The Benefits of Probiotics –Teaser Excerpt from The Paleo Approach

February 12, 2013 in Categories: , by

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The Paleo Approach by Sarah BallantyneThere are many topics that I am researching and writing about for the book that I’ve been meaning to write about for the blog for ages (the book just gives me a firm deadline).  I have decided take some of these topics (especially the more blog-sized ones) and publish them as teaser excerpts for the book (also because I think this information should be here too).

The book also contains a detailed (yet easy-to-follow) description of the components of the immune system, so when you read the book, you’ll already know why modulating Th1 versus Th2 versus regulatory T-cells is important and you’ll know what dendritic cells, antigen presentation and cytokines are. For a quick primer: Th1 and Th2 cells are over-activated in autoimmunity and cause damage (typically one or the other is over-activated).  Regulatory T-cells are supposed to keep all the other immune cells in check and suppress both over-activation of the immune system and autoimmunity (they tend to be deficient in autoimmune disease).  Cytokines are chemical messengers of inflammation.  Dendritic cells are a type of sentinel cell that detects foreign invaders.  Antigens are small sequences of amino acids on foreign invaders that are recognized by the immune system.   When a dendritic cell detects foreign invaders, they “show” the antigens to B-cells and T-cells (cells of the adaptive immune system).  Gut-Associated Lymphoid Tissue is the collection of immune cells and other tissues just inside the intestinal barrier in the gut.  Enterocytes are the cells that line the small intestine and form the barrier between inside the gut and outside the gut.

So, forgive the references to Chapters 2, 3, 8 and 12.  While you’ll have to wait until the book is out to read those sections, in the meantime, please enjoy this part of my section of probiotics (actually, probiotics are talked about in 4 separate sections-this section is from the chapter on healing foods).

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Consumption of probiotics, either as a supplement or in the form of unpasteurized fermented foods, can dramatically help modulate the immune system.  A vast number of scientific and clinical studies have evaluated the various effects of the commensal bacteria in the gut (those healthy gut bacteria) and/or probiotic supplement of specific bacterial strains on various aspects of the immune system.  The cliff notes?  It’s all good.

The exact mechanisms behind the many observed benefits of probiotics remain largely unknown.  This may be because different bacterial strains have different effects on the body and interact differently with the immune system.  For example, some probiotic strains stimulate production of cytokines (those chemical messengers of inflammation) that promote Th1 cell development (which may augment the immune system to help fight infection and prevent cancer).  Other probiotic strains stimulate production of cytokines that promote regulatory T-cell development, thereby providing that all important immune system modulation needed in autoimmune disease (see Chapter 2).  Yet other probiotic strains, including several lactobacillus strains, are beneficial both in diseases of compromised immune systems and diseases of excessively activated immune systems.

It has been shown that probiotics interact with dendritic cells during antigen presentation during the initiation of adaptive immune responses, meaning that probiotics are useful in preventing immune-related diseases (see Chapter 2).  However, they also affect the effector phase of adaptive immunity, so they can be used as a treatment for established immune-related diseases (this applies to both immune-related diseases like asthma and allergies but also autoimmune diseases).  In fact, probiotic supplementation has been shown to be beneficial in a variety of autoimmune conditions, including:  autoimmune myasthenia gravis, inflammatory bowel diseases, rheumatoid arthritis, multiple sclerosis, and autoimmune thyroid disease.

It used to be believed that probiotic supplementation and the consumption of unpasteurized fermented foods provided health benefits by re-inoculating the gut with beneficial strains of bacteria and yeast.  Having a healthier variety and types of gut microorganisms would then be responsible for the positive benefits of probiotic supplementation.  However, recent scientific research puts this explanation into doubt—at least in some cases.  A recent study of diarrhea-predominant Irritable Bowel Syndrome demonstrated that the administration of probiotic supplements did not to alter the composition of the gut microflora.  It’s important to emphasize that probiotic supplementation was still beneficial.  This implies that the benefits of probiotic consumption might be directly due to the interaction of those probiotic bacteria (and yeast) with the gut-associated lymphoid tissue (see Chapter 2) as it passes through the body, at least in some cases.

There are clearly still some situations where probiotic supplements do have profound effects on the gut microflora.  For example, studies have shown differences in the composition of the gut microflora after taking antibiotics in people who supplemented with probiotics compared to those who didn’t.  There may also be more impactful effects on those with bacterial overgrowths.  Probiotic microorganisms have the capability to affect the gut microflora through a variety of mechanisms, including: reducing the acidity in the intestinal lumen (the area in the middle of the “tube” that forms the gut), competition for nutrients, secretion of antimicrobial compounds by the probiotics themselves, stimulating the production of antimicrobial compounds by your cells, and preventing adhesion and interaction of other bacteria with gut epithelial cells.  In these ways, probiotics may help to “correct” gut dysbiosis.

Beyond restoring balance to the gut microflora and modulating the immune system, research has shown that administration of probiotics can have a direct effect on the tight junctions between enterocytes in the gut—resulting in decreased intestinal permeability.  So, taking a probiotic or eating food naturally rich in probiotic organisms can directly help heal a leaky gut.

As already mentioned in Chapter 3, what you eat has a profound effect on the types, relative quantities and location of different bacteria growing in your gut—this effect is largely independent of the benefits of consuming fermented foods or taking probiotic supplements.  However, consuming probiotics has the great potential to speed healing and modulate the immune system and should not be underrated in importance when dealing with autoimmune disease.

Some researchers are taking on the task of characterizing the precise effects of each probiotic strain on the human body (recall that there are approximately 35,000 of them among all humans).  Certainly some strains have already been isolated for their anti-inflammatory and immune modulatory properties, yet others for their abilities to improve the barrier function of the gut or the ability to reduce visceral hypersensitivity.  It is completely possible that in the future, probiotic supplements will be tailored to address specific health problems by providing specific strains known to counteract those issues.  However, until then, the best focus is on variety.

Because different probiotic strains have slightly (and sometimes vastly) different effects (which may also depend on your genetics, level of inflammation, and current gut health), the best way to ensure complete modulation/regulation of the immune system is to consume as many different probiotic strains as possible.  So, where do you get variety?  You actually get far more variety from fermented foods and soil than you do from most supplement available (that doesn’t mean that probiotic supplements aren’t useful—see chapter 8 for more information specific to probiotic supplements).  Every time you make a new batch of homemade sauerkraut, the probiotic organisms within it will be slightly different.

So, what are good food sources of probiotics?

  • Raw unpasteurized sauerkraut
  • Raw unpasteurized lactofermented vegetables (kimchee, beets, carrots, pickles)
  • Raw unpasteurized lactofermented fruits (green papaya, chutneys)
  • Raw unpasteurized lactofermented condiments (relishes, salsas)
  • Water kefir
  • Milk kefir grown in coconut milk
  • Kombucha
  • Beet Kvass

Some form of probiotic should be consumed every day.  It is typically understood that a small amount several times per day is more beneficial than a large amount at one sitting.  When you first start consuming probiotic foods, it’s a good idea to keep the amount very small (as little as 1 teaspoon) and see how you feel.  Some people with severe gut dysbiosis can have dramatic gastrointestinal symptoms from probiotics.  If one probiotic food doesn’t work for you, try another.  If none of them work for you, you may have more luck with a supplement or just might need more time to heal your gut before introducing probiotics.  It’s okay if you need to follow The Paleo Approach for a couple of weeks before adding probiotic foods (for more information, see the Troubleshooting section in Chapter 9).  The amount you eat at any given time can then be slowly increased over the course of several weeks.  (Making probiotic foods in your own home will be discussed in The Paleo Approach Cookbook)

An often underrated source of probiotics is soil.  Soil-based organisms (SBOs) have not been as extensively studied as the lactobacillus and bifidus genus of bacteria.  However, they are normal residents of a healthy gut, have been shown to be potent modulators of the immune system, and supplementation with SBOs has been shown to be beneficial in diabetes, chronic fatigue syndrome, insomnia and Irritable Bowel Syndrome.  Soil-based probiotic supplements are available (see Chapter 8 for more information).  You can also get exposure by playing in the dirt (a good excuse to take up gardening as a hobby!) and by growing your own vegetables organically (or buying locally-grown organic vegetables) and eating them without washing them.  Okay, you can rinse the big clumps of dirt off.

Interested in learning even more about The Paleo Approach? This video from my YouTube Channel is just a quick tour (the book is so big that giving you a broad overview takes 13 minutes!) but you get to see just how comprehensive and detailed this book is.


Barbara, G., et al., Mucosal permeability and immune activation as potential therapeutic targets of probiotics in irritable bowel syndrome, J Clin Gastroenterol. 2012 Oct;46 Suppl:S52-5

Bittner, A.C., et al., Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial, Clin Ther. 2007 Jun;29(6):1153-60.

Chae, C.S., et al., Prophylactic effect of probiotics on the development of experimental autoimmune myasthenia gravis, PLoS One. 2012;7(12):e52119.

Corridoni D, et al., Probiotic bacteria regulate intestinal epithelial permeability in experimental ileitis by a TNF-dependent mechanism, PLoS One. 2012;7(7):e42067

Fooks LJ and Gibson GR Probiotics as modulators of the gut flora. Br J Nutr 2002 88(Suppl 1):S39–S49.

Gerritsen, J. et al., Intestinal microbiota in human health and disease: the impact of probiotics, Genes Nutr. 2011 August; 6(3): 209–240.

Kiseleva, E.P., et al., The role of components of Bifidobacterium and Lactobacillus in pathogenesis and serologic diagnosis of autoimmune thyroid disease, Benef Microbes. 2011 Jun;2(2):139-54.

Kobayashi T, et al.,  Probiotic upregulation of peripheral IL-17 responses does not exacerbate neurological symptoms in experimental autoimmune encephalomyelitis mouse models, Immunopharmacol Immunotoxicol. 2012 Jun;34(3):423-33

Le Bert, N., et al., DC priming by M. vaccae inhibits Th2 responses in contrast to specific TLR2 priming and is associated with selective activation of the CREB pathway, PLoS One. 2011 Apr 1;6(4):e18346

Michail, S. & Kenche, H., Gut microbiota is not modified by Randomized, Double-blind, Placebo-controlled Trial of VSL#3 in Diarrhea-predominant Irritable Bowel Syndrome, Probiotics Antimicrob Proteins. 2011 Mar;3(1):1-7

Ng SC, et al., Mechanisms of action of probiotics: recent advances. Inflamm Bowel Dis. 2009;15(2):300–310.

Ruemmele F.M., et al., Clinical evidence for immunomodulatory effects of probiotic bacteria, J Pediatr Gastroenterol Nutr. 2009 Feb;48(2):126-41.

Shida, K. & Nanno, M., Probiotics and immunology: separating the wheat from the chaff, Trends Immunol. 2008 Nov;29(11):565-73.

Shida K, et al., Flexible cytokine production by macrophages and T cells in response to probiotic bacteria: a possible mechanism by which probiotics exert multifunctional immune regulatory activities, Gut Microbes. 2011 Mar-Apr;2(2):109-14

Schiffer, C., et al., A strain of Lactobacillus casei inhibits the effector phase of immune inflammation, J Immunol. 2011 Sep 1;187(5):2646-55

Tlaskalová-Hogenová, H., et al., Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases, Immunol Lett. 2004 May 15;93(2-3):97-108.

Tsilingiri K & Rescigno M., Postbiotics: what else?, Benef Microbes. 2012 Dec 27:69-75.

Soil-based organisms improve immune function: shift cytokine profile from TH2 to TH1, Posit Health News. 1998 Spring;(No 16):16-8


Thank you for this. Although I think it is rare, when I took a probiotic supplement to help heal my leaky gut, I became constipated. What should I do in this case? I was taking the supplement twice a day. Should I just try to take it once every two days or so to avoid constipation? Because of my various food intolerances, I can’t eat fermented foods or yogurt.

Yes, I would definitely scale back (sounds like they are exacerbating an overgrowth which happens to me too if I overdo it) and have a look at what prebiotic foods are in your diet (sources of inulin fiber or very starchy vegetables). You can also play with taking them on an empty stomach versus with food and see if that makes a difference. I most often take mine on an empty stomach now.

Thank you so much for explaining all the details! Understanding the “Why’s” of paleo makes it easier for me when I look longingly at other people eating non-paleo foods ( or even paleo foods which I need to restrict due to autoimmunity). At least I know what that particular food I want would actually do to my body! I love your blog and you are amazing at making complicated topics easy to understand. I wish I had you as a resource when I took biochemistry and cell biology in college ( I am an engineer…they were really hard classes for me!). I’m looking forward to the book 🙂

This is great! Can’t wait to get my hands on your book. I have a question about probiotic supplements. Is there a particular time of day or meal of the day that you recommend taking your probiotic supplements with? I use Biokult and it simply says to take with food 1-2 times a day. Thanks! 🙂

Great blog post, thank you. I guess the old saying, a little dirt never hurt, is true. I heard a story on the radio that our children don’t play in the dirt, and get enough dirt in their mouths, compared to our grandparents, and that might be related to a higher occurrance of asthma in our children’s generation. So interesting.

I am totally sold on the probiotic idea (I have been for years), but I seem to have difficulty implementing the idea with my 13-month-old. When she was young, I tried some (HMF Natogen, Jarro) and she broke out in hives. I attributed this to the small amount of dairy, so we switched to Klaire Labs Infant. I started with 1/4 tsp., but I should have been wondering right then–the HMF Natogen scoop is more like 1/8 or maybe even 1/16th of a tsp. It’s tiny. A 1/4 tsp seemed like a lot, and I probably just over loaded her system. Anyhow, it gave her very loose stools and she threw up the next day (in a chipper, happy kind of a way a 13-month-old can throw up and still go on with life…). I am afraid to try anything right now. Jeesh. At least she really likes beet and ginger sauerkraut! 🙂 I am curious about the sauerkraut though–is it too salty for kids?

Every little glimpse you give us into your book makes me so excited for it to be published, and so grateful that I found your blog last year. Thank you so much for sharing your knowledge and research with the rest of us!

My baby is teething on chunky homemade saurkraut and fermented parsnips. She seems to adore the sour flavors. Ocassionally, she will accept a bit of bone broth, well diluted, in her sippy cup (she’s 11 months old today). My older kids were weaned during my WAPF days and, while very adaptable to traditional foods, not quite as accepting as their baby sister.

Great article! How much fermented food do you think it takes to benefit? For example, would a 1/2 cup of saurerkraut per day provide any benefit, or is that too little?

That’s a great amount! People experience benefits at different doses. I would say anywhere between a Tbsp and a cup per day is a good amount. There’s not really compelling reason to eat more than that.

Great news about your book and awesome article about probiotics! I find it very difficult to find reliable information on appropriate dosage though and generally suggests that people start very slowly and gradually. Do you have a specific target in terms of billion of CFU / day for people using probiotic supplements?

I was just reading about water kefir and came to your site to see if it was okay for autoimmune paleo – happy to see it on the list – I think I’ll be trying it! I decided to look into the paleo diet because in the past year I’ve developed intolerances to many of the foods not eaten on paleo – gluten, dairy, rice, etc. I’m hypothyroid, but I don’t know if it is from autoimmune or not (apparently it runs in my family), but I’m hoping the autoimmune protocol will help with the food intolerances and many other health problems – migraines, fatigue, etc. I’ve preordered the book – can’t wait to get my hands on it!

I have worked with several patients that did not have an improvement in symptoms with probiotics but did beautifully with fermented foods. I believe that you usually have better results when you stick closer to things in their natural forms. I stopped washing my organic produce a long time ago! Also of interest is some great work being done to determine how our immune system and gut decides what is harmful and what friendly. It appears to begin in utero and in the first weeks of life. What we are exposed to at that time has a big impact on our immune system and what our body considers to be ‘normal’ intestinal flora for the rest of our lives. So a probiotic that works well for me may not be helpful for the next person. Whether we both have the same medical diagnosis or not. This is a great site and I can’t wait for the book!!

I have a 4 year old with eczema and am doing AIP with her. What do you recommend for probiotics for kids? Mostly cultured veggies?
Also, is sauerkraut made with whey not allowed?

There aren’t many probiotic supplements that have been tested on kids, so I would recommend talking to your pediatrician about specific recommendations. Cultured veggies are a great choice. The only potential issue with lactofermented veggies started with a whey culture is possible food sensitivities to the whey. If you aren’t sure whether your daughter is sensitive, it would be better to stick with wild fermentation for now.

In the article above you mention: ‘”And of course, you can skip ahead to Chapter 12 to start making probiotic foods in your own home.” I have bought your book “The Paleo Approach..” and it has only 9 chapters. I very much interested in your advice to how to ferment food and could not find chapter 12. Did you mean another book? Or another edition of your book? Thank you

I apologize. This excerpt was published before the decision had been made to divide The Paleo Approach into two books. The cookbook will be available in August. You can read more about the cookbook here: In the meantime, Sarah reviewed the book “Fermented” which is a great resource on the topic. You can read the review here: — Tamar, Sarah’s assistant

What brand of pro biotics do you recommend? I know there are some that require refrigeration and some don’t.

I recently began adding wk to my diet as well as resistant starch. I’ve already been 100% paleo for just over 2 years and lower percentage before that. The reason I gave up all cheats and dairy was because I became pregnant. About 3 months after he was born I developed HS. Only just recently did I figure out what it was. I worry about wk being an issue for me. I felt like everything was going into remission but yesterday I drank a full glass of wk and had a little outbreak. I don’t know if my gut biome is slowly working out the kinks (1+ month on wk and rs) or if the wk is causing outbreaks. Do you have any experience with this as being a trigger? I usually have no more sugar than a half banana in a smoothie in the morning each day and wonder if wk has too much sugar in it… Thanks. Hope this makes sense! 🙂

Which is better, kombucha or water kefir ? (I want to start with some homemade probiotics, other than sauerkraut). Thank you!

Hello! I’m just embarking on the AIP and I am planning on making some fermented veggies. Many recipes call for whey as an ingredient. Would whey be compliant? Thanks!

Can you point me to which probiotic strains might stimulate Th-1 production? I started taking Hyperbiotics Pro-15 Advanced Formula and Dental formula in August and saw an improvement in my (personally weird version of) dyshydrotic eczema and sinusitis, both Th-2 linked conditions. Geek me wants to know which friendly critters are my newest friends. Thanks.

To obtain kefir in my country (South Africa) is quite a mission…. but today I literally stumbled into a person who has milk kefir.

Now my question… will this kefi grow in coconut milk if it was formed in cow’s milk? Will it survive such a transplant? I believe I can’t use the cow’s milk kefir with Hashimoto’s?

Thank you

What about drinking water kefir or kombucha if having a sugar sensitivity? They are both started from sugar. I drank both in the past but after finding out about a sugar semsitivity, I have been cautious about trying again.

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