16 Things That Affect Your Gut Bacteria


A couple months ago, we explored many of the ways our gut bacteria affect us, focusing on the lesser known effects like anti-nutrient nullification, vitamin manufacture, and neurotransmitter production. Today, we’re going to discuss all of the ways (that we know) we can affect our gut bacteria. It turns out that the food we eat, the amount of sun we get, whether we eat organic or not, the supplements we take, and even the kind of nuts or chocolate we decide to eat – just to name a few factors – can change the composition and function of our gut microbiota for the good or for the bad. We may still have a lot to learn about this gut stuff, but the bulk of the evidence says that we do have the power (and responsibility if you care to be healthy) to affect the health of our gut microbiota.

Here are 16 things to do, eat, avoid, and/or heed:

Fermentable fibers

I’ve discussed this variable to death, but it may be the single most important pro-gut biome dietary modification we can enact. Without fermentable fibers, our gut bacteria just aren’t getting the food they need to maintain the population – let alone grow it.

Fermented foods

From sauerkraut to pickles to kimchi to kefir to condiments to “high meat,” fermented foods have been a consistent part of the human diet for many thousands of years. And while it’s unlikely previous generations had detailed knowledge of the gut biome, today we know that fermented food plays an important role in shaping the health of our guts. Yogurt, one of my favorites, often changes the composition of the gut biome for the better. But even when it has no effect on the population or composition of a microbiome, fermented food can change the way the existing population works. In one study, for example, bacterial strains isolated from fermented milk didn’t colonize the gut but led to increased microbial expression of carbohydrate metabolizing enzymes. In another study, yogurt and probiotic supplementation allowed lactose-intolerant subjects to tolerate a greater amount of dietary lactose by changing their colonic bacteria.

Fermented foods aren’t a “one and done” deal. You have to maintain an ongoing relationship with them in order to enjoy the full benefits and sustain the colonization. It’s more accurate to consider them necessary foods we need to eat regularly rather than supplements or medicines.


Even though we usually think of the polyphenols found in blueberries, red wine, green tea, and other fruits and vegetables as plant pharmaceuticals that we absorb and utilize instantly, their bioavailability in humans is controversial. Emerging evidence suggests we derive many of the benefits through interaction between phenolic compounds and our gut bacteria, which consume the glycan bonds holding the polyphenols together and render them available for absorption. The glycans are prebiotics for the bacteria, and the liberated phenols are more bioavailable to us. Even red wine polyphenols may have prebiotic effects on the gut flora (though keep in mind that some of us have different reactions to it).

Dark chocolate

Dark chocolate falls under the “Polyphenols” and “Fermentable fiber” categories, so this section was probably unnecessary. But c’mon: it’s dark chocolate, a combination of gut-supportive polyphenols and prebiotic fiber so delicious that we should welcome any and all justifications for its consumption, however redundant they may be.


Pistachios are another special package of fiber and polyphenols with potent prebiotic power. Other nuts like almonds aren’t too shabby, but pistachios beat them soundly in a head-to-head matchup, producing a biome richer in butyrate-secreting bacteria. And since they usually come in shells, overconsumption is hard if you’re worried about self-control.

Resistant starch

Resistant starch, or RS, is a unique kind of starch that humans by and large cannot digest. It’s not a fermentable fiber, but it acts like it. Upon its consumption, RS travels mostly unperturbed through the digestive tract into the colon where the colonic bacteria – who can digest the stuff – feast on it, get frisky, and reproduce. Multiple studies indicate that RS consumption generally leads to an increase in beneficial colonic bacteria and a reduction in pathogenic colonic bacteria, including a boost to bifidobacteria and a decrease in firmicutes.

Animal “fiber”

Carnivorous animals like cheetahs treat otherwise indigestible animal parts like prebiotics, displaying evidence of healthier gut bacteria when eating whole rabbits than when eating beef muscle meat. As animals with a long (pre)history of consuming other animals, it’s a good bet that humans retain this ability as well. The gristly bits at the end of a drumstick, the snapping tendons that floss your teeth as you eat a turkey leg, the crunchy cartilage you have to scrape off the oxtails with your front teeth, the skin on a pork belly – these are examples of animal tissue with the potential to affect our gut bacteria.

Vitamin D status

Vitamin D helps regulate the immune system, as we know. Low vitamin D status (or low exposure to UV radiation) is consistently linked to increased autoimmune disease, allergies, infections, and other immune conditions. Meanwhile, our gut bacteria comprise a huge chunk of our immune system, modulating the allergenicity of food fragments, crowding out pathogens, and regulating the development and maintenance of our immune cells. Could one affect the other? Absolutely. A recent paper in rodents shows that vitamin D status regulates the microbiome, with a deficiency causing dysbiosis and inducing colitis.


In last week’s Dear Mark, I discussed a new study showing that professional rugby players participating in an intense training camp had a more diverse (and healthier) gut microbiome than age and BMI-matched controls, despite experiencing a ton of acute stress (all the exercise). While the rugby players also ate more gut-modulating foods like fruits, vegetables, and protein and snacked less than the control groups, and this may have improved their gut diversity, this study is the first to shows that lots of exercise is compatible with and even supportive of healthy gut flora. The flipside is that lots of exercise without adequate support (recovery, rest, good food, sleep) will probably be enough of a stressor to negatively impact gut flora. Don’t overtrain and don’t undertrain.

Food variety

Much of the gut bacteria we get comes riding on the food we eat or our gut bacteria learn how to break down certain foods from the bacteria riding on the food. One example of this is that in most Japanese people, some of their gut bacteria have picked up the genes for seaweed digestion from the bacteria found on seaweed. The seaweed bacteria “taught” the resident gut flora how to handle the food. This gene transfer doesn’t happen with a single seaweed meal. They need sustained exposure to the seaweed and its bacteria. A recent study in fish even supports this idea: fish eating the most diverse diet had the least diverse gut microbiome.

So variety is good, just not too much. You want enough variety that you expose yourself (and your flora) to colorful fruits and veggies, fermentable fibers, and healthy fats, but not so much that you never eat the same thing twice. Eating some staple foods on a regular basis will allow you to develop the gut flora equipped to break them down. Be consistent.


Of course antibiotics affect the gut flora. Their stated purpose is to (negatively) affect microbial life. Use them if it’s medically necessary, but be advised that most antibiotics are indiscriminate killers WW2-era carpet bombing entire cities of bacteria. They get the pathogens (unless they’re resistant, of course) and the good guys, reducing microbial diversity and shifting the balance of the microbiome to favor unwanted strains. These changes may be lasting without serious and sustained prebiotic and probiotic interventions. Unfortunately, with even doctors prescribing them to patients with conditions for which antibiotics don’t help, medical necessity is difficult for the layperson to parse.


Like with fermented foods, we should think of probiotic supplements as friends. Not those friends you always tell “we should totally hang out more!” when you run into them but never do. Real friends. The ones you have over for dinner every week. The ones you include in group texts that go for months without breaking. That’s how you should treat probiotics – like real friends whose company you genuinely enjoy and who come in capsules and require refrigeration.

Take probiotics with food or 30 minutes before meals, as our bodies are “meant” to consume probiotics with food (i.e. fermented food); they seem to survive the transit through our gut when taken this way (as opposed to after a meal).


“Skeptic” science writers and corporatist apologists are quick to point out that glyphosate, the active herbicide used in Roundup, is non-toxic to humans. Roundup kills weeds by disrupting the shikimate pathway (PDF), a pathway involved in the biosynthesis of several crucial amino acids. Human cells are relatively unaffected by the herbicide because our cells don’t use the shikimate pathway. There’s nothing to disrupt. All good?

Unfortunately, no. Bacteria also employ the shikimate pathway, and we’ve got an awful lot of them living inside our bodies and handling some very important tasks, including immune function, digestion, production of neurotransmitters, mood regulation, and many more. This means our gut bacteria may be susceptible to Roundup residue on the foods we eat (and the air we breathe, the water we drink, and so on). This isn’t a big issue for people eating Primal because the biggest offenders are genetically modified soybeans and corn (and all the related food products) – two foods you likely aren’t eating. That said, your exposure may be elevated if the food you eat eats a lot of Roundup-laden soy and corn (PDF), like CAFO livestock, dairy, and battery-farmed poultry. All the more reason to favor pastured animal products.


Or rather, cessation of smoking. Smokers who give up smoking experience weight gain and more microbial diversity. The media reports focused mostly on the weight gain, but I think the shift in gut bacteria – toward the mostly beneficial Actinobacteria away from the Proteobacteria (home to “a lot of your bad guys”) – is the most significant news.


It takes time to build your gut flora. Initial changes happen rapidly, but sustaining them requires giving your bugs time to adapt and dig in. If you try resistant starch, don’t give up after a day. Give it a few weeks. If you try probiotics or sauerkraut, take them consistently for an extended period of time before throwing in the towel and assuming they don’t work. If you’re expecting your monthly gym foray to positively affect your gut, think again.


I almost forgot. Get dirty. Don’t be a clean freak if you can help it. I’m not saying you shouldn’t wash your hands after wiping, handling raw chicken, or dumpster diving, but be a bit more relaxed when it comes to getting your hands dirty. Garden, and don’t freak out if you misplace your gloves. Eat a fresh carrot pulled straight from the ground. Enjoy a soil smoothie twice a week. Pet a dog. Expose yourself to the outside world, soil and grime and dust and dirt and all, on a regular basis. I’m kidding about one of those (never garden without gloves!). Bacteria are everywhere – you really can’t avoid it – and most of it isn’t out to kill you.

Don’t be overwhelmed by this information. Don’t feel like anything and everything you do could have a drastic effect on your gut bacteria. For all the warnings and studies and focus, our gut flora are resilient buggers that have evolved – and are still evolving – to respond and react to the environment. If something affects them negatively, they can bounce back. And even in the case of major changes wrought by antibiotics or months of stress or medical procedures, you can help them bounce back.

Information like this should empower you. When I learn how the fate of my gut flora (or muscle mass, or bone density, or eyesight) ultimately rests in my hands, I’m excited and eager to assume the mantle of responsibility. That’s total freedom and it’s the most important thing in this life. It’s all we’ve got.

Thanks for reading, everyone. How do you feel about this information? Empowered, overwhelmed? A bit of both?

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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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130 thoughts on “16 Things That Affect Your Gut Bacteria”

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  1. I opened up my compost tumbler this morning and it smelled so good I almost grabbed a handful for breakfast… Is that going to far?

    1. NIMO, I’ve spontaneously eaten dirt from a rotting log because it smelled really good and a whole bunch of muck that was basically just sand from beside a river. It may be worth noting that both times I had been drinking.
      Other times when I was less zonked I’ve eaten small amounts of soil, like a spoonful, to get some bacteria.
      I didn’t notice any ill effects from any of this dirt consumption other than a taste that was not terrible but not good and a texture that was a little unpleasant.
      Why not give it a try, sample a tiny amount, it probably won’t hurt.

    2. try this
      50g coconut oil
      10g dark chocolate
      both melted over (not in) hot water
      then add to
      100g yogurt
      25g chia seeds
      1/4 teaspoon cinnamon
      Stir and eat. Yummo!
      Better than dirt or compost.

      1. I am going to try this, but with a “flax meal gel” and a Homestyle Coconut Milk based Kefir….cos I don’t have any compost!! (yuk-yuk-yuk! lol pun intended)

    3. I’ve often thought the same thing because my dogs sure do love to chow down on it!

    4. I know exactly what you mean. I love the taste of fermented codliver oil but sugary sweets etc turn me off. Get it on your hands and under your finger nails.

    5. maybe you could cook up a feed of compost worms- next best thing

    1. +1 I love ’em! A friendly reminder to watch out for the salt, though. Many of the commercially packaged pistachios are LOADED with it.

  2. This article is right where I am on my Primal journey. Perfect timing for me here. One quick question: can you expound on pre vs pro -biotics and what your products offer in that area? Thanks as usual, Mark!

    1. Prebiotics are things your gut bacteria eat, but that you usually cannot digest yourself. Probiotics are bacteria that you eat. Everything I know about his products can be found in their descriptions.

  3. I must admit that I have no problem over-consuming pistachios, shelled or not!

    1. I don’t always buy pistachios in their shells but when I do….

  4. Good information. I’ve recently discovered my local Kroger’s sells Kombucha, so I’ve been going to town on it. I need to incorporate some more RS into my diet….along with dark chocolate and pistachios. 😉

  5. Garden gloves don’t fit my hands well-I have too-short fingers for them, and cutting off the fingers only unravels the finger stitching, and the rest of the finger(s) end up coming apart. I’ve always gardened barehanded, and see no reason to stop. Yes, I wash my hands and scrub my nails afterward.

  6. The thing with the rugby players immediately brings to mind dirt–rugby players spend a lot of time in the dirt. Since they were professional rugby players, they travel all over the world, and “sample” soil bacteria from many different locations. It would be interesting to compare the rugby team’s gut bacteria to similarly high-performing but less “dirty” athletes.

    1. They might test the gut of professional Taekwondo fighters…same reason except instead of eating dirt, you might get the occasional foot to the mouth in a fight.

      1. Haha…. My only complaint about taekwondo. Being up close and personal with other peoples’ bare feet.

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  7. A soil smoothie? No thanks.

    I wonder if those rugby players had better gut bacteria because they face-plant into the grass regularly, while the controls merely on their fire-retardant-infused couches all day.

    1. There’s two whole posts about RS.
      Green bananas, powdered potato starch (personally I think the bananas are probably the better option).

      1. I’ve tried green bananas. They go right through me. HARD on someone with a sensitive GI system. But they certainly perform ‘as advertised’ in terms of being a RS.

        1. As far as I can remember cold cooked potatoes are full of resistant starch. I always eat them with some cold chicken fat to slow down the extra insulin. Nice treat with lots of fat.

        2. That sounds exactly like how Mark said a naive-to-RS digestive system would respond to not-small amounts of RS, especially if said system is sensitive. Had a similar experience with oregon grapes (pea-sized fruit) last summer. Possibly the concentrated pectin. I backed off to five or less during meals for a week, and then I was fine having them as a snack.

    2. I have a pdf if you’re interested. I can email it to you.

  8. Great post–had a good laugh over this bit of drollery: “That’s how you should treat probiotics – like real friends whose company you genuinely enjoy and who come in capsules and require refrigeration.”

    I’m disappointed that there was no mention of sucralose of other artificial sweeteners, however. Don’t they destroy friendly bacteria as well? So many paleo eaters rely on splenda for their occasional or not-so-occasional cheats. I used to pound sugar-free monster, thinking it was a safe indulgence. Then I learned the sucralose was harming my gut biome. Can anyone give me more info about this?

    1. I thought that was pretty funny too. I don’t know much about artificial sweeteners and sugar alcohols but I can say with quite a bit of certainty that sorbitol will decimate your gut bacteria if you have too much of it. Happened to me. If you want to read my little story on that check this link out. I commented under the article, which is about how sugar alcohols are generally regarded as safe and some may act as prebiotics, so you may learn something useful from that.

      1. What a great article, thank you! I thought sorbitol was one of the baddies because it once caused me great distress when I ate a bag of sorbitol candies; but in retrospect, it was probably just too much for my gut to handle at the time. Great to know sugar alcohols aren’t the same as other artificial sweeteners and might actually works as prebiotics!

        Regarding your story, it doesn’t sound to me like sorbitol wiped out your gut biome–if it’s a prebiotic then it should be food for the friendly bacteria. Sounds like it was other things that upset your system, or perhaps the sorbitol caused you a kind of distress, but didn’t actually harm your gut bacteria.

        1. Whatever happened, and I think there were probably numerous factors that led to me having a compromised digestion system, I think sorbitol was largely to blame. I’m sure it was mostly the syrup that did me in – had to be because of all the havoc it wreaked after I ingested it and it coincides with when things really started to go wrong, plus it coincides with my friend’s issues when she drank it. If it didn’t kill off a bunch of my gut flora I think it probably flushed a lot out as diarrhea, leaving my intestines pretty much barren, or fed the bad bacteria, leading to dysbiosis.
          However, here’s a list of a few other potential stressors / culprits that probably played a part, and it’s probably not a complete list:
          – I didn’t chew my food as thoroughly back then (I also ate nuts all the time and swallowing them in big jagged pieces probably made them scrape against my intestinal lining)
          – I was consuming lots of artificial sweeteners, including plenty of aspartame, via gum, energy drinks (many of which were probably too acidic and full of BPA), and various other products.
          – I was consuming a lot of sugar.
          – I ate grains regularly (which I seem to be able to digest well enough these days when I eat them, which is rare except beer, and since that’s liquid it probably goes through easier). My breakfast (or snack) was often a bowl of sugary cereal with milk. Normally I can handle sane amounts of dairy but with the problems I already had and with the grains, sugar, and whatever other crud in the cereal mixed in it probably did some damage back then. I also ate a lot of bagels (often grilled cheese, and with a big glass of milk or Nestle chocolate milk) and Kraft Dinner.
          – I was also mixing other foods indiscriminately. I’ve found that one of the most effective things to do for better digestion is to only eat certain food combinations or one food or type of food at a time. If you have gut issues, I recommend trying this if you haven’t already. In general, fruit is best alone, but ok with vegetables, and not too bad with nuts. Never mix it with dairy. (That means saying no to all those fruity yogurt cups). Vegetables pair decent with meat and just about anything that isn’t dairy. Nuts are best by themselves or with other plant foods, favouring vegetables a little over fruit, though they also seem to go alright with a bit of dairy and sometimes I mix nut butter with a natural sweetener without any apparent problems. I think legumes (maybe not peanuts) would be best with vegetables if you mix them with anything.

  9. Hi! New to the site…I’ve just started probiotic supplements, and was interested to read what I should be eating to make them more effective. I’d appreciate it if a more experienced reader could comment on what actual foods contain “fermentable fiber”, this is not a term I have seen before.

    1. ‘Fermentable fiber’ is also known as prebiotic [fiber]. They are plant fibers upon which our gut bacteria feed. Found in… most plants, really, though some have more than others and there are multiple types. Just one more reason veggies are awesome. This site has both a search bar and an archive organized by date and by topic, use them well.

      The simplest advice is get most of your calories from animals and most of your food volume from vegetables, and spend lots of time outside.

  10. From what I’ve read and understand (holistic/naturopathic practitioners) one of the best things you can do for your gut flora is to give up alcohol. Apparently candida can thrive on it and it does no good in regard to the good bacteria in the gut. I’ve noticed that the people that I know that seem least ‘healthy’ are the ones that drink the most – weather it’s wine, beer, hard liquor, etc. Independent of other lifestyle factors like diet, exercise, etc. Just an observation.

  11. Due to a strep infection, my doctor highly advised a round of antibiotics (amoxicillin) that I just finished up yesterday. I feel like 3 years of building my gut bacteria is down the drain, but I will be getting back to work building it up again! Probiotics, prebiotic fiber, resistant starch – they’re all going down the hatch. Great post Mark!

  12. I’ve had IBS most of my adult life so I’ve come to realize the hard way how many things can affect gut bacteria!

  13. Probiotics cured my daughter’s GERD. Thanks to a friend for tipping us off — her pediatrician was happy to let her stay on proton pump inhibitors indefinitely! 🙁

    What I would like to know is why, whenever my digestive system gets “off,” what always puts it right is eating beef or pork! There must be some beneficial effect of red meat on my gut microbes.

  14. Why “wear gardening gloves”? I hardly ever where them. Unless I am handling thistles or nettles?

    1. I wear (usually two layers of) surgical gloves under my gardening gloves, and when I come in, I have to wash my hands and forearms very diligently with good soap, and then use rubbing alcohol on a cotton ball to clean my cuticles and especially under my nails. If I don’t do all this (every time {sigh}), I often end up with “felons” — infections *under* the fingernail, requiring a course of antibiotics and antifungals… I think (well, I KNOW) I’m living in the wrong part of the country for me! Out in Washington State, I could (and did!) garden for hours with no gloves and no problems… since I moved to Georgia, I have to be exceedingly careful… my body seems to really dislike the local ‘bugs.’

      1. I enjoy a good vegetable garden as well. Something about getting out there, getting dirty, and enjoying the fruits of your labor is very satisfying.

        How’s the dirt in Washington? I live in TN and my county is notorious statewide for some of the worst dirt in the state….lots of clay and you’re doing good if you dig 2 inches before you hit a rock the size of your head. If anyone can guess which county in TN, you’ve earned a pat on the back!

        1. Hey Jacob,
          For GA, it’s not rocks below the “topsoil” (which is just slightly looser red clay) — it’s hardpan. ROCK-hard clay! When I garden, I have to use a pickaxe!

        2. Williamson? I’ve found rocks the size of my head when digging garden space… 😉

    2. I live in the clay belt too– I find extensive gardening without gloves dries my skin terribly, but regular gloves are cumbersome & make it hard to do tasks that require finesse. (I have small hands too.) So I’ve used surgical gloves for delicate stuff, & only use heavy gloves to protect against blisters while weilding the mattock, &c.

      That said, if I’m just pulling out a weed here or there, or harvesting some greens, I don’t worry about occasionally getting dirty!

  15. i would love it if you did an article on clays for detoxification, digestive health, how it may or may not inhibit microorganisms, or support good gut flora, and on specifically what clays you would recommend consuming.

    loved the 16 things on gut bacteria; it’s everything i’m already doing. thank you!

  16. all this talk about our secret gardens is exciting. It makes one think a little harder about the “where”s, the “how”s, and the “with what”s before any task is achieved, especially eating.

    1. I had a secret herb garden last year. 10 plants, six of which were females. I liked these plants, they were my… “buds”. hehe.
      They were only about a foot high each when I got booked and didn’t get released until, I don’t remember exactly because I spent half of the last year in and out of the local prison basically every month or two… at least a month later. I was anxious to see if they were still there. They were, and they’d grown to about six feet tall. The fertilizer I put around them when I planted them might have had something to do with that. There were a few fairly big weeds growing among them but they seemed not to be disrupting my plants, and there were little vines growing around some of them, and actually holding some of them up. It looked like symbiosis to me. I think the plants might have communicated to each other so they could all live in harmony. I talked to my plants sometimes because that’s supposed to be scientifically proven to make them grow better. I picked and enjoyed small amounts of buds from them frequently. I loved it.
      So, definitely, I want to do some more gardening: herbs and food, and some mushrooms if I ever get the chance.

  17. I was on some powerful antibiotics for a deep cutaneous staff aureus infection that would have killed Grok! Fermented vegetables and yogurt fixed my gut biome following the antibiotic regimen. Now I have cultured cabbage(sauerkraut) and garlic dill cucumber pickles going all the time. As a cue from MDA, I started using them together with RS to make “combiotic” foods. Potato salad made with cultured dill pickles and plain sheep’s milk yogurt is a staple in my kitchen. It is better after it sits in the fridge for a few days when billions of lactobacilli start assimilating with the RS in the cold cooked potatoes. If anyone is interested I’ll post the details in the MDA recipe blog if encouraged to do so.

      1. OK Diane and Bob,

        I have a new batch of pickles to make so I’ll photograph the process. Culturing pickles is a recipe in itself. It’s based on the one in Sandor Katz’ Wild Fermentation book. There is some good information on the web like http://www.culturesforhealth.com they sell basic fermentation supplies. The yogurt is http://www.bellwetherfarms.com It’s the best for savory applications like tzatziki and cold potato salad of course.

    1. I think that sauerkraut has done a lot of good for me in healing my gut. It’s one of my staples. Sometimes I eat pickles and olives and other fermented vegetables but generally I stick with the sauerkraut because it really seems to work and usually I can find some that’s reasonably priced.
      Often I eat some when I eat other plant foods for better digestion and sometimes I have some with protein rich foods for smoother bowel movements.
      And of course the number one reason I eat it is better gut flora in general.
      Careful though, because I’ve found when I eat a whole lot of sauerkraut I sometimes get minor pains, presumably due to its acidity irritating my stomach or intestines.

  18. I know this is kind of rare, but I wanted to comment in case anyone else out there is going through the same thing. It seemed the more I drank kefir, kombucha, and ate fermented foods, the sicker I became. So my natural health pracitioner did some blood work. Sure enough I put off antibodies to the yeast in these foods. This yeast is also often found on the outside of fruits and vegetables, deposited there by insect’s feet. So I have stopped consuming fermented foods, and scrub my fruits and vegetables to within an inch of their lives before eating them. It’s is no wonder sourdough bread made me so sick in the past. My Dr said it’s the same yeast.

    1. Gina,

      Lactobacillus creates an acidic environment that kills yeast so pickles, sauerkraut and acetobacter in cider vinegar are fungal antagonists.

      1. Even though the yeast have died, they could still trigger a reaction.

        1. Yes I agree there is the Herxheimer reaction. This is caused by the die off of bad organisms. Think of it as the carnage on the microbial battlefield. Some of the posts here describe feeling poorly after ingesting probiotics. My suggestion is to stay on the positive probiotics because feeling off is part of the changeover from bad to good gut biome. Its like have sore muscles after and exercise that has been neglected for some time. Perhaps Mark could do one of his creative summaries on the Herx process and the similar effects of grain withdrawals.

  19. The thing I like most about having healthy gut bugs is that few people linger in my office.

    1. HA! This is actually my secret shame. On low carb paleo, I NEVER farted and was very smug about I–I thought it was a clear indication of the healthiness of the low carb diet. Now building the gut biome back with probiotics and resistant starch, and YE GADS! I’m finding it hard to be socially responsible.

      1. Once you gut biome has balanced out, there will be bugs that consume the methane and other odiferous gasses, resulting in low- or non-smelly gaseous emissions. 🙂

        Sounds too good to be true, but it works most of the time. I find that when eating a food that hasn’t been in the mix for awhile (e.g. had cooked pak choi after not eating it for ages), a smelly fart or two may emerge.

        1. Well that’s good news. After a few months of resistant starch plus probiotics, I thought I was in the clear, but this week had a big flare up. New foods I guess. Never thought I’d be discussing this on a forum…

  20. A little confused as to when you’re supposed to take your probiotics. I have high quality stuff but the label says to take two hours AFTER eating while here Mark is saying we’re meant to take them “with” food. Any suggestions? thanks.

  21. Thank you for this information! I started taking a probiotic about a month ago, and did notice some digestive benefits initially, but on the other hand, I’m gaining weight when I should be losing (5 lbs in a couple weeks), and was curious as to whether this is “normal” and how long before I can expect to see positive benefits to my weight, or at least stop seeing gains. I haven’t changed my diet or exercise routine, just the probiotic.

    1. Do you take other measurements (around your waist/hips, or even a pair of jeans that are quite snug)? It’s probably a more reliable indicator of progress than the scale. The weight you put on could well be the increase in beneficial gut bugs, which will have no impact on your physical size. Does that make sense?

      1. Once when I was, I think, 5 years old, or if not then probably 6 at the oldest, I was at my grandparents for Christmas dinner and ate a lot, like I always would there. Then I felt like I had to plop a plump dump. Curious, I stood on the scale beside the toilet before and after. I may not have been standing on it properly one of the times but according to that scale I dropped five pounds. It baffles me to this day.
        Around the same age at another big family meal I ate a bunch of broccoli and then had to unload, and though my digestion was pretty sound as a kid, chunks of broccoli came out that time. I don’t think I’d eaten any prior for at least a couple days, so naturally my suspicion is that somehow, though most of my recently eaten food did what it was supposed to, that broccoli found its way out in what couldn’t have been any more than a couple hours.
        To me both of these events seem impossible.
        Apparently, that broccoli was in a hurry to reach The Outer Limits.

      2. Wow, that’s interesting – I had no idea bacteria could weigh so much! LOL
        I did take measurements recently and noticed a small increase in size but it’s small enough it could be attributed to bloating. Hopefully those extra gut bugs will help balance that out 🙂

        1. They may be small, but the usual figure is “outnumber your cells 10 to 1”. Obviously this is highly variable, but still.

  22. Mark,

    Another great post! I’ve been palying around with Kombucha recipes and created my Raspberry Kombucha, which I’ll post on my site soon…

  23. For most of you asking questions about what foods have RS, good options for pro and pre-biotics, etc, you really need to head over to:

    Richard, Tatertot Tim and Dr. Grace, along with many regular commenters, have posted many hundreds of links to research already done, what they have done to fix their gut biomes (Dr. Grace a couple of times), and the testimonials of many people who have had success and failures along the way.

    I personally have been doing resistant starch since January, and added in the soil based organisims (SBO’s) in April. I’ve noticed things like my body temp has gone up from 95.5 to normal 98.6 degrees, I don’t crave carbs, I sleep like a log, all sorts of good things. I’ve had my setbacks, in that RS didn’t work until I filled the ’empty cages’ with the SBO’s.

    Go read the posts that started the RS and gut microbiome revolution.

  24. Mark, you asked about whether this information leaves us empowered or overwhelmed, and for me that is the bigger takeaway from this post, actually.

    I’m beginning to see that approaching the primal (or ANY health) journey from an all-or-nothing attitude, getting stressed about the nitty gritty, and forgetting to let go and just live, can do more harm than good. THIS IS ALL ABOUT BALANCE. About being playful, as you so often mention – and we forget that.

    (This does not mean I believe in only doing this halfway, either. I strongly believe that if you want the full benefit of the primal lifestyle, you have to commit to it fully.)

    I have to admit that at first blush it DOES seem overwhelming to take gut flora into account on top of primal life, (and for me, following Sarah Ballantyne’s Autoimmune Protocol). But an important part of this journey is to take the knowledge we gain and be empowered, strengthened by it, and NOT turn it into overwhelm and a long list of dos and don’ts.

    When you are trying everything possible to build health out of perplexing physical challenges, you run the risk of running into overwhelm quite easily, especially when your lifestyle changes don’t seem to deliver results and you keep searching for the holy grail of that perfect combination of changes that will make you better.

    Thank you for that conclusion to remind us to keep looking at the big picture. Stress, after all, affects gut flora, too. For me the bottom line is that our microbiome needs to BALANCED. And that means a BALANCED mindset, too, otherwise we might be missing the point.

    Keep up the good work!

  25. I can’t be more overwhelmed. I stopped eating fermented food the minute I stopped eating dairy because I was only eating yogourt. When I decided that I should try to help my gut (most likely leaky) I tried fermented soy but I had the most horrible migraine ever. Now I’m scared to try the rest of the very expensive package.

    Also, I’ve stopped eating nuts because I can’t stand rancid oil and I stopped trusting my really sensible taste buds because even when I only eat the nuts that taste good to me, I end up feeling bad afterward. But I love nuts! They are tasty and filling. Any tips to buy FRESH nuts??

    1. Is there a reason you stopped eating all dairy? Many people eat yogurt and/or kefir while eating primal/paleo if it works well for them.

      Are you eating wheat and other grains? Those are a common cause of leaky gut. Also carbonated sodas, which is not generally known.

      To get fresh nuts, one idea is to buy them when the new crop appears in the store in the fall and freeze them. This is valid for temperate zone nuts such as pecans and walnuts. Also, buy whole nuts (not sliced almonds, for example) and store them in the fridge.

      Also, try different (for you) varieties such as macadamia nuts. Or, take a break from eating nuts if your gut can’t tolerate them at this time. My hubby couldn’t eat nuts until he stopped drinking sodas and let his gut calm down.

      1. Thanks for your reply. I stopped eating dairy because it was causing me headaches. I’ve tried to reintroduced them at least 3 times since with no luck.

        Fresh almonds are here now at the store but I don’t see how it will affect the stuck of dried almonds. Also, I have no idea when any other nuts “appear”.

        I eat rice and organic corn but the last time I drank soda must be 15 years ago. The problem with nuts is not my gut but that they cause headaches.

        1. Here are some other prebiotic alternatives you might try. I’ve tried all these without any issues.

          Fermented vegetables – Mark’s made posts about this topic along with recipes. His recipe for fermented dill pickles are delicious…and I don’t even like pickles!

          Kombucha – I just recently discovered my local Kroger’s sells a ton of varieties. The ones I drink typically have extra healthy things added into it like chia seeds, blue-green algae, acetic acid, etc.

          Greek Yogurt full fat – not much beats this. If you don’t have any negative reactions to yogurt, then knock yourself out.

      2. I find nuts and seeds one of the tougher foods to digest. I used to eat them in massive amounts but now it’s more like a handful here and there and I think that’s a much better way to go. I don’t make them a staple anymore. I used to eat them mainly for protein and because I found them filling. Now if I want protein I usually go for the superior animal sources.
        Despite all the hype over almonds, I’m not nuts about them, and much prefer some hazelnuts and occasionally pumpkin seeds, pistachios as a treat (because vendors seem to think that they are made of silver, gold, and platinum), or some pecans.

    2. Thanks Jacob!

      I just googled kombucha and I found a maker down town! I will go check them when I will go to buy soap soon enough.

      And no, I cannot eat yogourt, it’s actually yogourt with added lactase that made me notice my intolerance. Before that, it’s only milk that I was not eating.

  26. Anyone want to help me debunk this ridiculous little article about why you should supposedly not eat salmon?
    One of the reasons given is that’s it’s omega 3s are bad for you.
    (just pretend instead of this line, there’s the most epic facepalm .gif that exists)
    At the moment I post this my argument is at the top of the comments section. I think I did a decent job with it but I’m sure many of you have more knowledge on the subject than me and could probably give an answer more based on science, while mine relies mostly on what should be common sense.


    1. I’m not sure you need to debunk that article. Almost 100 percent of hundreds of comments basically told the author he was an idiot.

      1. hah, good point, nevertheless that’s just about all most of them did, without giving any reason why, so providing a few might be helpful to uninformed or misguided people reading the comments.

  27. Excellent information!
    The ecology of the gut is emerging as a vital ingredient for good mental and emotional as well as physical health.

  28. I’ve heard mixed things about resistant starch – some say helpful and others say it only increases all bacteria and can make gut problems worse.

    I’ve also personally had some issues with probiotics and fermented foods, although I may just have not found the right balance for myself. Or time. Giving it time after a lifetime of issues is important, as well as moderating stress, which is a huge thing for me.

  29. Mark,

    The last line of the Exercise section is “don’t overtrain and don’t undertrain.” This is my biggest struggle right now…how do we know what our exercise sweet spot is?? Thanks in advance

  30. Can someone explain how raw honey, which is certainly the most natural of sweeteners we consume, is compatible with this discussion on gut health when it is antibiotic and antibacterial? Is there some type of synergistic yen yang relationship with the prebiotics, probiotics we take along with a seemingly opposite effect of raw honey? What about vinager? Obviously I’m not an expert but shouldn’t we be looking for some sort of a PH balance here?

  31. How about prebiotic/RS candidates:
    isomalto-oligosaccharides (Quest Bars) and
    inulin/chicory root used as an alternative sweetener?

    That aside, being non-GMO won’t necessarily protect you from glyphosate (RoundUp) in your food. Farmers use it off-label on non-resistant crops to terminate growth for harvest, a practice euphemistically called “dessication”.

    Dessication is common with wheat (which is not GMO [yet], but which readers of this blog aren’t apt to be eating anyway). Dessication is a potential issue with other crops that must stop growing before being harvested.

  32. It’s unlikely that fermented foods, no matter how good they are, came in to common usage before the advent of agriculture, 10,000 years ago + or -. Before that, according to what this site has to say about it, our early human, hunter-gatherer, ancestors were eating tough, low starch, tubers to get their pre-biotics. But where did they get their pro-biotics? Or did they?

  33. Now, my health is pretty good. I’m happy with adding in a little more resistant starch and fermented foods but the idea that I ‘need’ to consume pro/prebiotics in a pill form each and every day offends me. Seriously, that’s what Primal has come to? The recommendation that you pop digestive pills on a daily basis. And, of course, there’s all the other supplements recommended. No.

    1. Our food, our homes and our bodies are so over scrubbed and sanitized these days…and that’s hardly primal. How are supposed to maintain a healthy gut microbiome without supplementing probiotics? Living in the modern age requires we do some things that Grok took for granted…
      My stomach is the happiest it’s ever been since I’ve started downing my daily dose of RS plus soil based probiotics in a nice tall glass of raw milk.

      1. Glad you’re happy with that Deborah. From what you say, another solution might be to worry less about scrubbing your food, body and home. Personally, I’m starting to think that there’s meant to be a degree of grit between the world and how we want it. The answer is to find a happy medium between getting everything exactly perfect and being completely at odds with our lives and bodies. Popping pre and pro-biotics as a standard is erring on the side of micro-management for me. It may not be so, for everyone. And, of course, there may be things I do that you would consider over the top. The fundamental point remains, however, that the way to real satisfaction should not involve constant dosing with pills. It just seems wrong.

        1. Living in squalor, getting dirty, not using soap, not caring about washing my hands unless they get annoyingly dirty, covered in chemicals, or out of respect if I’m going to be around other people is basically my norm, and I’ve gone over a month without showering (it was the winter and I was camping). The last time I was ill was an ear infection in the fall of 2010.
          I’ve gone from terrible gut health to decent gut health without ever in my life taking a single probiotic pill. I have eaten a lot of fermented food though.

        2. Totally agree, I just cannot get my head round the advice of eating fresh real produce, avoid all packaged processed rubbish etc etc, but it’s ok to pop pills on a daily basis and supplement with powdered “food”, and it’s always unbelievably expensive which seems to make people think it’s going to work wonders. I only wash in water too.

    1. I once watched an old Chinese woman carefully collect pieces of the “innards” of a rotting log by the river. Maybe she was collecting bacteria for her gut flora.

      1. Was it pieces of the log she was taking? I wonder if she was hunting for grubs.

    2. Pretty sure the dirt smoothie was the part he was kidding about in that list.

  34. I am so very confused about the (never garden without gloves!) comment. What is wrong with that? My assumption is he meant because of cross contamination between plants and their bacteria and not because its unsafe for humans. I assumed this because he said to eat a carrot with dirt on it or a dirt smoothie but made no mention of just kidding about those things. That being said, my confusion comes from being able to eat a dirty carrot but not being able to pull that carrot up with bare hands. Someone please clarify! Thanks!

    1. I’m not sure as well regarding gloves but I do have a lot of Black Widows in my back yard.

    2. He think he was actually kidding about never gardening without gloves. I’m pretty sure it was the dirt smoothie that you really shouldn’t do and he might have thought that that was clearer than it was. You can definitely garden without gloves, I do it all the time!

  35. Dear Mark, I won’t be the 1st to comment that you have a talent for reading our minds!

    My 1st comment/question has to do with fermented cabbage and the like to those with thyroid issues. As someone who’s thyroid markers suddenly went off line (hypothyroid), I scoured the internet (and MDA) for answers and finally arrived at Chris Kresser web site. In a 3 part series with Chris Masterjohn, they discuss the effect of goitgenic foods in general and fermented cabbage in particular on the thyroid gland.

    “Chris Masterjohn: Now, a lot of people think that cooking or fermenting cruciferous vegetables is going to get rid of the goitrogens, but that is not true. Fermenting actually activates them. It actually does the conversion to the thiocyanate right in the jar of sauerkraut. So, if you’re eating sauerkraut and kimchi, you are not getting rid of the goitrogens.” https://chriskresser.com/chris-masterjohn-on-cholesterol-and-heart-disease-part-3

    As of last week I sadly cut back on my fermented cabbage consumption and started to supplement with 380 mcg of iodine (kelp) and selenium (2 Brazilian nuts) to counter balance, to be followed with blood test in 6 weeks. In fairness, I also upped my carb again (sweet potatoes mostly). Due to elusive food energies (point of suffocation) and food restrictions, I thought that I mind as well switch to a Ketogenic diet. I now think that my symptoms are a failure of that attempt.

    I would love to get you take on an issue that plague many. And if not asking much what’s your opinion on “iodoral”? Readers out there – please report if you used it.

    My other comment/experience has to do with dirt and gut bacteria. After acclimating my feet with self-made 4m”m leather Huaraches (10K walks etc. over 3 months) – I spontaneously took them while walking in the park and managed to run barefoot (4K-2.48Mile) over grass (uphill sprints) and mostly hard sidewalk and asphalt without the slightest pain or a blister to show for. By the time I reached home (would have gone longer but there it was), I felt euphoric like never before (I’ve been running for nearly 40 years…. now if my abs were nearly as defined as yours… I’m tall and skinny and at 57 I am fit & toned then most of my peers). The part of my soles that touched the ground on the other hand was black as tar. Does this in any way have a positive effect on our gut bacteria; or does washing it away kill it, like in the NY time’s story (https://tinyurl.com/pxvbsob)?

    Thanks in advance and may I recommend that you try fresh pistachios? They are my 2nd best after macadamia nuts and so much tastier the dry ones, and, unlike macadamias they trick you to believe that you can eat more of them due to lower fat content. And addictive they are! Just get ready to end up with green fingers due to the dye they contain (harmless). Should be easy to get in California; no?

    P.S. You are welcome to address my thyroid question via your weekly “Dear Mark”. Also, my legs are still pain free two days later.

    1. And by that I mean that my reply was finally posted; I will wait silently for feedback from Mark.

  36. I’ve never heard of a soil smoothie. Can someone write down how to make one?


  37. Good info. I’ve been a tree trimmer most of my working life. Not a lot of places to wash up out in the field. My hard boiled eggs would look like dirt in my hands when I would eat them. Never bought into the over cleaning anti bacterial stuff.

  38. Important mention for FODMAP sensitive readers.
    Pistachios are High FODMAP & can trigger IBS like symptoms.
    Low FODMAP nuts are walnut, pecan, macadamia, pine.

  39. Question. Can OTC probiotics cause problems? I have started suffering from esophageal spasms which have landed me in the ER thinking I was having a heart attack. I love taking probiotics because it boosts my immune system, but the pain I have started getting from spasms is not worth it. Doc said spasms are a result of Gerd. I don’t get heartburn though, just spasms and a pain like someone put a dagger in the middle of my gut and is twisting it. I am a Celiac, but keep a constant gf diet. Can you “over do” probiotics? I take Ultimate Flora 30 Billion.

  40. I get dirty every day in the garden, but I stopped having dirt smoothies b/c I found out that soil has giardias in it sometimes. I don’t know how common this is, but giardias are not just in lakes and streams.

    Also, sometimes I have to spray poison ivy or other weeds that are impossible to get rid of any other way, and I use Roundup, as the least toxic herbicide available for perennial weeds anyway. (Annual weeds can simply be dug up or sprayed with vinegar.) I wear a mask and gloves and an impermeable suit. I think that’s pretty safe. Then I take a shower.

  41. Thanks Mark, I’ve had a feeling for a while now that probiotics are the answer to just about everything. They say they can even help Autism.. 🙂

  42. Interesting. I feel like I never eat the same thing twice (prepared in the same way) consistenly. Whatever I make for dinner and other meals is always different. I don’t have a meal rotation like other people do. Very interesting

  43. If you believe Roundup can affect gut bacteria, you need to cite studies to support it. Wouldn’t that be part of the very low LD50?

  44. I wonder if alcohol should be on this list.

    Does alcohol negatively affect your gut bacteria?

    Or, are beer and wine considered fermented foods and thus, good for your gut?

  45. I was told not to eat pistachios as most have mould. I eat macadamias, almonds and walnuts mostly and the odd brazil nut but dislike hazelnuts (unless in dark chocolate). Should I stop throwing away the activated pistachios?

  46. Nice post, though very long. I had to take 2 breaks to complete it fully. Being indian fermented foods are part of our everyday diet. There are many cases wherein, old grannies will suggest home remedies based diets for many illness.

  47. Dirt smoothies, love it! Have you checked out the book An Epidemic of Absence? It’s a great look into how our obsession with getting rid of germs and sterilizing everything my be adversely effecting our health.

  48. umm, I’m not sure if he was kidding about eating the dirt covered carrot or not. I’m a bacteria lover but think I might be afraid that the animals had crapped in my garden a few too many times to risk e coli contamination.

  49. I really enjoyed reading this thread…..I have just finished an antibiotic protocol for H.Pylori. I’ve decided to take a probiotic…will this also help kill the H.Pylori bacteria? Thanks!

  50. The number one deterrent to having healthy gut bacteria is consuming meat and maybe even any animal protein…

  51. Loved the information I just wish they would flat out just list what you should eat in avweeks time.

  52. A very important read and reminder for me here. Have been Primal / Paleo for several years, but “shit happens”, which in my case was pneumonia plus pleurisy….followed immediately by an empyema. I am 30 days in, of which 20 have been in hospital, have had more IV antibiotics than you could dare to mention, let alone surgery to drain the empyema.

    So I forgive myself for the antibiotics. They have (literally) saved my life.

    A month ago I was super fit, healthy, and with not much of a care in the world. Talk about a “grounder”, a reminder of one’s mortality. But I’ll be back. Beyond short walks with the dog there ain’t no training for some time yet, but I will be back and I will get there.

    This post is key to my recovery. Thanks Mark.

  53. Ya so after destroying the paleo philosophy with proof that a mostly raw vegan lifestyle creates the conditions for extreme healing, sustained health and wellness I also discovered through proof that cacao is a poison and if eaten like it is a food can destroy the gut, causing, candida and leaky gut and sever negative psychological effects. It is a drug. Nothing in nature eats cacao seeds that I am aware and if it does it’s not even remotely close in volume as human consumption. Any stimulant is a poison. This site is full of self satisfying information. As a long time paleo adherent and now a long time “defector” I am here to call bullshit on the movement. Get out of your own heads and evolve past this tripe lol

  54. Hi! Just wondering, does anyone know anything about antioxidants and whether or not they can help probiotic growth. I mean – if I ate antioxidant rich probiotic foods, would it help or not help or not even be a factor? Asking because I’m doing a science fair project on this topic. Thanks for the help 🙂

  55. I’m confused – what’s a soil smoothie, and why is it gardening without gloves that you’re kidding about, what’s wrong with that? Are you kidding about the soil smoothie instead? Hearing the whoosh over my head, would still be grateful for an explanation!