7 Things You Had No Idea Gut Bacteria Could Do

If you’re a regular Mark’s Daily Apple reader, you probably have at least a generally accurate if somewhat vague notion of the important functions performed by our gut bacteria. They’re a “big part” of our immune systems. They “improve digestion” and “eat the fibers and resistant starches” that our host enzymes cannot digest. Yeah, gut bacteria are hot right now. Everyone’s talking about them. And, since our host cells are famously outnumbered by our gut bacteria, 10 to 1, we need to be apprised of all that they do.

We don’t know everything yet – and we probably never will – but here are some of the most interesting and unexpected functions of our gut bacteria:

They learn from each other.

Bacteria are simple, straightforward organisms. They don’t have all the hangups that we mammals do, all the middle men and physiological bureaucracy between “us” and outside information. Bacteria can directly exchange genetic material – defense mechanisms, enzymatic functions, and other characteristics – from other bacteria they come into contact with in the gut. They’re very quick learners operating on an entirely different time scale.

One example: in most Japanese people, certain strains of gut bacteria have picked up the genes for seaweed digestion from the bacteria found on seaweed. The seaweed bacteria itself didn’t colonize the Japanese guts; only the genetic material transferred. Other groups whose gut bacteria weren’t exposed to the seaweed-digesting strains and never picked up the relevant genes have more trouble digesting the seaweed polysaccharides.

They improve our bone mineral density.

Feeding fermentable fibers to our gut bacteria isn’t just about the short chain fatty acids they produce in response. It’s also about the improved bone health, which occurs through numerous gut bacteria-mediated mechanisms: “increased solubility and absorption of minerals because of increased bacterial production of short-chain fatty acids from prebiotic fermentation; the enlargement of the absorption surface by lactate and butyrate; increased expression of calcium-binding proteins; improvement of gut health; degradation of mineral complexing phytic acid; release of bone-modulating factors such as phytoestrogens from foods; stabilization of the intestinal flora and ecology, also in the presence of antibiotics; stabilization of the intestinal mucus; and impact of modulating growth factors such as polyamines.”

They nullify anti-nutrients.

Phytic acid is an anti-nutrient found in seeds, grains, legumes, nuts, and many other foods. It binds to and prevents the absorption of various minerals, and high phytic acid diets have the potential to cause nutrient deficiencies. Unless you have the right gut flora.

Certain gut flora can actually turn phytic acid into inositol, preventing mineral-binding and releasing a nutrient involved in mood regulation and insulin sensitivity. The more phytate-rich foods you eat, the better your gut bacteria get at breaking it down (they learn, remember?).

There’s also evidence that the right gut flora can reduce the allergenicity of gluten and dairy proteins.

They manufacture vitamins.

When gut bacteria consume substrates, they produce various metabolites, the most famous of which are the short chain fatty acids butyrate, acetate, and propionate. But they also produce vitamins in the process, particularly vitamin K and the B-vitamins. According to Dr. Art Ayers, an optimally-outfitted human gut biome given sufficient dietary substrates can manufacture all the vitamins a person requires.

It seems Vitamin K2, that sweet little variant of vitamin K we love so much, can also be made in the gut. There’s very little direct evidence of this, but broad spectrum antibiotic usage leads to lower levels of vitamin K2 in the human liver. What we do make in the gut can absolutely be absorbed and utilized.

They form a large physical barrier against pathogens.

Bacteria are made of matter, even though they’re invisible to the naked eye. They take up physical space on the gut lining. They plug holes, fill nooks. They cross arms and stand together, steadfast against encroaching pathogens seeking residence. Sheer brute force is one of, if not the most primary immune function of our gut bacteria.

They represent a “second brain.”

The enteric nervous system, found in the gut, has more neurons than the spinal column or central nervous system. Long thought to be only concerned with directing digestive contractions, the enteric nervous system has a direct conduit to the brain: the vagus nerve, 90% of whose fibers are dedicated to communication from the gut to the brain. If you’ve ever gotten butterflies in your stomach from young love or anxiety (or both), or felt like you knew something “in your gut,” that may have been your gut brain relaying the message to your, um, brain brain.

Here’s where the bacteria come in: gut flora produce a ton of neurotransmitters, about 95% of our serotonin and half of our dopamine. Imagine if those voices in our head that seem to originate elsewhere are the result of your gut bacteria coming to a consensus position and delivering it via a chemical slurry of neurotransmitter secretions directly up to your brain? After all, the thoughts we have, the desire we feel, and the words we form come from chemical chatter between neurons. It’s possible that the brain can’t tell where the chatter originates, from “us” or the gut flora. Is there even an “us”? Maybe it doesn’t matter. Maybe “us” is closer to the truth than “me.”

They can make us depressed, anxious, obsessive-compulsive, and even autistic.

Researchers have long noticed that people with disorders “of the mind,” like depression, obsessive compulsive disorder, and autism, tend to also have gastrointestinal issues. It’s becoming clear that these aren’t chance correlations. The emergence of the gut-brain axis, the knowledge that gut bacteria manufacture neurotransmitters, and direct clinical evidence (albeit mostly with non-human animals) suggests that the gut bacteria disturbances are mediating the disorders. We see this in:

Gut bacteria help determine the nutrient content of our meals. They mediate our subjective interpretation of everyday life and our interpersonal dealings with others. They’re constantly learning new things and defending us from interlopers and communicating with and perhaps even telling us what to think and how to act. It’s almost overwhelming to even imagine.

Hopefully you’re beginning to understand why the gut biome is shaping up to be the biggest health story of the century and why we ignore it at our peril.

Thanks for reading, everyone. What’s the most surprising thing gut bacteria can do, in your opinion?

Primal Kitchen Mayo

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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180 thoughts on “7 Things You Had No Idea Gut Bacteria Could Do”

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  1. As an elementary teacher, I must admit that it frightens me to think of these correlations when I observe what children and their caregivers pack for morning “snack” and what schools now serve for lunch. Chocolate and candy (like straight sugar “pixie sticks”) at 10:30? Oh yeah, every single day. This despite the school’s healthy snack guidelines. It takes a village….

    1. Further evidence they’re trying to kill us off–now at a younger age!

    2. Yup, I witness the same thing at my school… a sugary snack at 10, a sugary dessert for lunch time, a sugary snack at 2, a sugary snack after school while waiting for mom and dad… *sometimes* a piece of fruit will be present during the day, but always some, so it’s therefore just as horrid to the blood sugar levels… :/

    3. It takes a village to do what exactly? Sorry. It takes two parents that properly care for their children. It the government nannies in the “village” that are killing us. I cite as Exhibit A–The food pyramid!!

      1. Her point I think is that we are all in this together. You can think of MDA as a virtual village, providing valuable information and a corresponding support group. Agri-business, large food processing companies and multi-billion dollar fast food companies are doing FAR more damage than the government food pyramid. The U.S. government is at least trying to protect citizens from pollution and toxins in the air, our food and water. Imperfect yes, but as a collective people we have to fight for change and get away from this knee-jerk reaction to demonize and blame the government for all of our ills.

        1. “The U.S. government is at least trying to protect citizens from pollution and toxins in the air, our food and water.”

          Why cannot property rights be used for environmental issues (like it used to be)?

          Last I checked govet. policies are responsible for adding flouride to water systems (a huge toxic by product spanning back to aluminum production) and radiating our foods (also from waste byproduct). Ahh, the good old “the solution to pollution is dilution). Let’s not forget the Farm Act which distorts market price or the food pyramid…

          You are correct regarding the collective people enducing change. The only direct, one-for-one vote for change comes from a true marketplace where people vote with their money, not the crony capitalism we have today, which by defintion of the mixture of state and corporations, is called fascism. Oh yeah, and allow competition in money because even that is a losing game under the current scheme.

      2. True, except not every child has two parents and many parents are uneducated in these matters.

        1. I can’t help but think that this is part of natural selection and survival of the fittest. If parents have so little common sense to blindly accept a statement from someone selling you something (ex: this is healthy) without question, then how are people or the government supposed to fix that?

        1. Survival of the fittest doesn’t fit the new paradigm. modern medicine has made it possible to keep train wrecks alive, sucking up resources, and racking up huge medical bills. Besides, “fittest” only means the organism able to adapt the fastest, not necessarily the organism in the best shape.

        2. Society takes all types to function. Ideally, some people spend a lot of type being analytical and figuring things out, following their nature, and a lot of others are needed to do various more gruntwork type things. Or maybe they are using their brains but applying it to other things like quantum physics, car repair or whatever. The rest should be able to trust the so called scientists to do what they advertise they do. And since 98% of people DO trust them, then survival of the fittest would mean only 2% survive? Not a very viable option. The scientific system needs to concentrate more on truth and less on grant money and handouts from big business.

      3. At 62 years old, pilot for a major global airline, relatives all over the globe, a CrossFit/MovNat/Kettlebell/Indian Club/Primal Scientist Coach for our tribe; I see it all. Some of my best athletes eat way outside the Primal Blue Print. My fellow airline craftsmen and women and my two PhD brothers can’t see this simple picture. Globally, forget about it. I spent a year in Africa and saw humans in better health than I see in the Western World. Perhaps it is the circle of life; a few will follow the path, most will not. At the core of the matter is the tribe verses the nation. Tribes are small verses villages are larger and too diverse. Only the people you can touch, love and protect can possibly understand. The rest will go their merry way. Be strong!

        1. Inspiring comment, ‘only the people you can touch, love and protect can possibly understand’. Makes me think that the key to this is the ripple effect, our modern tribes overlap so we need to gently and uncritically pass on our knowledge (or lead by example) and hope to effect greater change. I’ve managed to pull a few people along on my journey after transitioning myself and my children to this way of eating. Mark must’ve influenced hundreds of thousands by now, way to educate the village Mark!

    4. It is sad and frustrating that there is nothing that we can do about students who eat poorly. I have enough trouble getting my own son to eat properly. My wife works with autistic teenagers, and if she spoke up she would lose her job.

      1. I agree that It does take a village, but parent’s are such a large and critical influence in their children’s development that we [parents] CAN and DO make a difference, as well.

        Our children are subjected to, and barraged with, conventional “wisdom” in every aspect of their lives. But what they learn at home from their parents stays with them, even if we don’t think they are listening. We can arm our children with the information to make smart choices (and not just about nutrition) in dealing with conventional wisdom everyday.

      2. Oh my gosh – my sister worked with several autistic kids as a special ed aide at a school and what is you say is so true. One of the teachers she worked with was put on administrative leave because she tired to implement a no junk food rule in her class room. Parents lost their minds! Don’t try and take away parents’ “right” to feed kids what they want, by god!! This is ‘merrica! Even if it’s terrible for our kids!

    5. Um…I don’t always trust the village. After all, look at what the village (USDA recommendations) is promoting.

    6. I see a lot of this in my classroom as well. I started with my students last year and looped up with them this year. I practice what I preach and I speak with them regularly about healthy eating and physical fitness- it has actually stuck with the majority of them and they bring relatively healthy snacks. There are still two or three students who consistently bring in hot cheetos or little debbie snacks.

    7. Yes, my elementary age daughter tells me of horrifying lunches she sees made up of doritos, pudding cups, Soda!, etc.

    8. Couldn’t agree more. We insist our PP children (aged 4-5) have fruit every morning break, to the point of having a stock of apples and bananas in the fridge. It’s our second year with these kids so they and their parents are pretty okay with this now. It does smack a bit of the nanny state, but the kids lunches initially came with NOTHING unprocessed at all, and most of it, super high sugar ‘food products’, no nutrition evident. Awful. And autism like behaviours are on the increase, dramatically so. Anyway, at least they are eating one actual food a day, so we’re doing our bit for the village.

    9. When my son was in preschool, parents were required to take turns providing snacks. I would always send carrot sticks or grapes or something like that. Everyone else sent cupcakes and cookies. My snacks were the least popular 🙁

      When I was a kid, we only got one snack, after school. Modern preschools and schools inculcate our children with the idea that frequent sugary snacks are an entitlement.

  2. Another type of bacteria that have received a lot of attention of late in the literature are the so-called “segmented filamentous bacteria”, or SFB’s. These commensal bacteria have profound effects on the gut’s immune system, and they appear to play a role in preventing infections from enteropathogenic bacteria, such as E.coli and Clostridium in young animals and humans. They normally disappear at an early age, but if they persist, can promote autoimmune disease. Further evidence of the delicate balance between the right thing at the right time, and too much of a good thing!

  3. Once again it looks like all roads lead to the gut. It’s hard to stomach what conventional wisdom tries to stuff down our throats.

  4. This is great. I would add that research on other systems shows similar effects on the brain. For example, the heart can be a powerful effector of brainwave activity and also uses the vagus nerve as the primary communicator in the ‘heart-brain’ axis. These systemic relationships make more sense if you step back and understand the ‘brain brain’ as just another component of our bodily functions.

  5. The gut-brain axis leads me to believe that our conscious self is more than just a brain.

    If in some distant future we start to do brain transplants, will we lose part of ourselves if the gut and other organs are not taken as well? Should our entire neurological system, every nerve fiber be considered “the brain”?

    1. What a thought-provoking comment. I have nothing to add other than it made me think of Permutation City which has a similar theme although nothing to do with microbes…

      1. Makes me feel even sorrier for those people who have put their brains in dewars hoping for a revival at some point in the future.

        1. Yes, the bacteria and ENS is part of what makes us who we are, as well as what makes us human. Those people who decapitated themselves and froze their brain (CNS), in the hopes of one day being brought back to life for a chance at immortality, are indeed dead.

          I’ve done extensive research on everything in this article and more. What has been addressed in the article is only the tip of the iceberg. There are many amazing things that Scientists still haven’t pieced together yet. So much so, that I’m writing a book about the research I’m doing and a theory I’ve formulated. Utilizing the theory, I’ve managed to solve health issues etc. with ease.

          I keep hearing and reading about gluten being toxic, so I’m testing that theory out. I believe people who aren’t gluten intolerant possess the bacterial DNA necessary to effectively breakdown gluten. I’m hoping that I’m wrong and that any amount of gluten is bad, because if gluten is indeed all-around toxic then my biological processes will improve unfathomably to the point that it would be considered superhuman. A lot of revolutionary information will be coming out in a year or so allowing Medicine and many other fields to advance by leaps and bounds. However, it is a double-edged sword as there would be major positive/negative economic and social implications if embraced on a mass scale…

        2. Oh, yeah. Science fiction has all sorts of stories about what can happen. You are revived (unlikely) most likely in a society where you know nothing and with no money. And your social attitudes are *way* out of date.

          Anyway taking antibiotics can thus change who you are. Identity is such a fragile notion, mostly a social construct.

    2. I’ve had this thought as well and agree. I think if you were to transfer a brain, without the microbiome of any of the other things affecting it, that you could end up with two very different people. Maybe the “snapshot” of the brain when it’s transferred is the same, but being in a suddenly different environment could have a huge impact right away. If so I wonder what that would feel like. One moment you have this influence on your brain causing anxiety and the next it vanishes, or vice versa.

      1. Well, regardless of the gut-brain axis idea, being put in a new body would undoubtedly change who you are, because your sensory network would be different, your perception of reality would be different.

        1. Right, that’s what I was saying. I had a typo, it should have read “without the microbiome OR any of the other things affecting it”. I imagine the switch over could feel like running into a brick wall. Maybe not, but it’s interesting to think about.

      2. Just make sure you don’t use the brain in the jar marked “Abby Normal.”

      3. That assumes the true origin of consciousness is in the physical body in the first place. But if consciousness survives death, that means although affected by the body while attached to it, it does not need either brain or gut to survive.

    3. Yes! Read Candace Pert’s Molecules of Emotion for further info along this line; she died last year but during the 70s was forefront at discovering how widespread (around our body the brain is). She refers to the body-mind, well worth a read and it links up with the Chinese and Indian understanding of meridians, nadis and chakras. And remember Candance was a western Neuroscientist very much deep in her petri dish!

      1. I’ll add Lipton’s “Biology of Belief” to the suggested reading list. A similar concept to the body-mind connection, but from a biologist’s point of view. It’s a pretty easy and thought provoking read, too.

      2. If the complete neurological system is considered the brain then people will look at the idea of the body-mind with new eyes.

  6. Very interesting! My wife is very type A and prone to stress, anxiety, and mild depression. She also consumes a lot of junk food. Wonder if those symptoms would be reduced/eliminated if we got her gut biome under control….

    1. Good luck – you’ve nothing to lose in trying… except maybe an arm, if she is resistant 😉

    2. They would completely go away if she managed to balance and reinforce her body’s microflora. The operative word being ‘managed’.

      It is near impossible to do without having a firm grasp of the underlying mechanics. A Paleo diet helps dramatically, but it isn’t a panacea.

  7. It appears the way to a man’s heart is the same way to his brain.

  8. What brand/s of probiotic supplement contains L. helveticus R0052 and Bifidobacterium longum R0175?


    1. I am wondering the same thing; I have a probiotic formula from Vitacost called Probiotic 10-20 that has both B. Longum and L. Helveticus in it, but of course does not get as specific as R0052 or R0175, etc.

      I would also love to know what supplement has these….

    2. Jarrow Formulas Jarro-dophilus + Eps contains L. Helveticus R0052

      1. Thanks for the info on Jarrow’s product. The Bifidobacterium longum is a different strain. Anyone know if this really matters?

  9. Interesting that primal/paleo/ancestral nutrition arose into our collective consciousness ahead of the understanding of the role of the gut, and apparently is fully gut-friendly. So we knew ancestral health mattered but really didn’t know why……now we do.

    1. Yes! The philosophy of Ancestral Health makes intuitive sense–which is a “gut reaction.” Maybe those bacteria are nudging us in the right direction?

      1. It’s just cool that we’re circling the wagons back to real science of real human bodies that exist right here/right now instead of “primal/paleo” nutrition-speak.

        1. True that. Especially when one considers the effectiveness of paleo against the fallacy of the evolutionary theory.

  10. It would appear that taking a probiotic would be a smart move. Is there a good one on the market now? So hard to tell from all the competing claims.

    1. I’ve been taking Primal Flora (through this site), figuring they would try to formulate a good one. Also, check out the Cooling Inflammation blog–Dr. Ayers has been talking about this issue and recommending certain strains, not just the milk-based ones.

    2. Richard Nikoley recommends three different brands on his RS starter page. I just recently started taking AOR, and I’m liking the results so far.

      1. I jumped in with both feet and am doing all three: Primal Flora, AOR and Prescript Assist. I take two a day of each, along with my 4 tbsp of plaintain flour and a tsp of psyllium husk.

        I noticed a change in output almost immediately. The farting is finally slowing down as I get more of the good stuff into my gut.

        I am SO glad I found out about resistant starch, soil based organisms and gut biome. Making a major difference in my life.

        1. I actually just ordered some Primal Defense. I think I’m seeing some benefits from the AOR (better sleep, more elaborate dreams, better mood), but it hasn’t been as dramatic as some people seem to be reporting. Maybe the PD will make a difference.

      2. I have been using raw potato starch since January and have recently added cooked and cooled rice and potato. Also, taking a SBO probiotic (soil based) and another gut one with L biffa and Lacto whatever. I also took one that was only L Plantarum recommended for my hand eczema. I feel fabulous–calm, energetic, my aches and pains have receded. I sleep better and my eczema completely disappeared (nothing else seemed to work). It is hard to describe how pleasant I feel–but I do. 65 YO woman. I have been Paleo/Primal for 2 years plus LC and VLC. I t hink it was time for me to add some starch carbs back and Richard Nikoley’s site clued me into the resistant starch at just the right time. The new research is exciting and just what I needed to jumpstart a continued interest and enthusiasm for whole food eating. I am a believer on the gut bug issue!

  11. Love the “second brain” point. This needs to catch on if we want people to start medicating with food instead of artificials for all of the problems in the last point and more.

    1. There’s a relatively new field of research called “neurogastroenterology”.

      However, the Japanese have known for a long, long, long, long time about the connection between the “hara” (belly), and the mind.

      “Haragei” is the “art of the belly”, meaning intuition, instinct, gut-feeling, unspoken communication, mutual understanding, etc. This concept plays an important role in Japanese culture, and is especially evident in martial arts training, in which physically weak hips (belly) translate to a weak mind and a weak will.

      Western culture values logic, reasoning, and critical thinking (higher brain); Japanese culture values instinct and intuition. Valuing both and knowing when to use them is the best scenario of all.

  12. Thank you for including that little box a the beginning of your post. Often I’ll send friends to your site to learn more and they can’t figure out how to navigate to the basic material. PLEASE include that with all future posts. Thanks again for doing that.

  13. It would be great to have some follow-up posts on how to include probiotics to promote a more diverse and healthy gut flora. There are many different strains, and it would be great to get some ideas on how much to take, mixing and matching, etc. Eating fermented foods is simple enough, but when it comes to the supplement form, I feel I’m winging it.

    1. +1 – could definitely do with some specific advice, being in the UK makes it hard to just order primal supplements!

  14. I’m a little confused regarding raw honey and it’s antibacterial properties. Would taking raw honey negate the effects of probiotics? There are other foods like cabbage, lemons,turmeric, that are antibacterial as well. I know this sounds dumb but it would ease my mind to know how foods that promote and kill those little legions in our gut can coexist.

    1. Raw honey loses it’s antibacterial properties when it is diluted with water. Common sense dictates that if you consume it, then it becomes diluted by the stomach acids. What makes it a great antibacterial is it’s pH level. What makes it a great food is that it contains loads of different enzymes and minerals. Something most people do not know is that raw honey also contains… bacteria. One such bacteria is gram-positive and has been identified as being able to produce B12.

      I’m very curious about this specific bacteria and the conditions necessary that would allow it to produce B12. The reason being is that the bacteria can survive the stomach acids, which means it can reach our digestive tract and propagate. What if the right conditions are met in the digestive tract, allowing it to produce… B12? This would mean that honey doesn’t literally contain B12, but it does contain the prerequisite for us to produce B12 in our body naturally on it’s own if the right conditions are met.

      Now, if you desire similar antibacterial properties of raw honey inside your body, consume raw milk. It contains Lactobacillus, which naturally produces minuet amounts of hydrogen peroxide as a defensive mechanism.

      1. Fascinating. Do you still feel that raw honey ingestion might lend itself to our guts producing B12? Is this B12 bioavailable or an analogue version of B12 that gets produced? I couldn’t find any science online that has studied this so I am wondering where you came up with this honey/B12 connection.

    2. I have heard that coconut oil & cinnamon kill the bad bacteria without killing the good, but I don’t know how true that is. Most other foods that have antibacterial properties would kill some of the good bacteria as well as the bad, but not to the same extent that antibiotics do.

      1. I have a a question along the same line: eating to many (cooked?) starches feed the bad bacteria according to the GAPSdiet.
        I would love to take Resistant Starches ‘shortcut’ to rapidly improve my gut bacteria.
        But I hesitate on taking RS while being on this protocol. Because I just don’t know.
        Anyone with knowledge/experience on this topic?

        1. One food I eat is raw unprocessed coconut oil.

          When you cook food, the heat destroys vitamins, nutrients, and bacteria. Do not cook or microwave your food. If you heat up anything, do it under running water that isn’t ‘excessively’ hot.

  15. Eat dirt until fecal transplants are widely available. Dirty is good in so many ways!

    1. Fecal transplantation is already available and takes 5 minutes. The whole blender/ straining system is crazy. You kill off all the good bacteria who die on contact with air. Gloves. Harvest. Place in oral-type syringe (free from pharmacy). Inoculate. Trash. Done. 5 minutes. I first tested this with a dog who had, literally, 30 BM’s a day. Used ‘do’ from my other dog. (Try to leave do as intact as possible, using inside, unexposed part quickly.) next day…..dog started having regular bm’s ONE…about 10 minutes after eating. It made a believer out of me. This has also been done on people with a donor in the house/family for human use. Same exact technique. I know.

  16. Great review, Mark.
    There is no question that our gut bacteria is important for good health. The microbiota can also serve a therapeutic purposes. I have witnessed firsthand remarkable results with fecal microbiota transplant in the treatment of relapsing Clostridium difficile colitis. It will be interesting to see what other applications this therapy is useful for as more research is done.

  17. As someone who contracted Clostridium Difficile (I would NOT wish this disorder on anyone!) from an antibiotic prescription (which decimated my “good” gut flora), I can tell you that I’ve learned much about the gut since then. If you don’t include probiotics in your diet, think about doing so. If you consume sugar, think about eliminating it. The comments about systemic defense and gut-brain interactions in Mark’s article are spot-on. If you want good health, take care of your gut.

  18. I am for the most part primal, i have completely given up wheat and legumes. I am curious, how to build up gut bacteria. I had an autoimmune disease very young. I now have a primary immunodeficiency and get plasma infusions monthly. But before diagnosis, i was on 14 full spectrum antibiotics. i have not been on them for 6 mos now, and i am curious what other people do to repair their guts in conjunction with being primal.

      1. Great information from both of you. Thank you so much, excellent advice.

  19. Watch out for antibiotics as they can can lead to unhealthy gut bacteria along with things like stress and even over training

  20. Every part of our body does something important! Had no idea gut bacteria could play such a big part in depression, anxiety and OCD though. I do tend to be a pessimist, worry a lot and am definitely borderline OCD! I don’t think I have gastrointestinal issues though, but I was bloated for years before switching to keto.

    1. My herbalist said that typically where there is emotional upset there is usually a corresponding yeast over growth. Anger would also be grouped into that group you mentioned of depression, anxiety and OCD.

  21. I recently watched the documentry “Genetic Roulette”. It speaks of the gut bacteria taking on the properties of the BT corn and constantly producing the BT toxin (Bacillus Thuringiensis). Makes sense if gut bacteria can learn from substances it encounters. Another in a million reasons to avoid GMO’s…

  22. I’m working on the comment about 95% of the serotonin being made by gut bacteria. Not to nitpick, but that reference linked above says that the serotonin is made by gut cells, not gut bacteria. I knew SSRIs helped with Irritable Bowel Syndrome but I just assumed it functioned by reducing stress, not by working directly on the gut.

  23. Great topic! It seems that pasteurization and all of the preservatives added to commercial foods can have an significant effect on the gut biome. Do antibiotics fed to factory livestock end up in hamburgers? Does this effect gut flora of those who ingest it? Is it wheat or soy that causes complications or is it the residual glyposate herbicide in these foods that has adversely affected the gut biome? What good bacteria are suppressed by the sulfites, and sorbates in packaged foods and beverages? Perhaps those that crave fermented foods like lactofermented pickles and sauerkraut have a positive mind/gut biorelationship whereas the SAD dieter believes these foods to be rotten. Regardless of the facts, it seems our digestive system and flora performs best with organic foods

    1. “Do antibiotics fed to factory livestock end up in hamburgers? Does this effect gut flora of those who ingest it? Is it wheat or soy that causes complications or is it the residual glyposate herbicide in these foods that has adversely affected the gut biome?”


  24. I recently went to a dermatologist to see what the rash around my mouth was. I was told it was dermatitis and nothing worked to get rid of it except this low-dose antibiotic and topical cream, all for the low, low price of $300.00. I started taking the antibiotic, feeling none too wise, and reading about the relationship between the gut and the skin. I quit taking the antibiotic, (how counter-indicated is that?) and increased my consumption of fermented foods, probiotics and enzymes, and lo and behold, skin rash is gone. I had been using these natural things, then cut back thinking I was cured. I have a long way to go to heal a lifetime of gut abuse. I also came across some interesting information about the tongue, if you can see ridges from your teeth around the perimeter edge, your gut is not absorbing nutrients, and if there are deep crevasses in the center, your gut is not healthy. Who knew. I’m glad to learn more about my friends, the gut bacteria. I want them to be happy.

    1. That happened with my eczema–it completely cleared up after I began RS and probiotics and I have no luck with anything before

  25. So if the gut flora are exchanging genes with the passing foods, etc, and changing themselves – then what’s thebasis for the Caveman/paleo diet that we are stuck in our ancient past? Why shouldn’t we be changing with the newer food versions?

    There must be something hidden well behind a lot of curtains that’s is causing a rise in sensitivity to foods. Not just what we call modernity.

    1. Very interesting questions… I’m thinking it takes a long time to change the guts biome system to this newer poisonous way of eating.

    2. Yes, good question. Shouldn’t our gut bacteria be able to digest wheat gluten by now? Bacteria evolve a lot faster than humans do.

      I think that what’s “hidden behind the curtain” is not so much gluten, as chemicals found in processed foods in general (and bread is a processed food). Our gut bacteria may not know what to do with all these preservatives and chemicals. Also, broad-spectrum antibiotics that disrupt the normal bacterial flora.

    3. The bacteria probably adapt quite quickly, the problem is that our body has to deal with those new kinds of bacteria, the kind that thrive on a diet of sugar, chemicals, and almost no nutrition. The bacteria adapt quickly but the body is not adapted to those kinds of bacteria and the body is much slower to adapt. Sure they apparently found one adaptation in Japanese gut bacteria that seems to be for the good, but how many bacteria adaptations are bad for the body? Even the Japanese are experiencing more and more health problems these days as their diet changes away from what they traditionally ate. And we also don’t know all the details on that seaweed eating bacteria either. Japanese have been eating seaweed for thousands of years, it could have been something passed between the humans instead of gotten directly from the seaweed itself. We don’t know the details yet so it’s a bit early to hang your hat on any of this early research without looking back.

  26. Wow!! I knew that gut bacteria were very important, but I didn’t realize they were quite that important. 20-25 years ago, I became amazed at just how much supplementing with probiotics, feeding yeast, etc., helped to improve pastured beef cattle performance. Then I became interested in probiotic supplementation for humans. Even so, I never dreamed that gut bacteria played that big of a role. God’s creation (His divine design) is so amazing!!! Thanks for the info!

  27. Great summary, Mark. A book I’d recommend on this subject would be Michael D Gershon’s “The Second Brain” where I, too, read about the 95 % of serotonin production going on in the gut.

    1. Seriously…thanks to you and Mark, TaterTot, et al, I’m a gut groupie!

  28. I liked my lunch for today even more after reading this. Hard boiled eggs, sauerkraut (natural fermentation) potato salad (RS city) and some celery. My second brain should be happy….. if not I have some probiotic just in case, oh and of course some 85% chocolate for medicinal purposes.
    I did know about the Depression/Anxiety/OCD connection however, thanks to my fabulous herbalist. I couldn’t stop crying for no reason and she told me to go out and buy some probiotics and take them 4 times a day (five little pills) and by the afternoon that day I felt better and after two days I was all good. That’s when I realized that sugar fed the yeast…. that evil yeast. From then on I tell anyone who will listen to kick the sugar (includes anything that turns into sugar as well) and feed the gut to kill the yeast overgrowth. It works like MAGIC!!!!

  29. Scientific American quotes a neurogastroenterology expert: “The second brain contains some 100 million neurons, more than in either the spinal cord or the peripheral nervous system.”

  30. Fantastic bit of info. I look forward to reading more. I think it’s the coolest thing how the bacteria get used to what we eat (like the seaweed) that really promotes a local food table! I wonder if all our international food trading is causing some issues? Because the gut bacteria keeps changing?

  31. Nice to see this information all compounded into ONE place. I talk about this type of stuff with people all day, and its great to have an easy write-up laying out all the points.

  32. Thanks a million for this Mark. As one who has been living with Parkinson’s for 18 years (and holding up pretty well, thanks in no small part to my real food diet – not quite Primal but close – and 100 % positive outlook) I am very interested indeed to read about this. The site you link to about neurotransmitters and dopamine is fascinating. I have a ‘gut feeling’ this could to something really big.

    1. You might be interested in reading The Wahls Protocol by Dr Terry Wahls… one patient reported significant reversal of Parkinson’s symptoms in six weeks on her protocol.

  33. This is a great post and discussion.

    More research into our understanding of the Microbiome will help us:
    (1) value gut bacteria and take care to strengthen the immune systeam (i.e. less antibiotic use)
    but will also (
    2) force us to re-think / re-consider the Germ Theory!
    https://en.wikipedia.org/wiki/Human_microbiome https://en.wikipedia.org/wiki/Human_microbiome
    “This suggests that medical science may be forced to abandon only one-microbe model of disease, and rather pay attention to the function of a group of microbes that has somehow gone away.”

    Since this is the primary basis for our biological understanding of disease, the foundation to support our vaccination schedule, etc. etc. the transition will not come easy, nor without a painful fight and fall-out from BigPharma and other entrenched industry groups.

  34. I would love to know where to get these bacterias. I can’t wait to meet my asian ideal health-soul-mate to get a stool transplant.

    1. Find an Asian market and get some locally made non-pasteurized kimchi. Or make your own. Napa cabbage, carrot, daikon radish ginger and garlic. The “stool samples” i.e. microflora, are already on the cabbage.

  35. I have heard that eating fermented foods can heal Candida and then I heard that it can cause Candida. Does anyone know the truth to this?

    1. My understanding is that the fermenting bacteria create an acidic environment that the yeast don’t like.

    2. It depends on your initial gut health. When I first started the Autoimmune protocol (Candida is often present in people who have other autoimmune issues), I still consumed mushrooms, dried fruit, fermented foods and things did not improve. I discovered these triggers and my symptoms have improved drastically. But last week I consumed some home made sauerkraut that was still in my fridge and symptoms got a bit worse again. Not as bad as it did before though!
      For good coverage of the subject, read The Hidden Plague by Tara Grant. It is specifically about HS, but even if you don’t suffer from it like me, it is still very useful since this is a protocol more elaborate than AIP.

  36. I have recently started making a conscious effort to enhance gut flora. I include Saurkraut, Kombucha, probiotic supplements and yogurt into the mix and now appears i have oral thrush on my tongue. How could this be if i am supposedly improving my flora?

    1. Depending on the gut health you started with in the effort, it could be that yeast-based probiotics and other yeast-based products hurt you by feeding the wrong bacteria. See also my previous comment.

      1. Now that I think about it: If you increased your egg intake thinking the yolk is a nutritional powerhouse, it could be you increased permeability because of the egg whites. This happened to me and turned mild autoimmune issues into severe issues. I am pretty certain for me it was the egg whites that triggered it, because it was the only thing I changed since it became worse. I now don’t eat any eggs 🙁 only sometimes yolks if I can separate them completely from the whites.

        1. In general I would say: supplement with good pre- and probiotics, but decrease your probiotic food intake. Take L-glutamine supplements and drink lots of high quality bone broth. Supplement with fish oil and eat lots of fatty cold water fish (mackerel, herring, wild salmon). Do not eat any products with yeasts, molds (so no cheese, yoghurt, alcohol, dried fruit, mushrooms, etc.) and DO NOT EAT NIGHTSHADES OR GRAINS. Also, make sure you don’t eat any eggs. You could do yolks, but these are also tricky because even when separated from the whites, there still tend to be some ‘drops’ of whites on the yolk. Apart from the probiotic foods I would say the information on this and other paleo websites paints a nice picture of the do’s and don’ts to increase gut health in severely impaired gut flora (e.g. leafy greens, protein quality)
          But what you would do is very personal. It depends of the severity of your symptoms, your commitment and what you have already figured out about your food/supplement intolerances (I cannot tolerate Vitamine B supplement before 10 AM or probiotic supplement after 9 PM).

          Personally, because of skin issues I also supplement with zinc and Vitamine B and magnesium. Maybe you say manganese in English? I am considering starting calcium and selenium supplementation.
          Make sure you get enough sunlight and eliminate any stress you can. I try to tackle every stress issue separately so I do not need to change everything at once and every time I notice a significant decrease in inflammation in my joints, less bruises and healing more quickly.

          I have been at this pretty strict AIP for 2 months now, and have only started to see skin-related results since 1-2 weeks. My gut area started to feel better after a month. I never knew that was possible, but at some point I noticed the whole digestion process had changed and I also felt more at ease during the day.
          But according to more knowledgeable people (experts and n=1 experimenters), most people notice differences within 1-3 weeks.

          Every 2 weeks I have 1 or 2 days without any supplements. I plan to phase out most of the supplements and I want to start with probiotic foods soon as long as the results keep improving.

          Hope you can work with this… Good luck!

  37. Anyone have any good info on alcohol and gut bacteria? is wine, FE, good or evil for a healthy gut? It is after all fermented fruit juice.

    1. Most commercial wine has sulfites to kill off yeast and bacteria. Bars use sulfites or Campden tablets to clean the lines so if you are sensitive to tap beer and not bottle beer you may have an issues with sulfite based antibiotics.

    2. The GAPSdiet (dedicated to healing your gut and restoring the microbiom) does allow some dry white or red wine and eve a little bit of spirits like wodka.

    1. It wipes it out entirely. Leaves you vulnerable for pathogenic takeover.

      1. Are you saying alcohol wipes out your gut bacteria entirely? Can you cite references for this? If it were true, we’d see a lot of dead young alcoholics but we don’t.

    2. My understanding is that the colonoscopy prep removes the biofilms so the doc can see the intestinal wall, but many gut bugs are still floating around and/or are in the appendix. Haven’t had one yet, but plan to recover with a variety of prebiotics, probiotics, and fermented foods. If I ever get around to scheduling it, that is. I do want to get one because my grandmother died of colon cancer.

  38. Changing your gut bacteria will be a significant factor in treating mental disorders in the future hopefully as I truly believe that a lot of depression/anxiety/schizophrenia is related to an overload of more pathological bacteria in the gut. Not the only cause mind you but certainly a contributing factor.

    Studies in prisons show inmates behave better when fed a healthier diet and this may be due to the change in balance of their gut flora.

    Bacteria may also be the new mind control though as well as shown by this study from Melbourne –


    Patients who underwent a faecal transplant for gastrointestinal issues actually were more likely to vote for more left wing political parties.

  39. I tried the potato starch in small quantities, and it seemed to disturb my sleep in an unpleasant way. The line between waking and sleeping was blurred, my dreams were dreary, mechanical kinds of things (not vivid, kind of like a dull version of reality) because I was directing them, and I woke up tired after sleeps that would usually have been of sufficient duration. I hesitate to try it any more, despite a large container of potato starch sitting on my shelf. I eat plenty of onion, perhaps I’m overdosing on prebiotics when I add the starch.

  40. In terms of gut bacteria forming a “second” brain where brain chatter can be the consensus of many gut bacteria – we have decided that we may agree on this one.

  41. Wonderful post, thank you! I have mood disorders that are difficult to treat – Besides eating fermented foods, is there a way to get more of those specific strains mentioned in point #7, or a fermented food that does such things? Also, what’s a good way to test for all of this? I am still deciding as to whether Genova’s $250 Comprehensible Stool Analysis is worth it… I’d appreciate any replies, this is an important topic to myself as well as everyone 🙂

  42. Also, isn’t it true that serotonin and dopamine can’t cross the blood brain barrier? I can see how the gut microbiome could affect depression and anxiety nonetheless due to its ability to drastically turn down inflammation in the body, but I don’t see how the neurotransmitter production could ever have anything to do with it if the neurotransmitters never reach the brain in the first place.

    1. Neurotransmitters are the ‘messengers’ that ‘travel’ through the nervous system. Since there is a neural gut-brain connection in the Nervus Vagus these neurotransmitters can get to the brain….

      1. But neurotransmitters don’t do much travelling through neurons- their activity takes place in the form of being released in the synaptic cleft and then being reabsorbed. If you think the neurotransmitters are travelling through the vagus nerve, would you mind giving me a link to a study demonstrating this? I would be very interested in reading it.

        1. Oh dear,
          Alexander you’re absolutely right.
          i’ve been giving a reaction to fast. And gave that reaction from my, apparently rusty, knowledge as the nurse that I was 25 years ago ;-P
          Thanks for the correction.
          Indeed , information travels by electric impulses through the nerves and at the synapses the neurotransmitters play a role in transmitting the impulses on.
          I hope I have not misled too many MDA readers.

          But in answer to your original question: I found this:
          and this:
          See item IX and XI on this page.
          They state that serotonine is formed in the brain out of trytophan which get through the blood/brain barrier with the help of a carrier. Most serotonine however is used in the rest of the body.
          Dopamine is formed from tyrosine which is transported through the blood/brain barrier by the same carrier that transports trytophane.

          You would want to study the second link maybe a bit more. It has tons of information on what the neurotransmitters do and where they do it (brain or somewhere else in the body)

  43. Thanks for the great info Mark. I notice that the GAPS diet (Gut And Psychological Syndrome) is virtually identical to Primal except their insistence that fruit be eaten ripe vs. your suggestion to eat unripened bananas. Since both programs have gut health as a goal, I have to wonder who’s correct?

    1. The GAPS diet is a diet that has been implemented for over a decade (and is based on an even older diet). It is not about who’s right or wrong. It is virtually the same as primal but Dr Natasha Campbell-McBride started working with this diet long before the gut-brain connection was common knowledge and all these new research coming out. Changes can and have been made as I’ve read in her replies to FAQ on https://gapsdiet.com/uploads/FAQS_Listing_0114.pdf
      She keeps saying to learn to listen to your body because not everybody is the same and reacts the same to foods.
      I’m wondering myself about the resistant starches though. One of the main things on the GAPS diet is the avoidance of starches. The difference might be in the raw/cooled or cooked versions of the starches. I just don’t know if it would be wise for me, being on the GAPS diet, to take resistant starches
      I’ll put this question in these FAQ

  44. Ordinarily, I refer to Mark’s Daily Apple for scientifically supported content about nutrition. I am very saddened to see the sensationalism in today’s title. As a clinical developmental psycholist, there is simply no evidence that gut bacteria causes autism. While gastrointestinal problems often co-occur, they are not present in everyone. Inferring causality from a mouse model does not mean that translates to the human body. Before we go the way of vaccination scares, please temper your arguments.

  45. I have huge, huge objections to the pat statement in the post above (and Facebook post) that gut bacteria “make us… autistic.”

    It may be that continued research confirms there is a role for humans, and defines the extent of that role along with all the major cofactors (genetic predisposition, epigenetics, etc.)

    But there’s a huge difference between that mouse model showing reduced symptoms, and you saying that bacteria “make us autistic.”

    Being clear in communications like this is critical because the last thing we need is for laypeople to draw some paranoid, sweeping conclusion that you can CATCH autism from people (or schizophrenia, or other mental illnesses which may be partially linked to viruses or bacteria.)

    I really fear that pop-culture terror, and I don’t think it’s farfetched to think that misleading information will encourage that conclusion.

    Just imagine how it’ll go if people start deciding that some innocent kid in their child’s class is somehow a health threat.

    1. I don’t understand how you got “autism is contagious” from the article? The seaweed thing? If so, bit of a stretch…

      1. I don’t think it is; what I’m concerned about is that other people will.

        Don’t you think statements as above that “bacteria make us autistic” could cause people to conclude that “autism is contagious”?

        1. (And yes, it is a stretch. But no more of a stretch than the initial false statement, if you see what I’m saying….)

    2. I think she is making a perfectly valid point given lay-person interpretation that bacteria is often bad (and if it’s not, it is “spreadable”). The overall concept is sound. There is a large interpretive leap from mouse models to human genetic/biological composition. If the cause was this simple, we would have a cure. There is absolutely no strong empirical support (e.g., large effect size) for G&C free diets.The interplay is complex – with perhaps a reduction in maladaptive behaviors due to the pain associated with GI distress and the inability to tell others you are in pain. Sweeping statements such as these are misleading.

      1. Yes they may be misleading but they open the debate for real facts. Look up toxoplasmosis. It is a protozoan infection that has proven to affect behavior.

        1. Yes, I’m familiar with the concept. I don’t need to look it up. Toxoplasmosis has no relevance to the argument I’m making about using scientifically validated findings in your headline article. Again. There are no scientifically validating findings about toxoplasmosis and autism.

  46. I”ve been following the various threads on MDA re resistant starch but haven’t come to grips with the idea that rice (white, brown,…) has such as high glycemic index under normal conditions but then is not digested after being cooled.
    bottom line question: what is the GI of cooled, reheated rice?
    I’d love to eat rice if I knew it was really not an insulin spiker.

    Thanks for any opinions, data on this.

  47. Anyone have an opinion on gut testing/sequencing services (like 23andme for the gut?)

    Thanks in adavance

  48. I agree with the points in this article. See Dr. Mercola’s article, which explains the same things. Moreover, Dr. Mercola gives video instruction on how to ferment your own vegetables. He says that on small serving contains “trillions” of probiotics, which is more than you can get in an entire bottle of (very expensive) probiotics.

    Dr. Mercola’s article contains an interview with Dr. Natasha Campbell-McBride, a Neurologist who covers the topic of gut bacteria and its relationship to auto-immune and other disorders. Very interesting!

  49. So I have a question. For those that have gone on an elimination diet, who found that during the reintroduction/food challenge phase that their bodies are now reacting to food that they were not before, could this be caused by a change in gut bacteria vs a food intolerance? A friend of mine (veterinarian & behaviorist) and I were discussing this, and the same question had crossed my mind earlier (research psychologist). If so, that would mean you could build back up a tolerance by slowly re-introducing a food you now reacted to that you did not in the past. Of course then comes the question of what was causing leaky gut in the first place. Once healed, I know some food can be reintroduced. But if a food caused leaky gut in the first place, how would one know and avoid said food?

  50. So, on the phytate issue, am I concluding correctly that we should eat phytate rich foods, which are often out on a paleo diet (except nuts) to increase that bacteria? Does anyone knkow yet how long it takes? or if there is too much damage done along the way to make it worth it? It seems it would be valuable to give young children these foods (and possibly at least some gluten and dairy protein) to build up the right bacteria in them.

  51. This is exactly what I needed to read. I’ve been concerned about phytic acid lately, but now it seems I can relax a little. I find it fascinating how bacteria can transfer genes. That explains a lot about what causes some people to be sensitive to certain foods while others aren’t.

  52. I truly truly believe that the gut is the second brain, which is why I load up on probiotics and digestive enzymes! I have to baby the rest of the gut that I do have (I don’t have a large intestine)

  53. Mark, your post contains several factual errors, which you really should correct for the benefit of your readers, such as:

    1. gut bacteria (better known as sh*t) do NOT constitute a “second brain”

    2. they do NOT produce “tons of neurotransmitters”

    3. the article linked as a supposed reference to these erroneous statements speaks about the enteric nervous system, which indeed is often called “a second brain” and which in fact does produce the neurotransmitters you mention.

    Also, to be well-rounded, your post should at least mention that even the ‘beneficial’ the bacteria in the gut produce various toxins that get absorbed into the bloodstream and must be promptly neutralized by the liver; and if the liver can’t cope with those toxins, for whatever reason, the results range from mild dullness and ‘brain fog’ to delirium and all the way to coma.

    In fact, your confusion of the enteric nervous system with the gut flora suggests that a good purge, to clear the gut from bacteria and its toxic effects on the brain, is in order. Do that and enjoy the clarity of the mind 🙂

  54. I do struggle with OCD tendencies. What would be recommended to help the gut biome in relation to OCD?

    1. OCD can be the result of mineral deficiencies such as zinc & magnesium. If supplementing with zinc & magnesium, it is always a good idea to also take a multivitamin & mineral with them to provide the co-factors to help with their absorption & to not to deplete other competing minerals. However, correcting the gut biome would help you to absorb the minerals better from your food.

      1. I’m still very young, so I’m reluctant to rely on supplements and want to try and get most of nutrition from food if I can. What are good sources of zinc & mg? I know shellfish is a good source of zinc, if I’m not mistaken.

        1. That’s very wise. Below is a link to some very good information about zinc, which lists the amount of zinc in foods and explains how certain circumstances may increase your requirements for zinc e.g. infections, stress etc and how gastrointestinal problems can impair the ability to absorb zinc from foods. For example, more than half of people with an inflammatory bowel disorder called Crohn’s disease have evidence of zinc deficiency. https://www.whfoods.com/genpage.php?tname=nutrient&dbid=115

          Here also is the link about magnesium https://www.whfoods.com/genpage.php?tname=nutrient&dbid=75

      2. Hmm, it seems after beef & lamb, seeds like sesame and pumpkin are the highest in zinc and magnesium, but should I be careful to consume seeds in moderation due to omega 6 and phytic acid? Beef is quite expensive for me, and seeds would be easier…

        1. Well yes you would need to be careful due to omega 6 & phytic acid. You could try to balance out the omega 6 with lots of omega 3 from fish & grass fed meat or chia seeds or flax seeds. We do probably need more omega 6 than 3 & most experts agree that the omega 6:3 ratio should range from 1:1 to 5:1. However, most people eat between 20 to 50:1 which is why it is recommended to keep the omega 6 down & increase the omega 3. So it is important to get the ratio between the 2 right, but equally important, is not to have too much of either of them. Pumpkin & sesame seeds do actually contain a little omega 3, but it has to be changed by the body into a more usable form & they do contain a lot more omega 6 than 3.

          To reduce the negative effects of phytic acid, it would be best to soak or sprout them first.

          Pumpkin seeds are actually a very healthy food (One-quarter cup of pumpkin seeds contains nearly half of the recommended daily amount of magnesium & one ounce contains more than 2 mg of zinc.) They also contain trytophan to help with sleep.

          However, I believe it is best to eat a large variety of foods & everything in moderation, so if you could include lots of the ‘good’ sources of zinc & magnesium (see the 2nd chart) that should help. There are lots of vegetables listed.

          Another thing which would help, would be to optimise the gut bacteria, so that you actually digest everything you eat. Gut bacteria should help with the phytic acid as well.

          Also, try to keep your stress levels down, as stress dramatically increases your requirement for zinc. This includes getting adequate sleep, as lack of sleep puts a stress on the body.

  55. Down here in Australia our family subscribe to a PB diet having followed a ‘failsafe’ approach to our eating for a number of years. Check out the testimonials at http://www.fedup.com.au

  56. I’ve had digestive issues along with terrible anxiety. Endoscopy revealed, ulcer, hiatal hernia, and gastritis, so I was prescribed Prilosec. I still feel nauseous all day and have stomach pain. My question is: Is should I be taking the inositol powder? I had quit because I thought it was making my diarrhea worse. I also have diverticulosis.

  57. Fascinating stuff.
    I want to know all about how gut bacteria affects the mind. Since I started learning about it and read that we can actually get some bacteria in our brain that kind of controls us (like toxoplasma gondii) my interest in the human microbiome has greatly increased.
    I support the hypothesis that our gut is kind of like a second brain. Sometimes I get “gut feelings” that seem like dire warnings from some ESP source or certain bits of undeniable information and if I ignore them or shrug them off as temporary anxiety bad things tend to happen. Other times I get seemingly random urges or notions that when followed really help me out.

  58. Speaking of gut health, how do you feel about digestive enzyme supplentation, Mark? Helpful ? Harmful? Types n amounts ? Thanks !

  59. “They nullify anti-nutrients.” … wait… if the minerals that are being made inaccessible by phytic acid are being (or not being) absorbed in stomach, then how do the gut bacteria help, when they’re further in the wagon?

  60. Hi,
    You mention that the gut bacterial manufacture the neurotransmitters and link to an article that talks about how the Gut Brain produces them. From my research I find that the Enteric Nervous System’s neurons produce the neurotransmitters, and the gut bacteria produce several B vitamins, Vitamin K, Pantothenic acid, several enzymes, etc.. but I can’t find where they actually produce neurotransmitters. Although it is confusing because many of the articles I have found become vague when discussing “gut health”.. I’m understanding that there are 2 parts. The Enteric nervous system made of nerves, neurons, all that physical stuff similar to the Central nervous system – and then there is the whole colony of bacteria that work along with and help the nervous system, along with the rest of our systems to be healthy.

    Let me know if you have found any articles more specific.

    Love gut health! I’m speaking about it tomorrow and found your site doing research for my talk.


  61. Many valid points however many of us have mercury fillings. The leaching mercury kills good bacteria and we know the rest. Mercury is like taking an antibiotic daily until the mercury fillings are removed.