What’s Up With Your Gut? – Beneficial Bacteria and Good Digestive Health

Everyone knows (well, not everyone, but anyone who’s probably reading this) how crucial the early days of an infant’s life are for establishing good habits and healthy patterns for the rest of its life. What the mother eats while pregnant, what the child eats, delivery methods, breastfeeding duration, heck, whether you read to your children or plop them down in front of the TV – everything helps lay the groundwork for the rest of their lives. Exposure to bacteria is another growing concern for parents. Too little bacteria, and we risk allergies and significantly compromised immune systems later on. Too much isn’t as much of an issue, though we should avoid obviously harmful bacteria. It’s my general sense that most kids these days get far too little bacteria in their lives. They’re swaddled in protective clothing, forbidden from touching (or, perish the thought, licking) things, and doused in antibacterial liquid every other hour. How many kids play in the dirt nowadays? Build forts? Turn over stones in search of bugs? Roughhouse with friends? Far too few, I’d imagine.

While beneficial bacteria reside throughout our bodies, gut bacteria may be the most important of all. A substantial part of our immune system depends on these healthy flora (which will be the subject of a future post). People try to go about obtaining beneficial gut bacteria in ridiculous, counterproductive ways, but at least there’s a sizable public awareness of the subject. Most reasonably health conscious folks these days at least recognize the word “probiotic,” while many researchers are beginning to understand that the bacteria present in breast milk (Bifidobacterium) offers considerable benefits to an infant’s intestinal microbiota. Low levels of Bifidobacterium have also been linked to higher rates of eczema in human children, while giving chubby rats a Bifidobacterium supplement slimmed them down and improved their lipids. Breastfeeding has also been linked to lower rates of asthma in children – is Bifidobacterium involved here, too? There’s a good chance; the author of this study co-authored one last year that found “children who received antibiotics in the first year of life were at higher risk of developing asthma later on.” Obviously, antibiotics can kill both harmful and beneficial bacteria.

Gut flora is responsible for breaking down carbohydrates into short chain fatty acids. If you consider our gut flora to be foreigners – permanent alien residents, put another way – then you might say that humans cannot fully utilize starches without outside help. Technically, those gut organisms are foreign born, but a human without gut microbes is like America without its rich and storied history of immigration; immigrants made America and gut microbes make us whole. Indeed, we’re wholly dependent on our gut flora. You might even say we’re more microbe than man (gut flora outnumber the cells of our bodies by 10 to 1).

Until we’re born, the fetal gut is sterile. It’s just sitting there, accepting pre-digested nutrition from the mother, taking up space and generally living the slacker’s dream. But it works. The fetus doesn’t need a teeming, active gut, because all the work is done by mom’s gut flora. They’re breaking down the polysaccharides and the sugars, converting it into usable fuel, and diverting a portion of it all to the child. In a way, then, the kid is dependent on gut flora, just as much as you or I are. Once he (or she) is out of the womb, the child needs his own intestinal team. He’ll be eating, which requires digestion, and good digestion (especially of carbohydrate) just doesn’t happen without gut flora. He needs gut flora, and he needs it relatively quickly. That’s where the birthing process comes in.

Traditionally, birth allows the passage of microbes from mother to the sterile infant gut, a relatively quick process. Gut colonization isn’t exactly a “feature” of the birthing process, however, and it’s not like there’s a specific pathway designed for the flora to travel from mother to child. No, gut colonization arises organically. It’s common sense, really, if you consider what child birth actually is: a somewhat chaotic, unsanitary event, where fluids are being exchanged, stuff is sloshing around and mixing together, with this vulnerable baby in the midst of it. You’ve got a helpless infant sporting a fecund, totally accessible gastrointestinal tract and a perpetually open mouth. He’s just kind of lying there, maybe crying a bit, but he’s incredibly open to suggestion. To gut flora, this is prime real estate, ripe for the taking. By the time the cord is snipped and the infant’s butt’s got a handprint on it, the baby’s upper gastrointestinal tract has been partially populated with bacterial strains derived from the mother’s feces and the surrounding environment (the air, others in the room, etc). Breastfeeding provides another ongoing source of bacteria. It takes about a month for a newborn to establish a solid population of gut flora, and another year for it to resemble an adult’s gut contents. (Any wonder why C-section, bottle-fed babies might get off to a slow start?)

Raising kids isn’t just about bringing new organisms into the world. It’s also important to prepare them for what lies ahead, and the only way to ensure adequate preparation is with exposure and personal experience. Shortchanging kids now, whether by maintaining the ultra-sterile environment (Purel everywhere, no physical skin-to-ground/dirt/skin contact, zero exposure to the outside world, lots of antibiotics, etc) at all costs or feeding them a purely refined food diet, sets them up for poor health in the future. Getting enough gut flora is one huge step in the right direction, but there’s a bit more nuance, as researchers are learning. Getting a wide enough variety of gut flora is just as, if not more important in the path to good digestive health – and that goes for kids, teens, and adults, as well as infants.

Accelerated Evolution

Bacteroides plebeius is a common microbe that lives in the human gut, issuing various digestive enzymes to deal with various types of food. It’s a pretty basic example of gut flora, but researchers noticed something very strange while studying a marine species of Bacteroidetes. Zobellia galactanivorans, which lives on a type of red seaweed, contains a specialized enzyme designed for the cleaving of porphyran, a polysaccharide found in red seaweed. Simply put, this specific enzyme was meant to digest seaweed. The researchers searched the gene-sequence databases and found that the same enzyme was also present in human-borne B. plebeius. How did the digestive enzymes of an obscure marine microbe get incorporated into human gut flora? They looked a little harder and found that it was only present in Japanese B. plebeius, not North American. They had their answer.

When humans began arriving in Japan, around 40,000 years ago, seaweed became a staple. And, while most seaweed sold in stores is roasted (and therefore sterile), Paleolithic seaweed eating conditions were considerably less “sanitary.” Folks were eating lots of raw seaweed, teeming with bacteria, and those bacteria were communicating with the already present gut flora. We already know that bacteria enjoy accelerated evolution via gene transfer on a regular basis, but this was the first research to confirm that gut microbes learn from other microbes. They aren’t static. Our gut flora actually receives genetic information from foreign microbes passing through, borne by the food we eat, and they can alter their own genetic code to incorporate the new material.

That’s exactly what happened. Ancient human guts were exposed to new strains of bacteria with new digestive enzymes, and information was exchanged. Genetic code was transferred. And it happened really quickly; according to lead researcher Jan-Hendrik Hehemann, “a bacterium that can’t digest nori one day, can the next.” If those early Japanese had been eating grocery store nori, roasted and months-old, would they have been able to break down the prophyran? No. The seaweed had to be fresh, it had to be raw, and bacteria had to present and alive to survive the trip into the gut. Today’s sterile, refined fare is absent bacteria – good or bad. We irradiate, we pasteurize, we sterilize, and we roast everything that goes into our mouths. Is it any wonder we’ve got widespread health problems?

Clearly, humans evolved in a bacteria-rich environment. The food we ate, the ground upon which we slept, and even the water we drank sent a steady stream of microbial diversity into our bodies – and this went on for hundreds of thousands of years. It made for occasionally lethal infections, but it also made possible the digestion of a wide variety of foods, an ability that we continue to enjoy today. But that seems to be changing. Food is losing its bacterial kick, unless you go out of your way to incorporate microbes into your diet. In the past, as food became more “sterile” and we moved into cities and became successful with agriculture, fermented foods became staples. Nearly every traditional cuisine uses fermentation, in fact. Did they suspect something was missing with the increased refinement of the food supply? Maybe, but either way, they maintained a steady level of bacteria in their diets. We, for the most part, do not.

What Does This Mean?

This shows the probable arc of our evolutionary relationship with food. As we evolved and ate new foods, our gut flora evolved as well. It’s quite remarkable, really, and it shows just how fast evolution can occur. Humans don’t change that quickly, of course, but our gut microbes do, and we in turn change with our gut.

I think everyone of all ages, but kids especially, should eat a wide variety of foods. Avoiding refined foods isn’t enough. You’ve got to actively seek out new foods, “living” foods and raw foods. Don’t become a raw foodist, mind you. Just experiment. Try fermented foods, like kefir or sauerkraut. If most soil wasn’t filled with pesticides, heavy metals and other unknowns I’d probably even encourage you to eat some dirt. Since grubbing on dirt isn’t practical (or appetizing, for that matter) I also recommend supplementing with probiotics. If anything, we owe it to our next of kin to fill our bellies with tons of organisms.

What are your thoughts on gut health? Does it even cross your mind? Is this new to you? Or do you have a plan of attack to keep your gut happy? Fermented foods? Supplements? Share your thoughts in the comment board. Thanks, everyone, and Grok on!

AJCI Flickr Photo (CC)

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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110 thoughts on “What’s Up With Your Gut? – Beneficial Bacteria and Good Digestive Health”

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  1. Regarding the comment of “If anything, we owe it to our next of kin to fill our bellies with tones of organisms.”

    Do males have any influence on our offspring’s gut flora? Or is it really all about what is in the mother’s gut when the baby is born?

  2. Having been filled with antibiotics and steroids during my teen years for a number of ailments, I definitely wonder about gut health.

    In particular I worry about Candida overgrowth, given my medication history. I do have some of the symptoms of Candidiasis, but the symptoms are many and nonspecific.

    I make my own fermented cabbage in several varieties, and did make kefir with raw milk before deciding to give up dairy completely. I have never tried probiotic pills though.

    I would love to know more about Candida, as web searches turn up as much questionable info as factual evidence, and often it is hard to distinguish the two.

    1. My husband suffered from candida a few years ago and we had a heck of a time figuring out what it was. Only by chance did a friend recognize the symptoms I described and suggest that it could be Candida.

      After we found out what it probably was I did a ton of research and sorted through the information to find common threads to make a plan. Here’s what I came up with:

      1st, Eat only green veggies for 2 weeks – be sure to cut out ALL sugars, grains, yeast, anything fermented (even yogurt), cheese, mushrooms, fruit and to keep meat, eggs, nuts to a very minimum

      2nd, after your 2 week cleanse slowly add in more meats, nuts, eggs and acidophilus/bifidus and grapefruit seed extract for another 2 weeks. stil eating mostly vegetables.

      3rd, after that month you can start adding in yogurts and other good fermented foods to continue populating your gut with ‘good’ flora and resume normal eating being careful to monitor your reaction to sugars and yeast. You may have an ongoing problem that means you have to cut those things out altogether.

      by that point you should have successfully starved the bad flora and killed it off, thus noting a marked difference in your gut pain. it should even have dissapeared altogether.

      Hope this is helpful and good luck with the cleanse!

    2. Watch this video about gut health and gut-related problems! LISTEN to what she says.

      For the last two years I have had many different symtoms(akne, weakness, foggy brain and memory, digestinal problems, bad immunesystem..), which all have been mysterious and without answers. Until now, when I have seen this video, I clearly see how it is all connected – starting in the gut.

  3. We make our own sauerkraut and the grandparents regularly ferment foods for months at a time.. Yummy bacteria.

  4. Next up, the fabulous dirt diet! I kid, but this is all very interesting, in nature you never no beforehand what pillar you kick out will cause the whole thing to come crashing down. I’ve thought for awhile that our whole culture is a bit germ crazy.

    People often think of evolution as something that takes a long time, and it does with complex organisms, but the microbes can change overnight as the seaweed story illustrates.

    Also, usually no one ever really thinks of our bodies as an environment. Scientific American says we have more cells of other organisms inside our bodies than we have cells of us. Clearly this is not killing us, so you yhave to think that most of those things are beneficial or at least harmless.

    This is really a new frontier. I saw a documentary that said that any soil they examined had thousands of previously unknown microorganisms.

  5. Fascinating! I’m always grazing on seaweed when I go picking mussels, and I’m always grazing on cilantro, basil, etc. when they’re in my garden. It feels like a compulsion, and I don’t have compulsive urges around food as a rule. Maybe the instinctual drive to eat bacteria is what’s behind it?

  6. I have thought about this since I travel to mexico regularly and eat the local food when I am down there. I eat some yogurt a few times a week and have taken up drinking kombucha almost every day for both probiotics & alkalinity. It all seems good, but I really do not know, just having sucess on this experiment of one!

  7. Fermentation of foods is a human’s 1st stomach. Not making a case for eating grains, but it does break down phytic acids and assists in better digestion.

    Sauerkraut is FTW!

  8. Some of the questions raised by this post include:

    * Is it actually possible to substantially recreate the functional colon as it existed among our pre-agricultural ancestors without literally mimicking their entire life-cycle?

    * If not, are we then missing a vital piece of the Primal puzzle that limits in ways we don’t understand the very long term health we seek to achieve by eating just analogues of the food our ancestors ate?

    Answers, thankfully, always lead to more questions. 🙂

    On a note related to Mark’s musings about early infancy and laying ground work, I recently held out for my two month old daughter a piece of grilled steak just to taste and she went nuts for it. I don’t think I’m going to have any trouble convincing her that eating meat is “natural” for humans. 🙂

    1. at 2 months an infants stomach lining is entirely not capable of eating steak, even a taste does damage google “just one bottle”. The stomach lining closes closer to 10 months at which point the main food transitions from entirely breastmilk to including the same whole foods the parents eat.

      Infants being fed artificial breast milk are different of course as their stomach lining has already been severely compromised and thus the introduction of solids before 10 + months doesn’t do the same damage – because the damage to the gut has already been done.

      1. as soon as it can grasp and put things in its mouth, an infant starts doing so. your idea that it’s dangerous for an infant to taste things is ludicrous, when every observation of instinct and natural behavior tells us the opposite.

  9. Great post! My kids (4yrs/2yrs) seem to know this already, they put everything they possibly can in their mouth. So far they haven’t gotten sick, and part of me knows that in a ways it’s good for their gut.

  10. “How many kids play in the dirt nowadays? Build forts? Turn over stones in search of bugs? Roughhouse with friends?” Mine will thats for sure…At 14 months he has already eaten a significant amount of dirt. We regularly play outside and look at(and touch)all the bugs and rocks and stuff we can find. We do it because it’s just fun, but knowing that it’s healthy is a sweet bonus

  11. Just made some pickled beets, with homemade liquid whey. I’m addicted to the liquid whey 😉 One of those “makes you feel good foods”.

    I feel we’re only just scratching the surface on how important this subject is to our well being.


  12. Great article and I take probiotics for a few days at a time every few weeks. We eat a wide variety of foods and yogurt on a weekly basis to make sure our gut flora is good to go. Been throughout the world traveling and have only gotten sick once (Darn you Hungary!!!)

    1. Please post your recipe for ginger-berry fizz drink w/lots probiotics. Thanks

  13. I make and drink lacto-fermented berry or ginger soda. It has a little rapadura (unrefined sugar cane) left in it by the time it is ready but it certainly solves that taste for fizzininess and a little sweetness. It is full of probiotics.

    1. I would love a recipe for this! I have been seeing a nutritionist for a few months since a bout of pneumonia and sinus infections and surgery had me down all of last year. She is trying to get me to have more fermented stuff and it’s hard! I’m off dairy so yogurt is a no no for me too. She also wants me off of soda so this stuff sounds interesting! Maybe you could post a link for your recipe?

  14. Can we have more posts about food and stuff (sarcasm). We haven’t had a post on working out since the Brad Kearns post a month ago. Not counting the weekend links here and there. Just saying. It’s spring, good weather, for those of us who don’t live in Calf. And we’re itching to go outside and play, do new stuff. And you’re posting mostly about food? Really?

    1. Seriously. You need a permission from a website to outside and “play”?

  15. I have my own theory about being gluten sensitive.
    I wasn’t breast fed, I’m 48 now, and I was only 6 1/2 pounds when I was born. My mother started feeding me farina early to get my weight up. Maybe starting grains too early might have something to do with this problem.

    1. Yes, a lot of people believe this is true. The prevalence of giving grains to infants as their first food, when the stomach lining is too immature is widely thought to lead to gluten and other food sensitivities. I’ve also read that you can heal yourself from food allergies with a healing diet, however.

  16. I just scrub the majority of the grit off of the local organic produce that I get, but I leave it a little dirty. I figure that probably helps.

  17. Fabulous, Mark.

    I’ve been on this trail for a few weeks now from more of an experimental framework.

    What I’ve found and will be hitting on the blog is that often, especially for people with frequent heartburn or GERD, the gut flora problem is actually caused or exacerbated by low stomach acid levels, i.e., too high of a Ph, allowing bad bacteria to thrive & overgrow, squeezing out the good.

    So, it’s a vicious circle.

    I’ve been experimenting the last few weeks with taking HCL/Pepsin with my meals and the results have been pretty fantastic.

    1. You’re reading the Healthy Skeptic these days too! What a series he just concluded.

  18. …Oh, and what completes that circle is that some bad bacteria, such as h pylori, in-turn inhibit stomach acid production as they can’t thrive. Vicious circle.

  19. I’m an even bigger proponent of probiotics after recently killing what was likely a H. Pylori-related ulcer (I’ve had them before). I didn’t want to take antibiotics, and read a few things online implying probiotics worked very well in combination with antibiotics, so I decided to try them solo. I took supplements (about 8mil organisms/day) and downed kefir for several days and all my symptoms disappeared within a week, and haven’t returned even though I stopped the supplements. Now I take one–4mil organisms– every few days. So for mild pepticl ulcer or acid reflux symptoms I highly recommend trying this before resorting to drugs.

    I’m trying to incorporate more fermented foods into my diet. I’m a huge kefier fan, and the fruity “Synergy” brand kombucha drinks are my answer to yummy beverage cravings.

  20. There is nothing wrong with eating RAW meat as long as it’s from a grass-fed animal. And it also has to be slaughtered at it’s own place not down the assembly line of industrial meat of course. So do your research before ordering.

    I can’t digest denatured proteins. Pasteurized Milk turns putrid, meat turns into a foul smelling rock that takes 3 weeks to make it through my gut and then comes out really ‘angry’!

    Don’t eat dirt, parasites lurk in it.
    One reason why most wild pigs (e.g. european boar) have tapeworms. Anybody that was born and raised in the country side of europe knows that.

    1. bacteria ARE parasites. parasites, both single celled and larger, are part of the natural world, not only our digestion, but also our immune systems, work better with a moderate load of them than without.

  21. Not sure if this is an immune system response….or what. Recently broke out in what is called Pityriasa Rosea. Has been documented/studied for over 2 centuries. They don’t have any idea what causes it; fungus, bacteria, viral or autoimmune. It is very benign, some have a little itching. No scarring, no illness, no lingering effects except that it takes 6 – 12 weeks for it to go away. You will never get it again, so obviously the immune system kicks in. In the mean time, as the warmer weather returns I will be covered in clothing until these red blotches finally disappear.

    I guess what I am asking is if anyone has had any experience with this and is there anything I can do to shorten the time and if there are any theories out there about the cause. Because otherwise I am extremely healthy (makes people who know me LOL) and I would love to know what I did to get it.

    BTW I do work out in the garden/dirt and they say the prevalent time is spring for breakout. Also, the prevalent age group is 18-35, and here I am 60+ (maybe with the LC/HF lifestyle i have lived for almost 20 years fooled it into thinking I was younger than I am).

    Thanks for any info I can get.

    1. Karla
      I experienced the same symptoms, and after much research and many trips to the doc, I figured it out myself. In my case it was an auto immune response to gluten . I went GF and Df and it cleared up within days! Can’t tell you how much better I feel 🙂

    2. It’s viral. Zero biggie and was smart to choose such a healthy host.

  22. thought provoking post. i eat sauerkrat and strained goat yogurt but wonder if probiotics are wroth their weight in gold. i priced them recently at the health food store… $129 for a tiny bottle of capsules….seems ridicuously expensive without a lot of science to back it up…

    still curious of how much of a role stomach acid levels play with gut flora as well. is there any way to tell if ones stomach acid or gut flora needs assistance?

    1. Which probiotic was that? the best one on the market is Dr. Ohhira’s but 129 pills I don’t think it comes in. After that distant seconds are Garden of Life’s ‘Primal Defense’, Jarrow’s and than RPN’s ‘Gut Health’ from what I’ve read and used, but most of those are below the 50$-60$ price point.

    2. Yep, your digestion will suck!

      I had to drop in raw ACV and enzymes, + dialed back my fruit consumption last week to push out some stomach bug that moved in after I picked up a fast moving flu.

      Got out of the habit of making and consuming as much fermented stuff as I normally do for a while, so I’ve kept in the ACV & added back Kombucha too this week.

    3. Yes! I agree it is ridiculous when you can make your own fermented veggies for pocket change and get plenty of healthy probiotics.

  23. Water and Milk Kefir do a great job of populating the gut with beneficial bacteria and the milk kefir makes great smoothies!

  24. What about organic whole-fat yogurt? Aren’t there probiotics in that?

  25. The exponential spread of Clostridium Difficile (bad GI bacteria) suggests we are failing in this category nutritionally worldwide, as if we needed another reminder.

  26. Aside from the bacteria, allergens are also an issue for many people I know. I grew up in the middle of nowhere on a *gasp* corn farm in Nebraska. During the summer when it was particularly hot and humid (90%), the corn pollen would be a great, yellow haze on the horizon. Friends of mine, who grew up in major cities, had come to the farm to see what it was like and during the summer they were in complete agony!

    Of course, there are plenty of studies to show that farm-raised children have better immune systems and less allergies.

    I do have to agree overall with your statements, Mark, that children need exposure to good and bad bacteria. For city children, dogs and other house pets are great sources for all sorts of germs and bacteria.

  27. Don’t forget kim chi! It’s kinda like the Korean version of sauerkraut. The good stuff is really spicy, too, if you don’t like the flavor of kraut.

  28. there’s so much gut flora do for us.

    Both gutsense.org and coolinginflammation.blogspot.com talk about their use quite a lot if you want additional sources.

    Personally D3+ Probiotic have almost completely gotten rid of my GERD/IBS.

    Which is huge considering from middle school through college my winter usually went like this: Stop seeing daylight > get strep throat > get put on antibiotics > have horrible GERD/IBS till summer.

  29. Mark, can you please explain this: “Gut flora is responsible for breaking down carbohydrates into short chain fatty acids”


  30. I’ve never really thought about this but it makes sense. I’ve never been one of those people who has to have everything spotlessly clean and I am not a clean freak when it comes to myself either, obviously I wash my hands, shower and all the rest of it, but I don’t overdo it like many people do. I’ve got a better immune system than most people, only getting ill maybe once or twice a year, and that’s before I went Primal, so maybe I’m doing something right?

  31. Hey Grok/Mark… QQ I’m hurting on cash so at the moment its eat whatever the live in girlfriend cooks (trying to pick out the crap, but PB / pure paleo is touch on funds) anyhow, normally i do eat pure 99%. I do have the occasional ice cream after a long swim or hike during the summer, but my staple each day has been home made yogurt.

    what are your thoughts on this in the PB ‘BIG PICTURE’. As a dairy normally its well your an adult.. did adults breast feed for anything other than pleasure… but for the pre/pro biotic cultures therein would yogurt be a decent addition to our “modern acceptibles” (ie fish oil supplements, cooking techniques etc.). anyones advice would be appreciated!!!

  32. Currently i only eat sauerkraut once a year. On New Years day.

    Guess i need to get it in the rotation more. Does grocery store kraut have healthy bacterial, or do i need to ferment my own?

    1. Most kraut sold in stores has been pasteurized precisely to KILL those beneficial bacteria, along with any harmful ones that might cause legal troubles for the food companies. It’s similar to milk, you need to source your own to make sure it isn’t heated into oblivion which destroys many beneficial nutrients.

      You would be surprised how easy (and enjoyable) it is to make your own. I found a large 2-gallon container that I use to ferment, though it is only half full of goodies. I cover it all with a plate, keep it covered with the liquid that quickly forms after you salt and mash up the veggies, and cover it with a towel to keep out hungry bugs. Then I put it in canning jars in the fridge once it tastes good to me. Give it a try!

  33. yep, i make homemade yogurt from fresh milk, eat 50% of my animal foods raw and make saurkraut fresh with whey added to really get the bacteria working. no man-made probiotics necessary – just whole food and traditional recipes !

  34. probiotics are awesome, when i don’t have much fermented food to eat i have a probiotic pill, otherwise i have a little bit of really sour kefir now and then, and raw meat. Now that it’s spring i have all the fruit and veg coming up to look forward to fermenting (especially dill pickles – cannot wait till cucumbers are in season!!)

    Also, thought i’d mention a lecture i had a few weeks ago (im a first year med student) about allergies, and the lecturer had a few slides about how children who grow up on farms and drink raw milk have much less asthma and other allergies than city kids, (he said raw milk was a huge contributing factor in addition to the general farm lifestyle) and how scientists compared the gut flora of kids living in rural areas to city kids in eastern europe (the rural kids had much less allergy) and found the rural kids had much more bacteria in their guts





  36. I’ve got some kraut brewing in the pantry right now..and I make all the yogurt my family consumes.

  37. I need to add more fermented foods to my diet. I do not take a probiotic supplement and I do not eat any fermented foods that I know of.

    This article urges me to continue to learn more about gut bacteria as some other articles I have read recently has brought it to my attention.

  38. Lets make it really easy, head for a Korean restaurant. They’re fewer in number but tend to be more authentic then other ethnic fare. Most meals come w/ kimchi and a load of fermented fare. First timers should head for the Bi Bim Bop.

  39. Gut health is VERY VERY VERY important to me. I had a colectomy ONE YEAR (exactly) ago and my digestion really hasn’t been all that great since (or even before for that matter) but in order to keep my gut as “smooth” as possible I take digestive enzymes with probiotics and eat lots of healthy fiber!

    1. Second Emily’s question — I threw out Kombucha above but no one has discussed. I have used it with success but my experience is entirely anecdotal. We tried making it for a while but the stuff from the store tastes way better and I did not take the time to sort out the tea / flavoring aspect. I split a bottle with my wife daily, we both think it essential to gut health + PH.

  40. Perhaps we shouldn’t discourage our kids from picking their noses! Seems like an instinctive reaction they inherit?

    Perhaps adults might benefit also?


  41. 3 weeks into changing my diet so that my carbohydrate consumption dropped from maybe an average 300 + grams per day to below 80, I had a massive day long episode of diarrhea — the experince of which was so different from any I’d had in the past from infectious causes.

    I suspect that that, and occasional minor brief re-occurrences, may have a lot to do with massive changes in, maybe even death of, intestinal flora.

  42. The sad thing is that most people do whatever they can to do the exact opposite. Slather themselves in anti-microbial concoctions, wipe down FOOD PREP areas with chemicals that kill bugs. Imagine what those cheicals do to us!!!

    My 6 year old (who loves the dirt and all things outside) was asked, along with the rest of her class to “bring 2 large bottles of hand sanitizer to class”. I asked about it and the teacher mentioned that it prevents the spread of germs. The staff were worried about getting sick. Keep limiting your exposure to these bugs, and catching the flu will be the least of your worries.

  43. Hi there
    Have you heard of the drink Kombucha? I drink one every day. It claims to boost metabolism, digestion, appetite control,weight control, cell integrity, anti-aging……

  44. Lying Just to finally cover Kombucha, YES, it is full of probotics. Make it yourself if you don’t want to break the budget. It’s very easy to make:)
    Also, if anyone is really interested in the health of their gut, look up a guy named Konstantin Monastyrsky. He’s a wealth of knowledge on everything that has to do with guts and has been specializing and treating people with gut problems for many years.
    He has a few book out there and if you click on the “Store” link on his page, there is a product called GI Recover which contains a boat load of natural probiotics.
    I’m reading one of his books right now, Functional Diet, and it is very much in line with Primal Blueprint with one exception that the author doesn’t advocate a lot of vegetable consumption. Interesting stuff!

      1. We did it for a while. My wife got some of the culture and put it in a bin of tea and put it on the warming plate for a spell…don’t know the specifics but the folks we got the culture from loved what they made. We did not play around with juices and flavorings enough to get something that was really good, plus I always felt we were at risk of poisoning ourselves due to ineptness…so we buy it now but its $$$.

  45. That way you keep him on your board in case things don’t work out with Westerman/Hegarty, while retaining an open spot if you do hit a home run on the OOS guys. If you’ve already filled his spot and he does get back into shape and demonstrates himself to be Texas caliber, tell him your very sorry but there’s a numbers issue and offer him a greyshirt. He should have a number of options by that point.

  46. I just got back from a trip to Mexico, SICK AS HELL for eating street food on the last night there. My naturopathic doc has me on probiotics until I finish the bottle. I have a naturally sensitive digestive track that’s been ravaged by IBS most of my life. I LOVE kefir, but I figure I should probably eat more fermented foods.

    I was a pre-mature baby too (by three months!) AND a C-section birth too. No wonder I was always sick as a kid! Oh, and the onslaught on antibiotics I took as a child didn’t help either.

    Thanks for the article, Mark! As always 😀

  47. Awesome post, one issue with the rat study though. The rats were given bacteria that were genetically modified to produce a particular hormone (oxyntomodulin) that aids in weight control – rats given control bacteria that didn’t produce the hormone didn’t get the weight loss benefits. However, they did have significantly reduced plasma triglycerides when compared to rats that didn’t get any bacteria.

  48. As long as the mother and baby are both healthy, here is yet another reason to have a home birth. Think of the bad bugs lingering in a hospital and how all of those nice nurses colonize your baby’s gut with the germs they pass around. No thanks!

    Someone asked about the father’s bacteria. Yes good flora is important for him too. He passes fluids onto the mother and baby (kissing, sexual contact with mother) and it’s important for him to be healthy as well.

  49. We let our landlord know about our plans to relocate and she was oh so supportive. I sure hate to leave her. Can you believe that she gave us some rental guides and gave us the low down on bad properties? We trust her because we’ve read some bad reviews of some of the properties that she had mentioned.

  50. We had our first look at the fragarack at the BayMAC event and although there is nothing revolutionary about a magnetic frag mount, the fragarack product is a clean and modern take on a really simple concept and we really like how this frag rack aims to be as unobtrusive as possible.

  51. Exercise is a powerful immune booster, not to mention a very important component of good overall health. Regular, moderate exercise has been shown to lower an individual’s likelihood of getting sick. It also boosts natural energy levels while relieving stress at the same time.

  52. A work out plan does not have to be strenuous it can be simple with numerous benefits. Aerobics and sports are the most common types of performed health and fitness exercises.But for good brain we can take some supplements to improve brain fitness.

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  54. Proteins are body building materials that facilitate in development and enlargement of our bones and muscles. Fats are also necessary as they store and liberate energy, when required.

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  56. Mark,
    As a Newbie I am curious if a cleansing diet would be beneficial; getting all the crap out of my body before embarking more seriously into this new(old)primal lifestyle?
    Thanks for all your words.

  57. The website lists its local phone numbers that can be used for chatting. You just need to choose the number available for your local area. The free singles chat is absolutely perfect for who want to make friends through phone line.

  58. Can we have more posts about food and stuff (sarcasm). We haven’t had a post on working out since the Brad Kearns post a month ago. Not counting the weekend links here and there. Just saying. It’s spring, good weather, for those of us who don’t live in Calf. And we’re itching to go outside and play, do new stuff. And you’re posting mostly about food? Really?

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  62. The intake of vitamins and minerals varies from person to person, but there are some groups who are more nutrient-lacking than others. New scientific studies are seeing that we even have a genetic code that tells what nutrients we need more of as individuals.

  63. Mark

    I am curious about how the gut flora looks like for someone like you on your diet and lifestyle.

    Do you have a gut flora test done with some specialist labs like Genova or Diagnos tech and share it with us.


  64. If all that’s true, my son should be immune to everything. When he was a toddler, he would chase the chickens until he caught one, then sit under a tree, in the dirt, with the chicken in his lap and pet it until he got tired of that chicken and then do the whole thing all over again. He used to come in the house more dirt than kid, but he was happy and never got sick.

  65. I took daily doses of the probiotics sold on this site and after a few days I got cramps and diarrhea. So I went off them. Then a few weeks later I got a second bottle (thinking I may have had a bad batch) and I tried again with the same result. Any thoughts?

  66. i wonder what sorts of problems, if any, the guys on the international space station for a year had…..not many bugs floating around up there.

  67. I follow the GAPS diet by dr natasha campbell-mcbride. Below is a great video by her explaining gut health

  68. a few questions– any guidance is appreciated: (1) there are some who claim that enzymes derived from plant-based foods are not used by the body to aid in digestion because stomach acids eventually destroy the plant-based enzymes. That the only enzymes we use are those that our bodies manufacture on their own. Can anyone shed any light on this? … (2) re gut bacteria- do the bacteria “produce” enzymes that the body can use? Or does the body’s enzymes use but bacteria somehow? It seems there’s a symbiotic relationship between our own enzymes and gut bacteria- is there any more info on that anywhere? …and last question (3)- does the good bacteria come from our food, and if so is there a list of the good bacteria/food sources that must be consumed on a regular basis for good health?

    1. I heard that, although eating probiotic foods, and taking probiotics can improve your health, it is a temporary and limited improvement. I read, somewhere, that it is our resident bacteria that make the most significant difference to our health, and consuming other bacteria does not repopulate resident bacteria in adults. The conclusion I got was that consuming plenty of pre-biotics, which feed and protect our resident bacteria, is more important that consuming pro-biotics. And the best sources of pre-bioics were Jicama, and Jerusalem Artichokes.
      I also read that there have been cases of very sick people, with weakened immune systems, getting sicker when consuming probiotics, because they became overly infested by them.

  69. Hi! I may be completely crazy but in the UK mothers are told to avoid any foods with living organisms (yoghurt, unpasteurized cheese, kefir etc) during pregnancy so that diseased can’t pass to the unborn and vulnerable baby. However, this must influence her gut flora negatively and thus the bacteria that the baby ingests at birth is of a poorer quality. Could this be a reason why many babies today are not enjoying the full benefits of a sound gut flora?

  70. BS. Bacteria are bad for the body. All of them. Some are worse than others, thats why probiotics work is they are good relative to bad bacteria.

    Here is why baceria are bad:

    1. they make us fat. We absorb 25% more calories with bacteria present. Any wonder why we are obese?

    2. they make us sick. Virus’ are designed to infiltrate bacteria. Virus’ use bacteria to gain a foothold in the body to infect human cells. https://blogs.discovermagazine.com/notrocketscience/2011/10/13/beneficial-gut-bacteria-can-become-virus-collaborators/#.UQfz7Si9Kc0

    I use diatomaceous earth to mechanically kill the bacteria in my intestines and I can’t remember the last time I’ve been sick.

    Sure probiotics may be good if you don’t know of a way to keep all bacteria out consistently without antibiotics, but now you know how: diatomaceous earth. Make sure to take some metamucil with it to prevent constipation and get FOOD GRADE diatomaceous earth.

  71. From our birth our bodies know exactly what to do to best defend and heal itself. Our body is such a finely tuned machine that we’d be better off feeding it good food and getting ready for how good we would feel with all our cylinders firing. Take care of your body so your body can take care of you.

  72. The same flora that is in the intenstines, also populateo the vagina. Through natural birth the baby ingests fluids that contain the much desired bacteria.
    The first day the baby only drinks tiny portions of colonstrom which further help the proliferation of the bacteria.
    Babies born through c-section do not have the chance to get in contact with the much needed bacteria.
    The same applies to babies that have not breastfed.

  73. I guess this article is several years old, but I just read it and it made me cry! My daughter is 6 years old and she has had chronic stomach and intestinal problems her entire life. When I was in labor, her heart rate dropped, so they did an emergency c-section. They had to knock me out because the epideral did nothing for me. By the time I woke up, my baby girl was already on a stealth dose of antibiotics to combat whatever it was that made her heart rate drop (they had NO idea what caused it to drop, but they apparently don’t need a reason to drug people). She was to spend the next 7 days in the NICU being fed intravenious antibiotics and living on formula. I did finally get to start breast-feeding, but maybe the damage to her gut had already been done? She already had 3 counts against her.

    Could this be one of the reasons she has problems now? I have tried so many things, with no help from her pediatrician. She’s gluten free. I did an elimination diet for dairy, too, and she doesn’t seem to have a problem with it, but maybe I should try again. I would love it if I could get her to be primal/paleo, but she’s far too picky an eater for that. I do make grain-free breads and other baked goods for her as often as possible, but she can’t have any kind of tree nut at school, which limits what I can pack for her that she’ll actually eat. She throws up a couple times a week and complains daily that her stomach hurts. I’ve done a food journal and there doesn’t seem to be any pattern to what makes her hurt.

    I haven’t really investigated fermented foods (which I will right now), but is there a way to get a healthy dose of probiotics into a kid who may need serious gut help? She can’t do pills.

      1. Thank you so much for the suggestion! I have never heard of GAPS, but I have started reading about it and it could be what we need to do.

        1. Cati, what i am going to say is the core of what is really important to the extent that i know. You have to study about these topics:

          She might have leaky gut and SIBO. Check it.

          About leaky gut: she might have to close the leakage and create or raise the villi.

          Leaky gut: there are several ways to close the holes. Main drivers: bone broth, l glutamine, quercetin and colostrum.

          The best thing to create new villi is saliva and colostrum (burst training also enhances growth factors that may help…). It is difficult to find this piece of information: Saliva might be reduced, for example, by lack of iodine in her body or something obstructing the duct.

          You can close the holes in her gut, if she has them, but to raise new villi it is necessary that her gut has access to specific elements that make the new villi growth. Just closing the holes may not be efficient enough. Villi are key to absorb nutrients. I strongly advise you to study about it. Example:

          “Finally, colostrum contains a number of important hormones as well as growth factors, so named because they stimulate the growth of cells in a variety of tissues. For example, epidermal growth factor (EGF) and insulin-like growth factors I and II (EGF-I & II) cause cells lining the gut to replicate. This results in increased size of the intestinal villi that are the site of nutrient absorption. Therefore they are important in development of the intestines and also in repairing them following certain types of neonatal diarrhea. A variety of hormones stimulate and regulate the growth of other tissues and organs.”

          In addition, she might have biofilm in her small intestine, so that you wont be able to change the gut flora easily. Biofilm protect the “bad bacteria”. (Colloidal silver, NAC, apple cider vinegar, digestive enzymes)

          Probiotic (read about reuteri and glutathione combined). And copied this excerpt from another forum and checked it:


          (read the article below to understand the logic)
          Bifidobacterium infantis
          Bifidobacterium longum
          Lactobacillus reuteri (raises histamine in the short term but elevates anti inflammatory cAMP levels)
          But also Lactobacillus plantarum (lowers/inhibits tyramine and putrescine)
          Lactobacillus rhamnosus and salivarius and sporogene
          Lactobacillus gasser
          (Ema added conflicting reports on this one. Study shows it actually produces tyramine which is also a biological amine that those on low histamine diets may want to avoid.)
          And then the ones that seem to degrade histamine and be beneficial are lots of bifidobacteria species, but particularly Bifidobacterium infantis and then Lactobacillus rhamnosus and salivarius and sporogenes and Lactobacillus gasser


          Saccharomyces-Boulardii: I found a number of studies on its effectiveness in treating gastroenteritis, which some researchers havelinked to high histamine/mast cell issues.


          Lactobacillus acidophilus, Lactobacillus Lactis, Lactococcus Lactis, and Lactobacillus plant arum which do not have any effect on biogenic amines like histamine and tyramine.

          BUT NOT…

          Lactobacillus casei (produces histamine and tyramine)
          Lactobacillus Bulgaricus (increases histamine alone)”

          BACK: Finally, one of the most, maybe the most important thing againt allergies and auto-immune diseases is Vitamin D in appropriate doses: higher than 60 ng/ml. Probably 10 minutes sun (at noon -12h) will help her. A viable solution is to buy a lamp that enhances the production of vitamin D. The most famous is SPERTI and use it for 5 minutes a day. Remember: she cannot wash the skin after a sun bath (the vitamin D takes a time to be absorbed through the skin), so that she should limit the soap to strictly necessary areas (armpit, hair, feet…).


          Those problems are likely to be interconnected. Vitamin D and immune system, Leaky gut, small or absent villi, bad gut flora (each strain has a different property for health function. Study it a lot.)

  74. I am looking for a natural to cure my h pylori. can you help me with supplements? Thanks!