Last updated September 7, 2017 by Lisa Richards, CNC

Can Probiotics Make It Safely To Your Intestines?

Probiotic bacteria can pass safely through your stomach

One of the best ways to improve your digestion and general health is to take some good quality probiotics. But how can you be sure that those little pills you take, each containing billions of good bacteria, actually make it through to your intestines? After all, they have to get through the acidic environment in your stomach first, right?

Luckily, there’s no reason to be concerned. Probiotic bacteria, whether in a commercial form or in probiotic yogurt, are perfectly capable of making it all the way through your digestive system. The evidence shows that oral probiotics can colonize your intestines and even pass all the way through your digestive system without any problem at all.

Probiotics Can Survive In An Acidic Environment

If you read my post on the acid/alkaline balance in your gut, you already know that your intestines need to be slightly acidic for optimal digestion and a strong immune system. The good bacteria in your intestines play a large part in this.

Lactic acid bacteria, for example Lactobacillus acidophilus, are a good example. As part of their metabolism they secrete small amounts of lactic acid and acetic acid, lowering the pH of their immediate environment and making it more acidic. In fact, the word acidophilus literally means ‘acid-loving’ in Latin, and they are well-suited to surviving an acidic environment.

Another factor to remember is that these bacteria usually spend very little time in your stomach. If you take your probiotics after eating, they will mix together with the liquids and saliva in your stomach. And around 50% of this liquid will pass through to your intestines within 30 minutes of your meal, taking many of the probiotics with it.

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Lastly, your stomach may also be less acidic than you think. For example, immediately after eating your stomach pH typically rises to a level of around 6.0. This is only mildly acidic, and should be reasonably easy to survive for most of the bacteria in your capsule. In fact, something like 75% of probiotic bacteria will survive a short exposure to this kind of mild acidity.

Research Has Shown That Probiotics Survive The Digestive Tract

This is not all theory. There is actually lots of research demonstrating that probiotic bacteria can make it safely though your stomach. Here are a few of the research papers, along with a relevant quotation from each one.

Recovery of Lactobacillus rhamnosus GG from human colonic biopsies (Alander, 2003) 
“The colonization of Lactobacillus rhamnosus GG (L.GG) in five human colonoscopy patients was studied … In all patients L.GG was the dominant faecal lactic acid bacterium as a result of the administration.”

Analysis of the Fecal Microflora of Human Subjects Consuming a Probiotic Product Containing Lactobacillus rhamnosus DR20 (Tannock, 2000)
“The composition of the fecal microflora of 10 healthy subjects was monitored before (6-month control period), during (6-month test period), and after (3-month posttest period) the administration of a milk product containing Lactobacillus rhamnosus DR20 … DR20 was detected in the feces of all of the subjects during the test period, but at different frequencies.”

Intestinal transit of an orally administered streptomycin–rifampicin-resistant variant of Bifidobacterium longum (Fujiwara, 2001)
“It is clarified that BL2928SR [a strain of Bifidobacterium longum] has the ability for long-term survival in the human gastrointestinal tract, and alters the composition and metabolism of the intestinal microflora.”

Colonization and Immunomodulation by Lactobacillus reuteri ATCC 55730 in the Human Gastrointestinal Tract (Valeur, 2004)
“Dietary supplementation with the probiotic L. reuteri ATCC 55730 induces significant colonization of the stomach, duodenum, and ileum of healthy humans, and this is associated with significant alterations of the immune response in the gastrointestinal mucosa.”

How To Ensure That More Of Your Probiotics Survive

Commercial probiotics can be expensive supplements, so you should make sure that you absolutely get the most value from them that you can! There are two simple tips that you should follow to achieve this.

First, take your probiotics immediately before or during your meal. Eating a meal temporarily reduces the acidity of your stomach and makes it easier for the probiotics to pass through. This means that more will survive the journey through to your intestines.

Second, take a brand of probiotics that contains lots and lots of bacteria. You should be aiming for at least 10 million CFUs per capsule to start with, and then increase your dose even further when you feel ready. Some of these bacteria are bound to die during transit to your intestines, so the more that you ingest, the greater the chance of an effective colonization.

If you need more advice on how to choose a good probiotic, check out our Ultimate Candida Diet program. It tells you everything you need to know about the low-sugar diet, probiotics, and antifungals that you need to beat Candida, as well as giving lots of tips on how to choose an effective probiotic.

Filed under: Immune System, Probiotics
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  1. Susan says:

    All it does is give me diarrhea

    1. That’s probably a sign that you have some imbalance in your gut. Try a smaller dose first!

    2. Anna says:

      What you do if u suffer from direaha

    3. Rach says:

      My Mom says Align cured her diarrhea. It blew me up with my IBS-C

  2. Carrie says:

    What is the best probiotic to take?

    1. I usually recommend the Healthy Origins 30 Billion probiotic

  3. Elizabeth says:

    I find that most probiotics are made to treat diarrhea and I am a suffer of constipation. Can a person who has candida be constipated.

    1. Yes certainly! Taking a spoonful of olive oil after each meal can help (plus its an antifungal too). Probiotics help to restore balance to your gut flora, so they can actually help with both constipation and diarrhea.

      1. Hayley says:

        What kind of probiotics do you take?

        1. Lisa Richards says:

          I like the Healthy Origins probiotics

    2. Nica says:

      Elizabeth, all throughout my first pregnancy I had to take Colace for constipation. This time around I started probiotics when I got pregnant and I haven’t had a need for Colace at all! They also resolved an ongoing yeast infection that I couldn’t get rid of using the standard yeast infection treatments. I LOVE MY PROBIOTICS! 🙂

    3. Rebecca Quinones says:

      Try Coffee enemas if you suffer from constipation… it is non habit forming and actually trains your colon to eliminate waste…. If you are constipated, that also means your ability to detox IS ABSOLUTELY COMPROMISED! It also supports your Liver in the process of detoxification. The Body ecology diet is also a Candida diet and coffee enemas are part of the process that is encouraged

  4. Marilyn Cole says:

    Firstly, thanks for all the info on your website, I was guided here by a friend who has you ebooks etc.
    My problem is, most of the foods you recommend to fight a candida overgrowth, I am allergic too.
    I am struggling, realizing that if I want to heal, I will have to stick to a very restrictive diet of very very few foods.
    My allergy list is so long. I get instant headaches in the same place when I have eaten something I am allergic too.
    I have checked medically MRI scans etc. as I didn’t realise that allergies were my problem. I have known I have candida since 1985, at that time I managed to get it under control and stayed on a candida diet for many years, but then…life changed
    Any help would be appreciated…

    1. Chezbk says:

      Have you been checked for leaky gut? Allergies to certain foods are secondary there is usually a primary problem my husband has had amazing results check out info from a guy called ‘wilding ‘the truth about echzma good luck

  5. Art says:

    This article is fake, those of you that feel it worked, it’s 1) you stopped eating crap and replaced it with yogurt or 2) are having placebo effect. Science proves this article false. Bacteria in intestines will make you sick if consumed and bacteria that survives stomach acid is called food poisoning

    1. Lisa Richards says:

      “Bacteria in intestines will make you sick if consumed” — So I guess you haven’t seen the thousands of research studies into probiotics? And I guess you’ve never heard of the microbiome?

    2. Mr Oz says:

      Art, you are so uninformed.

    3. Joe says:


      You are an idiot! Food poisoning is caused from bacteria that are PATHOGENIC! The strains that are typically recommended as probiotics are not pathogenic. In fact, that is one reason you need to continually supplement; these strains do not permanently colonize at typically high enough numbers in many individuals, and therefore must be supplemented to maintain effective # of colonies in the intestines. Please read one or more of the numerous citations in this article and get educated. Unfortunately, ignorance is not a placebo effect!

    4. Jean says:

      False. My thesis revolves around probiotics and these little guys are proven to help several processes in your body. Also, yogurt is a good source of probiotics, so what exactly are you trying to prove here?

    5. David says:

      Please do research before you post anything,it makes you look stupid lol sorry.

    6. Rebecca Quinones says:

      This is a troll

    7. Tonya Ryan says:

      Wow.. you really need to do your research! I have helped not just my grandmothers IBS, to baby’s colic to injured/orphaned wildlife. Probiotics are so important, look up what they used to do during WW1!! They actually ate a healthy persons decal matters to stop dysentery in soldiers.

    8. Shari Priddy says:

      This is absolutely the very best diet/ program to heal your gut! I started in January 2016 and lost 56 lbs in less time hat 3 months! I am post menopausal and over 50 years old! Even when I was young I didn’t lose weigh that fast. My digestion was healed and I had no more heartburn/acid reflux. Healing the guy is the key to health and this program is the best! Lisa has made it simple and down to a science! I tell everyone about how great it is! Thanks Lisa!!

  6. Linda says:

    Question to all – When really is the best time to take probiotic pills? I want to improve the health of my 3 yr old who has eczema patches in the creases of her elbow and on her calves. I don’t give her any dairy and she (of course) refuses to eat sauerkraut. I also know I still need to clean up the rest of her diet some more, but I do need to start taking care of her gut flora. Well, the probiotics I give her which is –> “Primadophilus Kids” by “Nature’s Way” says one tablet daily BETWEEN meals which contains 3 billion CFU (Lactobacillus rhamnosas, Lactobacillus acidophilus, and bifidobacterium longum) per tablet. If optimal time for taking probiotics is WITH food, why would this bottle recommend between meals? Thanks! 🙂

    1. erac says:

      Have you tried removing Wheat/Gluten from her diet? Skin conditions are related to those foods usually.

      1. Krissy says:

        Was going to suggest the same. Had eczema horribly on hands and feet. Hubby said I had the roughests hands ever. Eliminated gluten/wheat and my body is completely different…smoothest, softest hands ever and the clearest face and skin ever. My tummy feels great and depression mood swings and irritability is gone…it amazes me how gluten affects people and they are quick to cover it with medication or a pill.

  7. Jill says:

    Hi Lisa,
    Thanks for the post. One question. While the research you quoted and many more establish probiotics as beneficial, the research does not indicate the timing of the probiotic. (ie are they taking them before, during, after a meal) Nor do many of them indicate the method (ie capsule, mixed with water, etc). Do you have any research articles that have included that variable?

  8. Jack Stewart says:

    I’d like to take all my supplements when they have the best chance to make it to the intestine and escape the stomach acid. With this in mind when is the stomach acid lowest? Would it be low when the stomach is empty? When food is eaten don’t enzymes in the stomach activate the stomach acid and if so wouldn’t the stomach acid be highest when food was being digested in the stomach? Would taking a supplement with alkaline foods be a good idea because there would be less stomach acid? The supplement I am most concerned about is SOD. I take a SOD supplement without a glisodin binder as I have gluten sensitivities.

  9. Maria Wigley says:

    How about homemade Kefir milk? I’ve heard it’s way better than popping synthetic pills and cheaper!

    1. Lisa Richards says:

      Yes! Homemade kefir is a fantastic source of lots of different probiotic strains.

  10. Tom says:

    When the probiotics reach the intestines, do they survive there a long time? It seems like they would multiply and reach a steady level, as all the other microbes do.

    1. Lisa Richards says:

      Lactic acid based probiotics tend not to colonize very well (at least not as virulently as pathogens like Candida do). Taking them in large amounts can help. Soil-based probiotics tend to colonize more effectively too.

  11. Hannah says:

    Thank you for this post, I’ve been trying to find some actual information (based on scientific research) for ages, but just been met with people’s assumptions.

    You suggest taking probiotics with or before food, so that they meet a less acidic environment in the stomach – but does this count with kefir? Everything I’ve read says to drink kefir on an empty stomach?

    1. Wiley200 says:

      A food-based probiotic is different because the food will help to neutralize the stomach acid itself. Kefir can be taken with or without food.

  12. Ernest says:

    Now Foods recommends taking their reduced glutathione between meals as research showed oral glutathione did not make it into the bloodstream and it was theorized that stomach acid broke up the glutathione protein destroying the benefits. Stomach acid is minimized at morning and fastest transit through the intestines is achieved then too, so to sneak supplements past all the digestion it would seem best to take the supplement with lots of plain water to speed transit. Now foods also added milk thistle and alpha lipoic acid to rebuild any of the glutathione broken down by digestion. They seem to rely on the scientific method of observing patients results with honesty instead of just double double blind studies which are expensive. I tried their supplement and it seems to work for brain inflammation or kinan inflammation of the brain or brain fog turning me into a “numbskull” at times. It has been forty years searching for this and it appears to be reliving some sort of “depression” caused by inflammation. Anti depressants did not work and the whole theory of some types of depression caused by inflammation which was discarded with the advent of anti depressant drugs seems true. Thanks to everyone for all of their great work on this, physicians and patients too who are making the observations. If it means anything, I am an engineer by education trained in the scientific methods and I respect all the old scientists who made their observations long before the double blind study requirements of modern medicine which doctors use to criticize the whole food supplement industry. Yes, there are problems, but drug pushers methods are problematic too. By and large, allopathic medicine has failed me and millions of others, while the simpler methods of naturopaths like Jesus and Luke have often times helped me tremendously. Sometimes you have to do your own experiments to find what works.

  13. Donna says:

    I have a problem with gluten but I love sandwiches. I can live without pasta, biscuits and cornbread. I also was told rice and oats have gluten, is that true? Is there a bread alternative for burgers and sandwiches? Any help or recipe is greatly appreciated.
    As for probiotic supplements, I have spent a fortune with no results. I started Greek whole milk kifer 3 weeks ago and my constipation has gone and eliminating is a new normal for me and I feel great. All though it takes 2 months to colonize in your gut…3 weeks have worked for me. I can’t wait for full colonization because health starts in our gut. I drink 8oz each morning on an empty stomach. That’s the best way and only once a day. Good health to everyone…it’s a process that has to be preserved and disciplined. Thank you for any feed. Hugs 😍.

  14. Donna says:

    I also want to say drinking bone broth is amazing for your gut. I buy the beef broth from Giant grocery store. It’s awesome…it tastes like the broth from your pot roast. Yum. I also eat organic mixed greens like popcorn. It’s hard at first but I have not acquired a taste for them and that helps tremendously. And this is less expensive than the processed and junk food. Happy healing.

  15. Donna says:

    I have tried the gluten free bread in the freezer, but it doesn’t work for me…no flavor and it has to stay frozen. Don’t like frozen sandwiches and not toasted bread for everything. I

  16. Theresa says:

    I have had my gull bladder removed. So I have a lot of acid. I take probiotics. Have had continued diarrhea on and off. Should I continue with probiotics or are they making me worse?

    1. Lisa Richards says:

      Hi Theresa, I’m sorry but I don’t know much about gall bladder removal. I do see elsewhere online that people are recommending probiotics after doing this, but I would check with your doctor just in case!

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