Probiotics and Stomach Acid

A question I frequently get is about probiotics and how to protect these possibly beneficial bugs from the very harsh stomach acid. There is more to this question than meets the eye, so let’s look at several parts of the probiotic picture. First, probiotics are bacteria, present in yogurt, other dairy products, and pills. The hope is that these probiotics will establish a presence in the lower gut and render beneficial health effects.

Probiotics Are Live Organisms

Dysbiosis: The Reason You’re Not Losing WeightAs such, they can live or die under a variety of circumstances. One such circumstance is time. Some bacteria make spores which can live for many years and then blossom and grow. Most probiotics do not make spores, so they gradually die off if they do not find a comfortable place to grow, meaning a moist, warm, friendly environment like the colon. However, when a probiotic sits on a shelf in a store, the bugs gradually die. The longer they are in a warehouse or on a store shelf the fewer live bacteria will be present. Refrigeration likely prolongs the life of probiotics but we don’t know for which ones and for how long. Most manufacturers will not tell you.

We also don’t know which ones our bodies need. A good bacterial strain for one person may not be as effective for another. When you consume probiotics, you’re hoping the bacteria you consume is the bacteria your unique gut needs.

Yogurt and Probiotics

You can be sure that yogurt and other such dairy products have fresh, live bacteria in them. Plus, it is refrigerated. These are two good things. However, we do not know how many bacteria are in a serving and manufacturers do not put this on the labels. You could be getting a very small dose which would not be enough to make a difference. Additionally, many of these bacteria will be killed by stomach acid, especially when eaten with food.

Aside from not knowing the amount of good bacteria you’re consuming, the other downside of yogurt is the sugar content. Typically, yogurt contains a large amount of sugar. If not sugar, the manufacturer will replace it with a manufactured sweetener. These sweeteners have been shown to cause gastrointestinal issues, which are the issues many individuals try to alleviate by consuming probiotics in the first place.

Probiotics and Stomach Acid

Here is the tricky part of the probiotic puzzle. Stomach acid is very, very strong. It does and will kill the majority of bacteria that get into the stomach each day. So, how do you protect the probiotic bacteria you take from this “bacteria execution chamber” which everyone has inside them? Here are some things you can do. First, take the probiotic on an empty stomach. When the stomach is empty, it is not making much acid. You can open a capsule and mix it with a small amount of water. The stomach will empty out the liquid in 15-20 minutes but will keep food in it for 60-90 minutes. During this time it grinds the food up and mixes it with acid and harsh enzymes which are designed to get the food ready for absorption in the small intestine. Another trick you can do is to mix the probiotic with some bicarbonate of soda, a strong alkaline powder. This will neutralize the stomach acid temporarily until the probitoic can get through the stomach.

Coating a Probiotic

Some manufacturers will enteric coat capsules. Enteric coating is a polymer barrier on oral supplements. This helps protect supplements from the ph (i.e. acidity) of the stomach. Another substance is called alginate which coats and protects the bacteria until it gets into the small intestine where it is safe. Again, we don’t really know how well this works. It sounds like it should. You have to check with the manufacturer to know if this is part of their production technique.

So here are the summary points:

  • Use a refrigerated probiotic which has just come onto the store shelf. The longer into the future is the expiration date, the more live probiotics are likely to be in the capsule.
  • Take a probiotic on an empty stomach with 4-6 oz of water. Even better, twist or cut the capsule and empty the powdered bacteria into a glass, add the water and a teaspoon of soda bicarbonate to neutralize the stomach acid.
  • Yogurt is great and most people get a good feeling that they are doing something good for their gut. We don’t know how much, but the advertisers tell us we will almost live forever if we eat their product. Consider the amount of sweeteners in the yogurt product. If you’re trying to manage your blood sugar, yogurt may not be the right option for you.
  • There are some probiotics that are helpful for certain gastrointestinal diseases. Your physician is the person to help you make the right choice.

Prebiotics and Probiotics

No discussion of probiotics would be complete without mentioning prebiotics. A prebiotic is not a probiotic. A prebiotic is a specialized plant fiber that easily gets through the stomach unchanged and the feeds the good colon bacteria which everyone already has in their colon. That’s right. We have over a 1000 species of bacteria in the colon and many of these are the good gals and guys. Feeding them good prebiotic plant fiber is the key to creating a rich furnace of potent good bacteria. When the body has a good balance of bacteria in the gut, it experiences many important benefits, from easier weight management and improved immune system to better mental health and resistance to stress.

When you consume prebiotics, you can be sure that you’re reaping all the benefits that come with them since they aren’t destroyed in the body. You can also be sure that what you’re introducing is beneficial. Unlike yogurt that contains good bacteria that may not be helpful to your unique gut, prebiotics fertilizes the good bacteria you already have in there.

Learn more about the differences between prebiotics and probiotics.

For additional information about the health benefits of prebiotics you can view published research on


  1. LLR says:

    So I’m new to all this. Dealing with diverticulitis, maybe IBS, hall bladder removed few years ago. My Dr. suggested probiotics. Info on your website is very informative. My question is: I have for years taken Omeprazole (heartburn). Will this have any negative effect on my using probiotics & prebiotic?

  2. Paul says:

    Have a search on the internet. A study has shown that taking some glucose -at the same time I think, raised stomach ph and let the bugs through. Hope you find the article.

  3. Julie smith says:

    I get my probiotic from melaleuca. It does not need refridgeration and is equal to eating ten cups of yogurt in one capsule. I have multiple digestive issues and this really helps me

  4. Joe says:

    I am very curious about how probiotic tablets (no matter how potent they are and able to withstand stomach acid) would be able to outnumber the dominant bacteria that produces gas, after the good bacteria have been wiped out by a course of antibiotics.
    How one expects a die-off of the bad bacteria which colonizes the whole intestines that amounts in trillions can be overcome by a capsule that contains some billions of the good bacteria?
    I wish that someone could explain how this is possible.
    Thank you

  5. Sandi says:

    I have been using proton pumps for the last 14yrs and have just had an endoscopy which has found multiple polyps in my stomach. I am also just about to have a colonoscopy done. I have been vomiting after food, sometimes 4 – 5 hrs after for over 10 years. My Dr didn’t seem unduly worried, but would just change the dosage.
    I have taken myself off the proton pump and have tried to change my diet by having organic veg, less meat and having the odd green smoothie. I also have started taking aloe vera gel. But I am finding my oesophagus and stomach is sore and I have burning stomach acid.
    I did try taking probiotics but was told not to take with aloe vera. Help I need to know what to do best for my stomach.

  6. MKM says:

    IBS and Autism – Looks at specific carbohydrate by Elaine Gotschall (search the net for her book- BTVC) and also on yahoo u have a group to guide u

    Also look for autism articles on site

  7. MissyNP says:

    Recent medical studies are proving the worth of bacterial flora in the gut. Of 20 patients with refractory C.diff infection (caused by antibiotics that incidentally or purposefully kill gut bacteria and parasites) who had failed traditional and holistic measures were given a feces transplant orally (from healthy people undergoing a colonoscopy and tested for communicable diseases over time) 16 were cured after the first capsule (enteric coated) and two more after a second treatment.

    The reality is that in the future current studies will prove that our overuse of antibiotics (kills normal bacterial flora) and overconsumption of meats (the digestion of which may bind neurotransmitters produced by normal flora) alters our healthy microbiome to our detriment. The consumption of naturally fermented foods, modestly cleansed root vegetables or probiotics may not be the cure all everyone is hoping for but they are the best we have now. However, chronic consumption of probiotics is not necessary and can be very costly. Once recolonization of the flora has occurred, continuing the supplement daily is unnecessary. Changing diet is absolutely key and avoiding antibiotics if at all possible are the keys to a longer, healthier and disease-free life. Eating an abundance of fresh homegrown pesticide-free fruits and vegetables, reduce all animal product (yes, vegans have better guts, fewer acquired diseases and much less gastric distress then non vegans-but we are talking healthy choice vegans not those eating twinkles and drinking diet colas instead of meat for their energy) and reducing or completely eliminating processed foods.

    It is painful to change our eating habits and sedentary lifestyles, but it is just this way of life doing damage to our bodies and it is a hard reality ( even for me a farm- raised girl who ate meat at every meal until college) to accept the necessity of these changes. The studies will prove over the next 5 years or so how very important the role of healthy normal flora of our gut is as their role in producing neurotransmitters for use locally and systemically as well as the role of detoxification of our foods is revealed. Their role in processing carbohydrates or not processing them plays in the cause of obesity will also be revealed sooner rather than later and we may end up taking poo-pills (promising when all probiotic supplements failed) to help those of us with bad guts. As palatable as this sounds to some, as a healthcare provider, I think a healthy lifestyle is more so.

  8. Damascus Cain says:

    Great thread… No one has mentioned one of the most important aspects of probiotics. The quantity. The stomach does indeed kill most (as much as 90% depending on your stomachs health) of the probiotics we consume and nothing can be done about this. It’s a good thing, otherwise we would be bloated and gassy all the time from eating fermented foods and or foods with probiotics in them. This can be dealt with by simply taking a double dose twice a day. The real enemy of probiotics is the quantity per capsule. These strains are all canibalistic in nature. They eat one another… In my personal experiments, I have found that the only probiotics that actually work have no more than two strains per capsule. A war with two armies is better than a war with 25 armies all attacking each other. If you must have more than two strains then but them severally in blocks of two and take them at different times in the day.

    Despite the comments written here, I have found that probiotics do indeed work best if taken when you first wake up and again just before bed.

    Probiotics are not needed for those with a healthy gut. It’s a waste of money. However, they are life changers for those suffering from SIBO, IBS, CROHNS DISEASE and CANDIDA.

  9. Theresa says:

    IBS : give him mainly brown rice to eat, maby also rolled oats to bind as fibre

    ( poor boiling water over oats and cut up dates, let it stand with plate covering it, after ten minutes add some coconut butter and raw cacao, even a little cream .)

    … Tastes delicious…..

    .. Smoothies are also good with added psyllium husk, only a little at a time with banana, chia seeds, maca powder, mesquite powder….plus other super foods…….. He may really need nutrition rich foods to give home added support.

    If there are enzymes present in the food 75 % of the food will be digested in the first part of the stomach where little stomach acid is present, ……..

    Adding digestive enzymes to cooked food helps tremendously with digestion and therefore assimilation of nutrients.

    Making a salad dressing with Apple cider vinegar, raw honey, extra virgin olive oil, unrefined salt, plus whatever else …..

    helps build hydrochloric acid production ……

    which most people today over 40 are deficient off….the food do not digest properly and the body takes strain trying to compensate…..

    .IBS needs to be treated with all these aspects considered,,,,,pre…biotics are probably more important,,,also digestive guidelines ,,,,, enzyme rich foods…No cool drinks or sugar…..consider sprouting sesame, pumpkin and sunflower seeds and combine in banana rich smoothie…..

    So much to be done…..seems like a lot but is actually simple…..and of course lots and lots of bone broths….

    Good luck.

  10. Pat says:

    I have enjoyed reading all of your comments. i am trying to find an answer, to whether it would be safe to take probiotics if chewing them, as my son 55yr old, who is autistic is suffering from what the doctor thinks is IBS, with loose bowel movements. the doctor has no idea about probiotics. I am desperately in need of facts.

    • Brianna says:

      Pat, Please review the information on our web-site. We firmly believe that our Prebiotic fiber will do wonders for your autistic son. You are the ideal candidate to try what we are doing. Shortly, you are going to see more and more information (and we already see this happening) linking the gut to issues of autism. It is an area we are focused on, both short and long term. Please give us a try. As far as probiotics and the thought of chewing them, few bacteria can survive stomach acid…. That is why most probiotics don’t work. Bacteria is destroyed by the acids found in the stomach. This is why I only recommend “enteric coated caps” for any probiotic use. However, Prebiotin is a soluble fiber and is not effected by stomach acid in anyway. Prebiotin enters the colon unharmed, as nature intended. Prebiotics should be your first option. We hope you give us a try and let us know how it goes. Thanks.

    • MLT says:

      Have you looked into the GAPS diet? I highly recommend it for and ASD

  11. Pierre says:

    I find it highly doubtful that consuming bicarbonate would be sufficient to neutralize stomach acid.

  12. Debra S. Meyers says:

    ok thx for your help. i would like to, however, post a comment which might help people in search of treating intestine bacteria: i have found it beneficial to alternate probiotic formulas because i seem to bulid up a tolerence every few months or so. i basically listen to my body. when i am in alot of distress and my energy level declines i switch brands and formulas. i have also found caprylic acid extremely beneficial, especially in higher doses than recommended when in distress.

  13. Debra S. Meyers says:

    ok i guess other than lacto there are not any effective probiotics to treat stomach bacteria. but dont u need stomach acid to aid digestion. besides coucunut oil what do u reccomend. ok any other suggestions

  14. Debra S. Meyers says:

    to reiterate when using probiotics a brand with live cultures which are refrigerated works bests.

  15. Debra S. Meyers says:

    i am looking for probiotic that doesnt bypass stomach. the energy coated ones do not treat stomach bacteria for they bypass stomach.

    • Eddy says:

      I am a physician and I have to mention that the stomach is strile. Just very few bacteria can survive its acidity. Helicobacter pylori is an example which is responsible for peptic ulcer. Obviously Stomach does not need pre or pro biotic.

      • Brianna says:

        Actually the stomach may not need a pre or probiotic, but the colon certainly does. The problem with Probiotics is that few bacteria can survive stomach acid…. That is why most probiotics don’t work. Bacteria is destroyed by the acids found in the stomach. This is why I only recommend “enteric coated caps” for any probiotic use. However, Prebiotin is a soluble fiber and is not effected by stomach acid in anyway. Prebiotin enters the colon unharmed, as nature intended. And we all need prebiotic fiber for optimal gut health.

  16. sachin says:

    Still not clear – Probiotics produces acid themselves ( Lactobacillus in yoghurt) – they break food into lactic acid -If they are themselves producing acid – how they help in reducing acidity?

    “Lactobacillales or lactic acid bacteria (LAB) are a clade of Gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod- or cocci-shaped bacteria that share common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation.”

  17. Biochemisty says:

    A cow gets zinc from its diet because it is a herbivore. It has rumen a gut with four compartments in the stomach. Plus they have herbivore teeth. A cow chews the food for hours and has very different gut bacteria. This is why it can get zinc etc. from plant matter. A human is an omnivore. Humans have omnivore gut and teeth. God (if you believe in God) or Nature if you dont believe in God – made humans that way. Omnivores who think they can become herbivores simply making a decision can’t change the fact that they were born an Omnivore.

    • RXX says:

      That’s actually not true. You are talking about very superficial things there and completely forget about chemistry. What omnivore means in humans is a slight adaptation to eating more that a herbivore diet (we adapted because of times of famine and also because we discovered the fire). Bears are omnivores too and look what different teeth they have. Humans don’t have such teeth. Also, the teeth movement in humans is just like that of herbivores. Besides, there is a ton of examples of vegans and vegetarians who feed themselves correctly and live well after 100 (monks in every region of the world, for example). Stop believing the meat eaters propaganda, experiment yourself and open your eyes to see the real examples out there. Humans were never designed to eat meat. It’s too harsh on our systems, it kills the good gut bacteria (proven) and shortens our lives. This is real science and real life experience, not propaganda.

      • Jennifer says:

        Surely if we were vegetarians we would have eyes on the side of our heads instead of at the front like most carnivores do?

        Why also do we not produce cellulose (an enzyme found in herbivores that can break down cellulose); instead we produce proteases and lipases so we can digest both animal protein and fat?

        Why also do we not have 4 stomach’s like cows do? Surely if we were exclusively vegetarian we would need that. It’s true that we have a long intestinal system but that is because we can make the best out of both food types (animal and vegetable)

        Clearly we are omnivores

        • Jennifer says:

          That was meant to say cellulase not cellulose; darn auto correct

          • leguman says:

            Take for example the lemur, he has binocular vision, just like predators do, and it feeds on lots of fruits and insects. People tend to omit that humans were eating a lot of insects before the modern meat era and there are a couple of studies that show that the eyes on the front of our heads simply helped us catching those pesky little buggers.

    • Michael Smith says:

      LOL, Trans-herbivores

  18. Mikal Lawton says:


    Sorry, but stomach is strongest when the stomach is empty not when it is full. Medical doctors get that wrong every time. Stomach acid is neutralized during eating and does not kill the probiotics. Think about eating fermented foods or raw vegetables with soil organisms.

    It is the same silly thinking as saying vegetarians don’t get much zinc and you have to eat meat to get zinc. Well….how do you think the cow assimilated zinc into its meat, from eating plants. Also, stomach acid does not destroy enzymes. It doesn’t make sense that nature would supply all these foods with beneficial enzymes only to be destroyed in the stomach.

    I tend to not listen to the medical community because it has become corrupt in search of financial gain and the patient is no longer important anymore. You and I are just statistics.

    • Biochemist Ph.D. says:

      Yes, stomach acid DOES destroy enzymes – it hydrolyzes all proteins (which is why diabetics must take insulin – a protein hormone – by injection. If they took it orally it would be hydrolyzed in the stomach and could not have any effect).

      Nature supplies foods with enzymes beneficial to the *original* organism – not for those organisms further along the food chain. Those proteins (whether they be enzymes, hormones or structural proteins) are useful to the consuming organism ONLY as a source of the amino acids that the consuming organism can use to build the proteins beneficial to the consuming organism. That’s why those not eating meat must eat “complementary” foods – to obtain the complete range of the 20 natural amino acids that are required for optimal health, along with the cofactors (vitamins and minerals) that are required so that the enzymes that perform all those millions of biochemical functions every minute are completed and can do their jobs.

  19. Stu says:

    Some people suggest freezing capsules of castor oil so that they open further down the digestive tract. If this works, perhaps it would work for probiotic caps as well.

  20. jodi says:

    Thank you Terry Dixon I will read these!

  21. anabela brandao says:

    Please inform me of the amazing eating plan!

  22. Terry Dixon says:

    Diverticulitis and almost all bowel and gut diseases can be sorted by reading “Grain Brain” by David Perlmutter and “The Miracle Of Coconut Oil” By Bruce Fife MD. Excellent publications by Doctors who have done the stats and studied the surveys world wide. My wife and I have established an eating plan that has changed our lives and amazed the local medico’s.

    • Gary says:

      I’d like to know more about your eating plan as well. Thanks!

      • Emma Holloway says:

        I would like to no more about your diet. I am interested in eating good probitics. I have problems with stomach acid, also. What would u suggest? I have been using Papaya Enzyme, which seems to work, thats taken with a couple of sips of coke. 4 tablets with a meal. Please share your diet plan with me, thanks in advance

  23. Anthony G. says:

    Hold on a second. “… whey (wheat) protein…” What does whey have to do with wheat besides *nothing*? That line there will confuse people to thinking whey has or comes from wheat.

    I wouldn’t recommend using bicarbonate just for this purpose. There are better ways than to neutralize stomach acid IN the stomach. The capsule content in a small amount f water is what i’ve been doing for a long time *I have troubles swallowing capsules & tablets*

    Another option is to look for what companies like Renew Life is doing…entric-coated capsules that open ~ after 2 hours.

  24. vinu says:

    There is always an inherent danger in trying to bypass stomach acid.
    Stomach acid breaks down proteins into amino acids (denature). People who took proton pump inhibitors which block stomach acid, had intact proteins being absorbed. This resulted in them developing allergies to those food items. Likewise, if the probiotics have other food proteins, defeating the stomach acid with say bicarbonate of soda, will cause intact food proteins to get absorbed resulting in allergies. This is a danger with any oral vaccine also.

  25. al non says:

    Whey is a milk protein and not a wheat protein. Perhaps you are confused because there is an element of milk (casein) that is often accused of being similarly detrimental to gut health as gluten. However, i don’t think casein is included in the whey protein fraction (i could be wrong here though)

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