Gut Flora and Your Healthy Immune System

Last week, I discussed the importance of gut flora in the digestion of food while briefly touching on its role in early immunity, including the development of asthma and eczema – both of which are immune issues that appear to be exacerbated or caused by disrupted gut flora in children. But it goes much further than “just” asthma and eczema. Our gut flora plays a massive role in mediating our entire immune response. Think about this little factoid: the human gastro-intestinal tract houses the bulk of the human immune system, about 70% of it. And foreign gut flora actually aids and abets our innate immune response system by improving the function of our mucosal immune system and providing a physical barrier to invading microbiota. Before I get into that, though, let’s go over what we mean by immune system.

Some time back, I wrote a post discussing the three tiers of the human immune system:

  1. Anatomical barriers – Skin is the basic line of defense, along with mucus membranes and other physical responses like sweat, tears, and salivation, against the intrusion of foreign bodies and antigens.
  2. Innate/non-specific immune system – The innate immune system is the broad, generic response to bacteria and viruses that have made it past the anatomical barriers. Imagine bacteria entering through an open wound and the resultant inflammation, which is pretty much the body’s attempt at a catch-all response. Technically, the physical barriers are included in the innate system.
  3. Adaptive/specific immune system – The immune system can learn and improve its response to specific microbes over time and with repeated exposure; this is the adaptive immune system, and it’s only present in jawed vertebrates.

It’s generally accepted that gut flora affects and informs our immune systems, and how it does so, though a complicated, multi-faceted process, is beginning to be teased out by researchers.

Intestinal flora helps determine the quality of our mucosal immune system in several ways. First, it provides a physical barrier to colonization by foreign, deleterious microbes. As I mentioned earlier, infants receive the lion’s share of their gut flora from the mother (and surrounding environment) during birth and for the first year or so. This is a crucial time, because the first bacteria to gain a foothold are able to establish a long-lasting, mutually beneficial relationship with the host (that’s us). Good bacteria settles in and keeps bad bacteria out – for life (ideally, barring disruption of the population by poor diet and excessive antibiotic usage), which is why early intestinal colonization is so incredibly important for healthy function later in life. Though we’re talking tiny, invisible organisms, living quarters in the gut are still finite, and there are limits to how many microbes can be established. Compromised gut flora populations, for example, can allow harmful yeasts and bacteria to flourish. Healthy gut flora populations protect against invading microbes by simply taking up space and generally being more proficient at obtaining nutrients than the intruders. They’re playing defense, and informed, experienced defenders who know their way around always have the advantage.

Next, intestinal flora communicates with certain features of the immune system to help them focus on invading microbes. Ever wonder how our immune systems determine which bacteria to attack and which to ignore? After all, foreign microbes are foreign microbes, and immune cells aren’t “intelligent.” There’s got to be a mechanism behind it, some sort of “safe word” that causes immune cells to pass over the trillions of foreign bacteria residing in the gut. Good bacteria talks to the lymph nodes and provides a safe word, and the lymph nodes’ stromal cells produce “normal cell” antigens that tell the immune system not to attack the good bacteria. This conserves resources and improves the immune response by making it more efficient.

Intestinal flora can even influence the growth and formation of organs crucial to proper immune function. Take the thymus, for example, the primary function of which is to produce T-lymphocytes, also known as T-cells. T-cells are a type of white blood cell that has two functions. Killer T-cells destroy the body’s own cells that have been infected by viruses or bacteria; this prevents the offending microbe from replicating and causing more damage. Helper T-cells stimulate the production of antibodies. Both are vital, and both are made possible by the thymus. The thymus, in turn, is dependent on intestinal flora: formula-fed infants have smaller, less productive thymuses than breastfed infants. Okay, but how do we know that it’s the bacteria in breast milk making a difference? What’s one big thing that sets breast milk apart from formula? Beneficial bacteria, specifically Bifidobacteria, which is only present in breast milk. One recent study confirmed the effect of bacteria on thymus size when it compared thymus sizes in breastfed infants, standard formula-fed infants, and infants fed a fermented formula populated with Bifidobacteria. Infants given standard formula had smaller thymuses than infants in the other two groups; thymuses in infants given the fermented, bacteria-rich formula were similar in size and function to breastfed infants.

The study (PDF) of germ-free mice offers clear evidence that the presence of intestinal microbiota impacts the development of immune systems. Mice raised in isolation chambers, completely free of gut flora, exhibit a host of immunodeficiences: systemic lymphopenia, or low levels of lymphocytes, a kind of white blood cell extremely important to immune function; hypoplastic, or underdeveloped, lymphoid structures with compromised immune function; and poorly formed high endothelial venules, which are crucial pathways for the normal immune cell response. Colonization of germ-free mice with normal levels and species of gut flora, for the most part, normalizes immune function and structure.

90% of cells in the human body are microbial; a mere 10% are “human.” Perhaps it’s time we start redefining exactly what it means to be human. We couldn’t function without foreign gut flora. We’d be quivering and helpless, chronic hypochondriacs by necessity. Any variance in diet would probably immobilize us, and the mildest, gentlest pathogen would have its way with our tender bodies. It would be a bad scene all around.

Every organism – at least the larger, multi-cellular ones – has similar relationships with foreign microbes. The difference with humans is that we are consciously aware of their existence, and we devise methods to eliminate them from our bodies and our environment. Wild animals do not fret about such things; they live in ignorance of the teeming bacterial hordes handling the internal machinations. Oh, they may have protectionist instincts, like shying away from harmful or spoiled food, but they aren’t making the conscious decision to avoid bacteria. We have antibiotics, and soap, and surgical gloves, and gas masks. Our entire modern existence can perhaps be described as the avoidance of nature. Nature’s a scary place, with dark, dismal caves, dangerous predators, poisonous plants, and uncertainty, so we built walls, planted crops, tamed animals, and discovered fire. Humans are of “mother nature,” but we number in the billions only because we rejected and excluded her. And that’s the tricky part of being human, isn’t it?

Clearly, the best path for proper immunity is the early establishment of a healthy population of gut flora, ideally initiated immediately after birth. If you’re reading this, you’ve most likely been born, probably for quite some time now, but that doesn’t mean you should throw in the towel. On the contrary, we adults, more than anyone else, need to know the importance of gut flora. If we have children, it’s up to us to ensure they receive the proper exposure to beneficial bacteria. As for adults, the avoidance of sugar, vegetable oils, and lectin-rich grains and legumes to the inclusion of animal fat, protein, Primal starches, and leafy vegetables is a safe way to promote a healthy gut. Eating fermented foods and trying probiotic supplements may also help.

For anyone who’s still interested in this subject, I’d strongly advise you check out Dr. Art Ayer’s fantastic blog, Cooling Inflammation. Art suggests chronic, systemic inflammation stemming from disrupted gut flora as the root of most, if not all, diseases. He may be onto something here.

Let me know your thoughts in the comment board. Thanks for reading!

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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82 thoughts on “Gut Flora and Your Healthy Immune System”

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  1. Any thoughts on the use of non-antibacterial soap helping to increase exposure to healthy bacteria? I have recently moved away from anti-bacterial soap for this very reason. While I haven’t seen any definitive studies, I have seen a few articles that touch on anti-bacteria soap hurting our immune system and our overall health.

    Thanks for all the great insight Mark!

      Yes, antibacterial hand soap causes infertility….don’t use it.

      I wrote a nice informative story for ERGOparent magazine…which can now be found on ERGObaby blog. (link above.)

      Breast milk is crucial for babies to populate their guts with beneficial flora. Thank you, Mark for highlighting this extremely important fact.
      We were born to eat at a breastaurant before anything else for this reason!
      Aloha from Maui, where we are raising 100 regenerative-design, grass-fed, intensively grazed cattle and chickens. Cheers!, Claire

  2. Great post Mark. It really makes you think about what you’re putting in your mouth when you think about what’s going on inside you.

  3. I would emphasize the avoidance of sugar and inclusion of fermented foods in ones diet. That has helped me tremendously after numerous rounds of antibiotics.

    I also wanted to add getting outside and playing in dirt. Do some gardening, get kids outside digging and playing in mud. There’s tons of natural good bacteria outside, we just need to get out there and surround ourselves in it.

    1. Yes – play in dirt – do some gardening!

      May is right around the corner (my birthday month) which means its time to garden if you are a Michigander!!!

      I was not at all into gardening for the first 21 years of my life. But, now that I am primal, I have a STRONG interest in it and will be helping my parents in the yard frequently!

      When I buy my own home, I will have a MASSIVE garden. 🙂

  4. I used to wash my hands an absurd amount of times. Today, I enjoy washing them only when it is 100% necessary.

    I am happy to read these gut articles. I do not consume any fermented foods or foods but have been wanting to for a while now.

    Thanks for the education Mark!

  5. I find it humorous that this rash of posts about the health benefits of healthy bacteria come just prior to the release of PrimalNutrition’s probiotic supplement.
    That being said; it all makes sense, and I’ll still buy the probiotics for my family and myself.

    1. At least he’s not saying “the only way to repopulate the gut is with probiotics”. I find fermented foods to be much more potent than any probiotic I have tried. That said, probiotic supplements are useful to have around, especially when traveling.

      1. What type of fermented foods do you eat? Do you need to buy them from a health food store, or can you make them yourself?

        1. I am from Korea and we eat a salad dish call Kimchi. There are several kind of Kimchi, some very spicy, but simple one is just pour salt over cleaned Chiness cabage(Chopped & drained well)until wilted, it will take few hours. Put cabage in a jar and pour over water and more salt until water taste right(enough salt make does it) and leave in a large jar for a few days in room temperature,water should be covering the cabage. Once it is furmented You can keep in the refrigerator for months. You will love this.”Good Luck”

    2. Yes, the impending product definitely has an influence on these posts, but probably not the way you’re thinking. I believe in probiotics and take them myself. I’ve been doing a lot of research on them lately to ensure that I can get 100% behind the product I’m developing. The more I dig into the research the more I’m convinced that probiotic supplementation makes sense. It’s been on my mind with all the R&D work I’ve been involved in, so I felt compelled to share it with the MDA community. Read the studies linked to, think critically and then find something that works for you. Grok on!

      1. I know you’re not doing it as some scare tactic Mark: I’m sorry if that was unintentionally implied. I simply recognized the connection and laughed to myself.

  6. Very useful information, especially for new parents. Circumstances require our baby to be mostly formula fed, but I’ve been working in kefir and lactofermented veggies on the side. Not to mention that wonderful reflex all babies have to smear their hands on everything possible and then suck their fingers. I think he’s going to be fine.

    But I wonder, what happens when we take antibiotics as adults? Not that we should, but a full course over several days has got to be devastating on gut flora. Can we ever fully recover from such microbial genocide, if our first-year bacteria are so essential?

    1. Timothy, you might want to check out GAPS and SCD diets which are essentially primal diets with more emphasis on fermented foods and rebalancing/repopulating gut flora. I do believe we can recover, but it does take some work. I was not breast-fed and went through many many rounds of antibiotics. After a few years of this diet style I am finally recovering.

    2. researchers now think that in some cases, the appendix can hang on to its store of bacteria and repopulate us with our native strains in cases of diarrhea diseases but i do think some antibiotics wipe us out completely, appendix included. i know in some cases they give antibiotics to appendicitis patients instead of surgery.

  7. Very interesting, and I second the idea of Dr. Ayers being onto something. His research of bio films is fascinating.

  8. Good post! I was a victim of over-using antibiotics for a period of 5 years. I have been on a similar diet, but a few foods allowed on PB, aren’t allowed on the diet I am currently on. Food has cured some symptoms and I’ve seen remarkable results. Again thanks for your insight on such topics!

  9. “90% of cells in the human body are microbial; a mere 10% are “human.” ”
    mmmm… maybe I’m not understanding this correctly. Does this say that 90% of the total number of cells in our bodies are microbial? or that 90% of the total number of TYPES of cells are microbial? The latter, right? ok then!

    1. 90% of the total is what I’ve always heard. I guess the microbial cells are just so much smaller than the normal “human” cells that they actually outnumber them.

  10. I recently subscribed to your blog.
    I don’t understand your attitude to grains. When I say grains I mean grains and not white bread and cereal. Grains is the primary food in many parts of the world, especially in poor countries. I don’t think even there is enough meat in US if all people started following your advice. Not to mention that most of the meat in the stores is from hormone/corn fed animals. Vegetables are also expensive, and not everybody can afford eating just vegetables and meat. World would not survive without grains.

    1. “Grains is the primary food in many parts of the world, especially in poor countries.”

      No argument there. Yes, grains are a cheap source of calories.

      “I don’t think even there is enough meat in US if all people started following your advice.”


      “Not to mention that most of the meat in the stores is from hormone/corn fed animals.”

      Yep, another problem.

      “Vegetables are also expensive, and not everybody can afford eating just vegetables and meat.”

      Yes, there are cheaper ways to eat.

      “World would not survive without grains.”

      7+ billion without grains? Yes, quite possibly true, too.

      So, yes, I agree with all of your points, but it doesn’t make grains an optimum or even good food choice on the individual level. Take a look around the site, read my book and stay in touch!

      1. I’d like to note:

        If we weren’t growing all those damn grains, we could be growing real food on that land. Or maybe some animals?

    2. So long as you assume current farming, the world cannot survive without grains. However there are a lot of things farmers could do (but don’t because the money is in grain) that change the picture.

  11. I’m your cautionary tale. I was placed on powerful antibiotics for an abscessed tooth back in 2002. After years of living a high stress, processed food life I developed IBD, specifically Ulcerative Colitis, two weeks after the course of antibiotics was finished. After three years of medications, treatments (both conventional and holistic) that are too lengthy and grim to get into, I had my colon removed. It was either that, or die. If my doctor had just recommended taking probiotics while taking the antibiotics (which kill all bacteria – good and bad), my story could have been very different.

    This is definitely an interesting read. My only reservation is the Science Daily article, “Why Doesn’t The Immune System Attack The Small Intestine?” The immune system does in fact attack the small intestine in the autoimmune condition Crohn’s disease. In fact it can attack any part of the gastrointestinal system from mouth to anus. A quick and dirty overview:'s+disease
    However, a HEALTHY immune system (where the T-cells recognize the antigens properly) the immune system does leave the small intestine alone. I kinda felt they needed to make that distinction in the article.

    But on the whole, right on. I have been a big supporter of probiotics, and good nutrition for years. Bad health is an excellent motivator for personal reform. Keep up the great work!

  12. Imagine if the majority of land now tilled for government reimbursed grains was readapted/allowed to revert back into the grasslands they were before the advent of industrialized farming………..grassfed protein (and what an improvement to our environmental impact).

    I have actually found I eat less of even protein when I am eating low carb/high saturated fat, sounds strange I know. We are glutenous americans with our meat portions………is this because of the corn fed beef.

    As for cost…….my grocery bill is smaller, even with buying grassfed protein/dairy…….but again I don’t buy all the other ‘stuff.’ Try it for a week’s shopping trip. Just buy vegies, meat, butter, nothing else………You might just be surprised.

    Thanks Mark for all the information, insight, other websites to ponder and inspiring me to speak out.

    Wish I could have joined the group at Primal Con. Looked like tremendous fun and information.

  13. My daughter is 2 years old and has had stomach issues since birth. At 6 weeks, she had blood in her stool and was only able to tolerate a formula broken down to the amino acid level.(I was only able to breastfeed for 9 weeks and she bled on breastmilk) She had a colonoscopy at 9 months to determine the cause of the bleeding. She had C. Diff bacteria present, but no other cause. She is not able to tolerate any milk products.

    She has been nearly primal for about 3 weeks and is showing improvement with her stomach issues (less pain, constipation, etc).

    I had antibiotics for Group B Strep upon her delivery. Could this have caused her troubles?

    I have not started any probiotics yet. Any recommendations for her age?

    1. I’ve been giving my two year olds Nature’s Way Primadophilous for kids. They’re chewable so it’s good for this age. And they seem to be working well to help both of my girls with some stomach issues they’ve had. Good luck!

    2. I also have a daughter who had the antibiotics at birth. She has allergies to gluten, dairy and is very affected by red and yellow dyes. When we pulled these foods out of her diet, her balance, coordination and language developement leapt. She takes Vitamin D, A and a probiotic called Bifoviden.

      1. Hi Dave, does your daughter currently drink milk? I have pulled my daughter from soy and have started her on almond milk. She is not liking it very much. Any other suggestions for non-dairy milk that young children will drink?
        Also, what type of reactions did your daughter have to the yellow and red dyes? Hyperactivity, stomach pain?

        1. Kefir is a great source of probiotics and can be made with water and other sources if milk/dairy cannot be used. Do a google search on kefir and water kefir and you’ll get a ton of info.

          Better and much cheaper source of probiotics than a supplement.

        2. She drinks rice milk now when she wants it or we need to cook with it. Not very primal but it’s working. She gets all the normal milk nutrition from veggies and fruit along with meat. This is really all she can eat without stomach, sleep and learning issues.

          We have a nutritionist that suggested pulling the red and yellow dyes because they are “neurotoxins” and she was a bit behind in the motor areas and language development. She was almost passive too but now has increased activity and awareness. The nutritionist says that the dyes affect each kid in their own way though.

        3. Have you tried coconut milk? You can also make coconut kefir which is fermented and will give her some probiotics.

        4. Thank you for the advice and information! It sounds like probiotics will definitely help her repair her gut. I won’t worry so much about the milk, either. Thanks again for the support.

    3. I used to give my son goat milk which seemed to help. If it is cold, they can’t tell the differece.

  14. Calling Mark Sisson out on the release of his probiotic is weak, at best. Sure, he has something to sell (don’t we all ???) but I have followed this site for several years and I know that he has our health at the heart of his mission. After all, what else do we have if we don’t have superior health? Grok on, Mark!

  15. awesome post! i read cooling inflamation a well and am intrigued at overcoming lactose intolerance, which is iwhat i am experimenting with now. starting with suerkraut, kefir and strained goat yogurt and eventually going to add bck raw goat cheese and see if it has helped.

    anyone have experience with this?

    1. My husband and son both had “lactose intolerance” until they eliminated grains, and gluten in particular. Now they have no symptoms. I can’t say how long it took, it just became apparent over time that their issues had cleared up.

  16. Thanks Mark. I have an adaptive immune deficiency and I am working on changing my diet to be as good as possible. I like the idea of fermented foods but could you provide more information?

    1. Haha, they also don’t wipe their asses as much as we do … there are some aspects of civilization that still make it great to be homosapien! Ever watch a dog return to its vomit? How far back down the ladder would you like to go? 🙂

  17. My cats wash their paws about as often as I wash my hands (I don’t wash my hands that often ;))

  18. I just recently started taking probiotics and I am fermenting some saurkraut as I type this. Once the bottle runs out I will be sure to use Marks probiotics. Now if I can just convince others of healthy gut flora. I know so many people who’s children get on antibiotics…then are sick again in 2 weeks….then back on antibiotics! Why can’t people understand we are meant to eat REAL FOOD and not processed fake food substitutes?

  19. Hi mark’s daily apple

    What is a primal starches?

    Is rice high in lectin?

  20. Our immune system like all our systems needs a workout to stay in shape. The constant drive to live in an asceptic environment (hand-sanitizer beside elevator buttons)isn’t helping us. Kids raised in householdss with pets suffer fewer allergies. For a great insight into our relationship with parasites and our evolution along side them, try “Parasite Rex” by Carl Zimmer.

  21. Hey Mark,

    I have to say that you have truly been an inspiration on how I look at diet and fitness and the results that I have seen since implementing your ideas into my life have been phenomenal. I thank you and wish you a ton of success in spreading the grok message to more people 🙂

  22. I gave my 8 month old (at the time) probiotics after a breakout of eczema and it went away. He is now 5. He has had asthma for a couple of years. I started him on probiotics again and this is the first year he hasn’t needed an inhaler. We are also careful about sugar, which I agree makes a difference. We all take them now.

  23. Hey Mark; might wanna check out “Enterogermina”. It’s the biggest selling probiotic in Italy and I bet it really packs a punch.

  24. I like the article about the gut! If you want to see a proof that you truly are what you eat and drink, check out this video. Don’t eat while you are watching it!

    It will make you think about what your gut looks like on the inside. It made me wonder and I decided to buy the Kangen machine and have been drinking this water for the last 3 years. I have found that it has been the best tool in our family’s natural medicine chest and it’s absolutely worth every penny. So, find someone to give you the water to try, and try it for a month and see how you feel. If you have problems finding someone, let me know, and I’ll help you. It shouldn’t cost anything – just make sure that it’s real Kangen water, made in a Japanese machine, not a Korean imitation and you will notice a change in how you feel!

  25. How come your probiotics don’t require refrigeration? My doctor told me to avoid probiotics that aren’t kept cold. Am I misinformed?

  26. While this is an old thread – didn’t appear to be a newer one on the subject. Due to a round of c. diff here, my entire family is on antibiotics. We’ve started taking some probiotics to help counter the negative effects of the antibiotics, and we heard the same info as Mike above – from both the doctor and the pharmacist.

    Just curious about any science behind the need for refrigeration? We’re taking “Natural Creations Enterobiotic S-IGC” which requires refrigeration. It also has a lot of strains of probiotic, but vastly smaller numbers of CFU.

    I am trying to figure out whether it’s better to switch to the primal flora, or what the difference is. There have been a number of years of research on this topic since the product came out – so figure there might be a new formulation in the works?

  27. Interesting and informative article on gut flora. However, in your last paragraph you refer to what adults should avoid (sugar, vegetable oil, high dose lectin grains such as wheat) [all of which I agree] and what they should include (animal fat and protein) [This I do not agree with] You are obviously an advocate for a paleo based diet, but have you read the works of Professor T. Colin Campbell (Author of ‘The China Study’), Dr. Dean Ornish or Dr. Caldwell Esselstyn jr. These 3 men are huge leaders in their fields and I would recommend and encourage all of your followers to read their works and get a better understanding of why you should eliminate meat protein from your diet to bring about optimum health for not only yourself but for the planet also. Further more, If anyone is looking for further reading on just why some particular grains and in particular ‘wheat’ are so terrible for your body, you could look into the work of Sayer Ji titled ‘The Dark Side of Wheat. A whole food plant based diet such as that being advocated by these field leaders, could be just the answer some of your readers are looking for in terms of better sustainable health with longevity and vitality.

    1. Try eating organic animal products and then go back to that China Study. …I am hypersensitive to most foods. I cannot have regular meats not even when it is the same brand that I buy organic meats from. However, I survive on organic meat. Why? Because I can’t have too much fiber. My digestive system is too worn down. Plus, animals and their fats also contain vitamins and minerals that require fats to absorb and utilize. You can have those same vitamins and minerals in your body, but if you aren’t getting your fat requirement, then you wont be able to utilize them, which is just like not having them at all. Also, the human body requires different types of fats including cholesterol for many different functions in the body like like structure, digestive lining repair, and hormone production. Animals are a very necessary part of the human diet.

  28. Hi Mark

    Do you/or any other informed person on the forum, have an opinion on Lufenuron for combating yeast overgrowth in humans? I seem to have many symptoms that would point to me having this, I avoid sugar quite successfully, not perfectly, and eat a naturally fed paleo diet 95% of the time, I regularly take quality probiotics and exercise regularly and I have done all this for a few years, , my weight is near optimal at 12% body fat (male), but I cannot shake these symptoms though, I have friends telling me how good Lefenuron is for breaking down the cell wall of the yeast, however I do not really want to ingest a drug unless it’s really necessary and safe. please help.

  29. I wish to show thanks to you just for bailing me out of this particular trouble. I have a sheet all your articles. Thanks for this best post.

  30. Love following your insights Mark! Thanks for all the solid content aimed at bettering other people! And for Primal Kitchen’s amazing products!