. Here's my background: BACKGROUND: I had a colonoscopy and endoscopy in 2010, and chronic gastritis and GERD were diagnosed, and microscopic colitis. I didn't take any of the Meds prescribed, because I read about the terrible side effects. I've been gradually healing these conditions and the lining of my gut these past 2 years by: 1) working with various holistic practitioners 2) a nutrition plan recommended to reduce inflammation and heal the gut, etc. (See gapsdiet dot com) and also google online, plus probiotics, dig. enzymes, DGL, etc. 3)  In addition, extensive testing at holistic labs revealed parasites, allergies to dairy, gluten, nightshades (tomato, eggplant, peppers, tobacco) plus toxic levels of mercury and lead, so I've also been dealing with all that. Perseverance furthers!

    Submitted by Lee on
    September 12, 2013 - 10:22am

    Since beer increases stomach acid, would it help someone with LOW stomach acid?

    Submitted by BaselineFoundation on
    September 12, 2013 - 12:14pm

    There are better ways to handle it.  Do a search on our site and you can see all the articles about stomach acid.

    Submitted by Abbie on
    February 3, 2015 - 8:58pm
    Springfield , Missouri

    This article is amazing! Thank you for sharing! I am currently on protonix as I have acid reflex. Ive started eating more yogurt to increase my probiotics but it seems to make my acid reflex even worse. Any advice would be appreciated

    Submitted by henry on
    April 3, 2015 - 4:34am
    jakarta ,

    I'm really thankful for this article. The info is very elaborate. Thanks alot!

    By the way. I'm wondering if anyone has tried wakamoto made probiotic or if it's considered as one. I dont really believe in our local probiotic brand product. I live in southeast asia. I hv tried this wakamoto, its quite expensive. Im a little bit confused, if indeed wakamoto is a probiotic, why sometimes its effective sometimes it doesnt? Does it hv anything to do with the amount eaten? Or you need to supplement it with something else. And how long do people usually take probiotic? Until you are cured or you take it as daily supplement or you take it only when its necessary?

    Submitted by BaselineFoundation on
    April 3, 2015 - 12:53pm

    Hi Henry,

    You should read our article on probiotics:  http://jonbarron.org/article/probiotic-miracle

    Submitted by Sam on
    June 23, 2015 - 2:53am
    Pretoria ,

    Dear People

    The only solution is water fasting. Very difficult but beneficial - results received from 3-40 days of water fasting. Nothing else will heal the body. Please check with your doctor for those on chronic medication and read the bible for further info on water fasting.

    Submitted by Ann on
    January 7, 2016 - 3:59pm

    Do you think a colon cleanse can help stomach acid problems?

    Submitted by BaselineFoundation on
    January 7, 2016 - 4:45pm

    It certainly can not hurt, and will help with overall health.  However, Jon more specifically recommends:

    • Use digestive enzymes with all your meals.
    • Drink aloe vera juice.
    • Use probiotic supplements with confidence.
    • Use proteolytic enzyme supplements with confidence.
    • And, if needed, use apple cider vinegar or betaine hydrochloride supplements to make up for stomach acid insufficiency.
    Submitted by karren on
    January 15, 2017 - 1:01pm

    I have been having nausea for 3 weeks. I tried the 2 weeks of omeprazole but it didn't help. I just started to take enzymes before my meals and also started a probiotic. MY question is how long to t take to start feeling better?
    Also, I took a salvia and urine PH test that showed I was very acidic but I'm not sure how accurate it is.
    I want to try the betaine test but I've read take it on an empty stomach and also read to take it with protein during your meal.

    Thank you so much for any help.

    Submitted by Marian on
    April 18, 2017 - 10:18am
    Basildon UK ,

    I have a hiatus hernia (6 years now) and have been on lansoprazole all of that time. Prior to going on that drug I was throwing up after most meals as the food got stuck in my oesophagus. Had an endoscope and only the HH was diagnosed. I recently found out that PPI drugs seriously affect the absorption of some vitamins and minerals so I came off the drug. I got rebound acid awful but it settled down after about 5 days. However, now, 2 weeks after I have for the first time since about 5 years ago got the old problem back and tonight I threw up after my meal. Needless to say I have now gone back on the lansoprazole and I have purchased some liquid vitamins (expensive and very good quality). Will these vitamins be absorbed when my stomach acid is going to be depleted through these drugs? It seems I have no option but to take the drug. Thanks.

    Submitted by BaselineFoundation on
    April 18, 2017 - 4:10pm

    PPI drugs do not affect the absorption of all vitamins—primarily, just B12. And for that you can get sublingual tablets that absorb under the tongue and bypass the stomach.

    Submitted by Cindy on
    October 20, 2017 - 2:01pm
    London Canada ,

    I cough after eating. My Dr. says its acid reflux. I don't take the m3eds she suggested. Instead I take digestive enzymes and have been for 20 years before this coughing started. I have upgraded the enzymes on the advice of a naturopath but still cough. Any suggestions on what is the cause and how to resolve the problem.

    Submitted by BaselineFoundation on
    October 23, 2017 - 2:05pm

    For obvious legal reasons, we can not diagnose, just merely provide information.  That said, you may find this article useful: https://jonbarron.org/article/your-stomach-part-3

    Submitted by Cyndie on
    January 6, 2018 - 7:55am
    Inman , South Carolina

    My daughter is 14 and she has suffered with stomach issues for several years that have been treated with proton pump inhibitors to no avail. She now has bad acne around her mouth and lately belches a lot. Could all of this be indicative of low acid? As a teenager, her diet is not great because she is a picky eater, and I am very worried about her. I have even been told that she could have fatty liver.

    Any suggestions or advice would be appreciated.

    Submitted by Val Sinclair on
    January 31, 2018 - 2:36am
    Cambridge, UK ,

    I have LPR and the symptoms affect my job as a singer, iconstant throat clearing and excess mucus. One very strange symptom is a feeling of having menthol in my eyes, weird, and the same icy coldness hitting my throat as I breath in. Even the consultant laughs when I tell them that! But it’s alongside a burning tongue and a bitter taste in my mouth/throat. I burp as soon as I eat or drink. An endoscopy revealed a small hiatus hernia and mild gastritis. Changing diet seems to have no effect. I make my own yogurt and eat healthily. I wonder if I have low stomach acid and what your recommendations might be. Is it better to eat yogurt last thing at night? Your site is brilliant - many thanks.

    Submitted by Elam on
    August 9, 2018 - 2:51pm
    Lancaster , Pennsylvania

    This information was very helpful and mostly accurate. I agree that less stomach acid is made as we age. However, the explanation of digestion suggesting that processing and cooking food kills the digestive enzymes in the food isn't really based on nutritional science. Why would food come with special enzymes in them to help us digest them? Thinking that they have special enzymes for us to digest them presumes that they were created just for us to consume them, like they couldn't just exist for their own sake. Processing and cooking food is one big factor that helped humans develop into what they are. The digestive system in humans is quite small compared to the digestive systems in our ape and monkey relatives, who don't eat cooked food. Their systems need to be larger to slowly digest the uncooked foods they eat. Our digestive systems grew smaller because processed and cooked foods are easier to digest. Early humans, who began cooking food had to spend less time eating and foraging and all that extra time led to human culture. Processing and cooking whole foods is healthy. Processing foods and stripping them of most nutrition is unhealthy.

    Submitted by BaselineFoundation on
    August 10, 2018 - 4:48pm
    Submitted by Albert Tijerina on
    October 31, 2018 - 4:54am
    Elgin , Illinois

    Hello, I enjoyed this post! Thank you. I am 25 and started having symptoms of gout/ arthritis over a year ago. I’m still on my journey of healing and have come a long way. One question I’ve had is why apple cider vinegar flares up my condition. Maybe I take too much at once? HCL w pepsin does not flare me up at all but I’ve taken up to 6500mg at once with a meal and not felt a burning sensation. Does the HCL need to be taken with an acid based drink? Thank you!


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