Life In the Sanitized Bubble (Or Why Probiotics Are So Important)

For the vast majority of human history (and prehistory), men, women, and children had near-constant contact with the natural world around them. They were walking on the ground. They were playing in the dirt. They were digging for roots and grubs. They were eating with their hands. They were field dressing animals and wiping their hands on the grass. Nothing was sterilized; the tools to sterilize the environment didn’t exist. You could boil water, but that was about it. Bacteria were everywhere, and humans were constantly ingesting it. Even as babies, preindustrial infants nursed for almost four years, so they were getting a steady source of breastmilk-based probiotic bacteria for a good portion of their early lives.

The Agricultural Age: Farms and Fermented Foods

After agriculture and animal husbandry hit the scene, human diets changed, but their environmental exposures didn’t so much. Every day they interacted closely with the soil and/or animals (and their respective bacteria). And they also continued ingesting probiotic bacteria on a regular basis through the use of fermented food—for at least the last 10,000 years. Honey into mead, grains into beer, fruit into wine, alcohol into vinegar.

We know that fermented dairy has been an integral part of any traditional dairy-eating culture because fermentation is the natural result of having milk around without refrigeration. You take raw milk and leave it out for a couple days at room temperature, and it will begin to separate and ferment. Introduce an animal stomach and you can make cheese. Introduce specific strains of bacteria, and you can make yogurt or kefir. But the point is that dairy fermentation—and, thus, the consumption of dairy-based probiotics—was unavoidable in pre-industrial dairy-eating societies.

In areas without (and some with) dairy consumption, they fermented plants. Kimchi, sauerkraut, pickles, chutneys, soy sauce, miso, and natto are just several examples among hundreds.

Modern Diets, Modern Environments

Here’s my point to all this: probiotics in one form or another have been a constant input in the human experience… until today.

Today? We live sterilized lives.

  • We wipe everything down with anti-microbial agents.
  • We wash all our plates and eating utensils with ultra-hot water and powerful soaps.
  • We wear shoes.
  • We don’t touch (or see) dirt for days, weeks at a time.
  • We stay indoors most of the day.
  • We pasteurize our dairy. We render shelf-stable (and thus inert) our sauerkraut and pickles.
  • We sterilize our water.
  • We take antibiotics.
  • We eat processed, refined food that’s been treated with preservatives and anti-microbial additives designed to remove all traces of bacteria.
  • We employ tens of thousands of scientists, bureaucrats, and agents whose primary role is to ensure our food supply is as sterile as possible.

I get all that. There are good reasons for doing all these things, and on the balance I’d of course rather have clean water, clean food, and antibiotics than not, but there are also drawbacks and unintended consequences. We live in a sterile world, and our guts weren’t built for a sterile world. They’re meant to house a diverse array of bacteria.

What Are the Consequences Of Living a Sterile Life?

Hippocrates, the father of medicine, said that “all diseases originate in the gut.” The most obvious example, digestive issues, are some of the most common in the post-industrial world. Constipation, diarrhea, bloating, and general digestive distress affect tens of millions. Food intolerances and allergies, which also have a link to gut health, are rising.

Even conditions that aren’t intuitively linked to gut health, like autism or hay fever or even heart disease, may actually have a connection with the state of our guts or digestion.

At least since Biblical times (and probably earlier), humans have identified a connection between the gut and our emotions. “I’ve got a gut feeling…” or “I feel it in my gut.” Though it’s usually portrayed as “merely metaphor,” this connection isn’t spurious and can feel quite real. Remember when you held hands with that pretty girl or handsome guy for the first time? You felt those butterflies in your gut. Or how you had to rush to the bathroom before giving that big talk in front of your college class? You felt the nervousness and anxiety in your gut.

Evidence is accumulating that our gut bacteria can manufacture and synthesize neurotransmitters like serotonin and GABA, and even sex hormones like testosterone. We’ve even identified a legitimate physiological pathway running from the gut to the brain and back again. Couple that with the fact that gut health seems to play a role in depression, anxiety, and other related conditions, and it starts looking like our lack of exposure to probiotic bacteria could be triggering (or at least exacerbating) the rise in mental health issues.

Supporting Our Guts In the Age of Sterility

The foundation of gut health has to be diet: 1) Eating fermented foods to provide probiotic bacteria and 2) eating plant and animal foods that provide prebiotic substrate to feed and nourish those bacteria. That’s been the way of humans for tens of thousands of years—from ingesting soil-based and animal-based bacteria on the food we ate as foragers to directly producing and consuming fermented food—and it should remain the primary mode of probiotic procurement.

But there’s also a place for probiotic supplementation. Food alone probably can’t atone for the sterile existence we’ve built for ourselves. Food alone can’t counteract the several years of breastfeeding you didn’t get, the dirt you didn’t play with, the antelope colons you didn’t handle with bare hands, the untreated water you didn’t drink. You may get it now, but what about ten years ago? What about when you were a kid?

Evolutionarily novel circumstances often require evolutionarily novel responses to restore balance.

And probiotics aren’t even that “novel.” We’re clearly designed to consume probiotics in the food we eat, and probiotic supplements utilize the same ingestion pathway, especially if you consume them with food. The dosages may sound high. Primal Probiotics, the one I make (and take), contains 5 billion colony forming units (cfu, a measure of bacteria that are able to survive digestion and establish colonies in the gut) of good bacteria per dose—but that’s right in line with (or even well under) the dose of probiotics found in common fermented foods.

A single milliliter of kefir can have up to 10 billion cfu.

A cup of yogurt can contain up to 500 billion cfu.

A tablespoon of sauerkraut juice can contain 1.5 trillion cfu. Kimchi is probably quite similar.

A single gram of soil can contain almost 10 trillion cfu. A gram of soil is easy to consume if you’re eating foods (and drink water) directly from the earth.

Now, Primal Probiotics isn’t the only option. It may not even be the best option if you have specific conditions that other strains are particularly adept at addressing. (I’ll cover this in a future post.) But the way I designed Primal Probiotics was to be a good general, all-purpose probiotic with particular applications for Primal, keto, and other ancestrally-minded people living their modern lives.

For instance, one of my favorite strains I’ve included is Bacillus subtilis, the very same bacterial strain that’s found in natto, the traditional Japanese fermented soybean. B. subtilis addresses many of the issues we face in the modern world. It helps break down phytase in the gut and turn it into inositol, an important nutrient for brain and mood and stress. It helps convert vitamin K1 (from plants) into vitamin K2 (the more potent animal form of the vitamin). It can even hydrolyze wheat and dairy proteins to make them less allergenic.

There’s also Bacillus clausii, an integral modulator of the innate immune system (PDF)—the part of the immune system that fights off pathogens, toxins, and other invading offenders. Innate immunity is ancient immunity; it’s the same system employed by lower organisms like animals, plants, fungi, and bacteria. It’s the foundation of what we know as the immune response. What’s funny is that B. clausii has such a powerful effect on our innate immunity that one could argue B. clausii is an innate aspect of our gut community.

I’ve also included a small amount of prebiotic substrates in the latest iteration. I use raw potato starch (for resistant starch) and a blend of fructooligosaccharides and galactooligosaccharides. The prebiotic doses are low enough that they shouldn’t exacerbate any gut problems or FODMAPs intolerances and high enough to provide enough food for the probiotics to flourish.

Again, you don’t have to take Primal Probiotics. It’s my opinion that they provide the perfect combination of strains for most people’s needs, especially when combined with regular intakes of fermented veggies like sauerkraut and fermented dairy like yogurt, cheese, and kefir, but the actual strains themselves aren’t proprietary. You can find them elsewhere if you want to get individual probiotics. Hell, you may not even need a probiotic supplement. Depending on your personal health background, the level of sterility in your life history and current life (if you grew up on a farm drinking raw milk, for example), and the amount of fermented foods you currently consume, you may not need supplemental assistance.

But it’s sure nice to have around.

Anyway, that’s it for today.

How do you get your probiotics? Do you find them necessary for optimum health? What kind of benefits have you experienced from taking probiotics, either via food or supplementation?

Thanks for reading, everyone. Take care.

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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26 thoughts on “Life In the Sanitized Bubble (Or Why Probiotics Are So Important)”

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  1. I don’t like most of the fermented foods you listed. I do like heavy cream in my coffee and cheese. I drink two glasses of wine every day. Is this even close to enough? Would it be enough if I took your supplement? Or, should I hold my nose a gag down those fermented foods?

  2. I’ve had gut problems (gas, stomach pain, bloating) my whole life. The condition improved somewhat after adopting a primal lifestyle over 7 years ago, but probiotics (both via fermented foods and Primal Probiotics) never helped at all. However, my gut problems completely resolved 7 months ago when I went carnivore and took all the fiber out of my diet.

      1. Me too! I’m hearing so much about it’s benefits and people feeling great on. Would love an updated post on it and it’s variants if you have time Mark. Especially on it’s effect on gut health and why it might help so much and still produce good gut bacteria despite the lack of fermentable matter entering the gut.

        1. I second this. I’m leaning more and more toward trying it, if only I can find a way to afford to eat enough each day in the process.

      2. Hi, same here, my gut problems almost disappear if I stay away from fibre and starch but then my bowel movements stop. I thought eating plenty of fruit and veg would be enough but it isn’t. How can you keep a normal transit without eating any fibre? I wish I could!

        1. Most carnivores don’t appear to have a problem with transit (according to the Facebook groups), but I definitely do! I’ve taken 400 mg magnesium citrate in pill form but it doesn’t seem to help. However, getting magnesium via epsom salt baths has worked really well for me. Use 1 cup per bath and stay in for 20 minutes.

  3. Mark: For those with severe gut imbalances (candida) and who can’t take probiotics in supplements, what food source do you recommend for probiotics? Starting slow with sauerkraut or the juice of sauerkraut? Thanks!

  4. Most probiotics strains are histamine producing. You can google to find low vs. high histamine producing strains. But I find nearly all of them, as well as sauerkraut which I enjoy, cause runny nose, sneezing, etc. within an hour or less of taking them. So if my body reacts in this way, and it’s not uncommon (!), should I listen to my body and avoid them? I do a little better with a few single strain varieties but still react.

    1. Hi Laurie, please listen to your body. Avoid foods and supplements that make you react. You are’t able to clear excess histamine and/or your balance of gut bacteria are producing too much histamine. From what I know, there isn’t an easy way to tell which one it is, so it is best not to overfill your histamine bucket. We have all inherited a different hand genetically and then have lived in different environments and eaten different foods, so what is good for one person, may not be quite right for someone else.

  5. I find I react much better to my homemade ferments than I do to store bought ones.

    I make and consume every day – milk and water kefir, kombucha, and some type of fermented vegetable – usually kimchi.

    I honestly didn’t find that the store bought versions did much for me – now that I make my own, my gut health has improved greatly. No more bloating and very little gas. And I can eat almost anything without issue.

  6. You forgot to list the effects of RoundUp/glyphosate, which is an antibiotic. Saw a map the other day, the entire Mississippi watershed is sprayed with the stuff – and what isn’t sprayed gets rained on. We can’t avoid it.

  7. As usual, Sweden seems to be ahead of us in this area. Initial findings from a child wellness pilot program in Stockholm which includes monthly biotic seeding of park playgrounds with pelletized carcass and locally harvested ordure have been encouraging.


  8. Having good results with making Dr. Davis’ Wheat Belly ‘yogurt’ using this Luvele machine (has specific temperature controls that are needed) and Biogaia Gastrus. It contains patented Lactobacillus reuteri ATCC PTA 6475 strain and Lactobacillus reuteri DSM 17938. These strains have been researched for a very long time and offer great health benefit.

    Also used Biogaia’s Osfortis to make ‘yogurt’ and it turned out fantastic !

    Both found on Amazon.

  9. These have been true in Europe since about the Renaissance:

    We wash all our plates and eating utensils with ultra-hot water and powerful soaps.
    We wear shoes.
    We don’t touch (or see) dirt for days, weeks at a time. (women)
    We stay indoors most of the day.
    We pasteurize our dairy. We render shelf-stable (and thus inert) our sauerkraut and pickles. (boil or canned)
    We sterilize our water. (boil)

    Even in the 1970s, my mom was getting milk from local cows and bringing it to a near-simmer before putting it in the tiny refrigerator. She taught me how, because she couldn’t predict what life would be like later. I object strongly to ultra-pasteurization and even more strongly to homogenization. I think it makes milk taste like crap.

    The pickles thing, my granny was one of those who had the cellar with home canned goods, they may have been fermented, but for generations, they’d been putting up canned foood.

    My family’s cooking habits ensured that fermented things were not eaten raw, ever.

    I’m wondering if this is some sort of new theory we have that we should be more dirty. When people go to a country where sanitation is lax, they’re told to avoid food stands and not drink the water. When they ignore that advice, they often get sick. Some of them get sick for years (Whitney Dafoe for instance, communicates only by text message now).

    To say nothing of fungal irritations (ref: early articles by Bulletproof Executive) which can disable a person and make them question their own sanity.

    I think there is wisdom in sanitation that limits our exposure to pathogens. But I agree that using chemicals to enhance it is very likely to be counterproductive.

    One place where we have no choice but to use chemicals is water treatment plants. We’re recycling water, which is bizarre, but necessary. And in doing so we do a series of unnatural things to it.

    I hope this isn’t a stand against sanitation. Because slowing the entry of germs gives our body a chance to deal with it safely. I hope this is a stand against the increasingly desperate attempts to “kill 99.99%” of pathogens and every other bacteria, virus or fungus.

    I strongly object to claiming that probiotics make wheat or other allergens “less allergenic” because that’s not the real world experience of many allergy sufferers. That’s a myth that the allergy and celiac communities fight every day on social media. In fact, the growth media of probiotics is very often made with barley or other allergenic substances. Until I knew that, I didn’t understand why many probiotics felt like they were triggering my Celiac.

    This is a list of growth media used in industrial probiotic processing by just one company:

    Homemade fermented foods are something I trust to eat now, but store bought… not so much. There’s an art to getting the right germs into a fermented food without buying prepared (therefore risky) starters. The leaves of cabbage and the outer shell of whole grains carry just the right ingredients. Grapes are also a classic starter.

  10. There is yeast extract in many commercial growth media of probiotics. YE is usually a byproduct of barley fermentation from beer making (though not always). In the US, if it comes from wheat, it must be labeled yeast extract (wheat). But that’s only if the ye has to be labeled. Any “standard recipe” does not need to have all its ingredients labeled in a mixed product. This is how you get allergenic items secretly in everything. It’s not intentional, so much as it’s sloppy labeling. As a person with Celiac, it can really hurt me though.

  11. So, couldn’t I just eat the gram of soil mentioned in the article? It certainly is more cost effective.

  12. One of the best things I did a few years ago was get rid of anti bacterial soaps. I use a simple soap (Dr Broners) for most everything and I no longer have stinky towels, stinky sponges etc. The bacteria that survives apparently take care of the bad guys that make them stink.
    I may try your product Mark, it sounds good.
    I am beginning to think that most of my gut issues are from plants since I don’t typically have a problem when I just eat meats, eggs, fish. However, I do miss eating salads, fruits and veggies so I will go ahead and suffer with the resulting bloating and etc that go with eating them now and then…… but not every day!

  13. Wow, thank you for the tidbit about how many CFUs are in sauerkraut juice. I thought the supplements had way more than fermented foods but now I’ll just keep drinking my sauerkraut juice. 🙂

  14. Good “food” for thought! I’ve heard of diatomaceous earth…would this help with supplementing the dirt that we miss out on ingesting nowadays? Also, how come some probiotics seem to need refrigeration and other don’t? Does it benefit to consume a resistant starch at the same time as taking a probiotic?

  15. Love my fermented foods (especially kimchi) and probiotics. I live in Prague, Czech Republic – any chance you’ll be setting up your European distribution anytime soon? I’d love to get my hands on Primal Probiotics!

  16. My husband and I were discussing whether probiotics should be taken daily. As a microbiologist I am a staunch believer that probiotics and gut health are of enormous value to keeping our bodies healthy. I am curious though, your article states that you have included Bacillus subtilis and clausii in your primal probiotics however they are not listed as such. Could you explain?
    Thanks, Holly