Marks Daily Apple
Serving up health and fitness insights (daily, of course) with a side of irreverence.
23 Apr

7 Things You Had No Idea Gut Bacteria Could Do

BacteriaIf 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?

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Imagine you’re George Clooney. Take a moment to admire your grooming and wit. Okay, now imagine someone walks up to you and asks, “What’s your name?” You say, “I’m George Clooney.” Or maybe you say, “I’m the Clooninator!” You don’t say “I’m George of George Clooney Sells Movies Blog” and you certainly don’t say, “I’m Clooney Weight Loss Plan”. So while spam is technically meat, it ain’t anywhere near Primal. Please nickname yourself something your friends would call you.

  1. I just started on the resistant starch bandwagon and was a little skeptical at first. I really believe it has helped with my digestion issues.

    NOLA Paleo (new orleans) wrote on April 23rd, 2014
  2. 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….

    SEModiste wrote on April 23rd, 2014
    • Further evidence they’re trying to kill us off–now at a younger age!

      Wenchypoo wrote on April 23rd, 2014
    • 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… :/

      meg wrote on April 23rd, 2014
    • 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!!

      LCDR USN Ret wrote on April 23rd, 2014
      • 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.

        George wrote on April 23rd, 2014
        • “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.

          Paleo Bon Rurgundy wrote on April 24th, 2014
      • True, except not every child has two parents and many parents are uneducated in these matters.

        Lara wrote on April 23rd, 2014
        • 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?

          Zach rusk wrote on April 23rd, 2014
      • Amen!

        Lucylu wrote on April 23rd, 2014
        • 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.

          Jane P wrote on April 23rd, 2014
        • 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.

          Eva wrote on April 23rd, 2014
      • 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!

        Geoff wrote on April 24th, 2014
        • 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!

          Pip wrote on April 28th, 2014
    • 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.

      Roger Bird wrote on April 23rd, 2014
      • 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.

        Paul wrote on April 23rd, 2014
      • 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!

        KariVery wrote on April 23rd, 2014
    • Um…I don’t always trust the village. After all, look at what the village (USDA recommendations) is promoting.

      Mike wrote on April 23rd, 2014
    • 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.

      Cori wrote on April 23rd, 2014
    • Yes, my elementary age daughter tells me of horrifying lunches she sees made up of doritos, pudding cups, Soda!, etc.

      Colleen wrote on April 23rd, 2014
    • 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.

      Westie wrote on April 23rd, 2014
    • 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.

      cavenewt wrote on July 15th, 2014
  3. 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!

    Smileyprimaljulie wrote on April 23rd, 2014
  4. 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.

    Nocona wrote on April 23rd, 2014
    • Ha!

      Yasmine wrote on April 23rd, 2014
    • It’ll take me a little time to digest that pun.

      Tom wrote on April 24th, 2014
  5. 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.

    Sandeep wrote on April 23rd, 2014
  6. 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”?

    C L Deards wrote on April 23rd, 2014
    • 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…

      Tim wrote on April 23rd, 2014
      • 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.

        C L Deards wrote on April 23rd, 2014
        • 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…

          Scott Finley wrote on April 23rd, 2014
        • 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.

          WalterB wrote on May 2nd, 2014
    • 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.

      Rob wrote on April 23rd, 2014
      • 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.

        C L Deards wrote on April 23rd, 2014
        • 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.

          Rob wrote on April 24th, 2014
      • Just make sure you don’t use the brain in the jar marked “Abby Normal.”

        KariVery wrote on April 23rd, 2014
      • 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.

        Eva wrote on April 23rd, 2014
    • 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!

      Kelda wrote on April 23rd, 2014
      • 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.

        Paul wrote on April 23rd, 2014
      • If the complete neurological system is considered the brain then people will look at the idea of the body-mind with new eyes.

        C L Deards wrote on April 23rd, 2014
  7. 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….

    Jacob wrote on April 23rd, 2014
    • Good luck – you’ve nothing to lose in trying… except maybe an arm, if she is resistant 😉

      Westie wrote on April 23rd, 2014
    • 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.

      Scott Finley wrote on April 23rd, 2014
  8. It appears the way to a man’s heart is the same way to his brain.

    Cliff wrote on April 23rd, 2014
    • LMAO!

      Eva wrote on April 23rd, 2014
  9. What brand/s of probiotic supplement contains L. helveticus R0052 and Bifidobacterium longum R0175?


    barb wrote on April 23rd, 2014
    • 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….

      Joyce wrote on April 23rd, 2014
    • Jarrow Formulas Jarro-dophilus + Eps contains L. Helveticus R0052

      Ellen C wrote on April 23rd, 2014
      • thanks; I wonder if the strain really makes a difference?

        Joyce wrote on April 23rd, 2014
      • Thanks for the info on Jarrow’s product. The Bifidobacterium longum is a different strain. Anyone know if this really matters?

        Paleo Sapien wrote on April 23rd, 2014
  10. 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.

    John D wrote on April 23rd, 2014
    • Yes! The philosophy of Ancestral Health makes intuitive sense–which is a “gut reaction.” Maybe those bacteria are nudging us in the right direction?

      Tom B-D wrote on April 23rd, 2014
      • 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.

        John D wrote on April 23rd, 2014
        • True that. Especially when one considers the effectiveness of paleo against the fallacy of the evolutionary theory.

          James wrote on April 23rd, 2014
  11. 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.

    KK wrote on April 23rd, 2014
    • 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.

      Tom B-D wrote on April 23rd, 2014
    • I add kefir everyday to my Primal Fuel smoothie.

      eatsleepswim wrote on April 23rd, 2014
    • 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.

      Yasmine wrote on April 23rd, 2014
      • 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.

        Beth wrote on April 23rd, 2014
        • Ditto, potato starch twice a day has made a massive difference to me.

          Kelda wrote on April 23rd, 2014
        • What is AOR? thanks!

          Joyce wrote on April 23rd, 2014
        • Joyce,

          This is the article I was referring. AOR Probiotic 3 is one of three probiotics Richard (and Dr. Grace) recommends.

          Yasmine wrote on April 23rd, 2014
        • 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.

          Yasmine wrote on April 23rd, 2014
      • 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!

        Janet wrote on April 24th, 2014
  12. This post is inspiring me to get a scoby and start up my kombucha factory again!

    Lauren wrote on April 23rd, 2014
  13. 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.

    Dr. Anthony Gustin wrote on April 23rd, 2014
    • 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.

      SumoFit wrote on April 23rd, 2014
  14. 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.

    sean wrote on April 23rd, 2014
  15. 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.

    Debbie wrote on April 23rd, 2014
    • +1 – could definitely do with some specific advice, being in the UK makes it hard to just order primal supplements!

      Pip wrote on April 28th, 2014
  16. 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.

    victor wrote on April 23rd, 2014
    • 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.

      Scott Finley wrote on April 23rd, 2014
      • 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.

        Michelle Choi wrote on September 9th, 2015
    • 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.

      Christine wrote on April 24th, 2014
      • 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?

        Helene de Winter wrote on April 24th, 2014
        • 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.

          Scott Finley wrote on April 24th, 2014
  17. It took guts to write this!

    Dashui wrote on April 23rd, 2014
  18. Eat dirt until fecal transplants are widely available. Dirty is good in so many ways!

    John Campbell wrote on April 23rd, 2014
    • 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… 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.

      Marilyn greenwold wrote on May 22nd, 2016
  19. 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.

    Tom wrote on April 23rd, 2014
  20. 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.

    Bear wrote on April 23rd, 2014
  21. 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.

    Pat wrote on April 23rd, 2014
  22. Watch out for antibiotics as they can can lead to unhealthy gut bacteria along with things like stress and even over training

    jamie wrote on April 23rd, 2014
  23. 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.

    Gym Queen wrote on April 23rd, 2014
    • 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.

      2Rae wrote on April 23rd, 2014
  24. 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…

    Cindy wrote on April 23rd, 2014
  25. 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.

    Cliff wrote on April 23rd, 2014
  26. 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

    jack lea mason wrote on April 23rd, 2014
    • “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?”


      cavenewt wrote on July 15th, 2014
  27. Mark great article, question for you.

    First, I obviously want a more health gut now! Would you still consider the two articles below the best recommendations for protecting and promoting gut health?

    Perhaps a definitive guide is coming soon?

    Luke wrote on April 23rd, 2014
  28. 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.

    Wendy wrote on April 23rd, 2014
    • That happened with my eczema–it completely cleared up after I began RS and probiotics and I have no luck with anything before

      Janet wrote on April 24th, 2014
  29. 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.

    tom LI wrote on April 23rd, 2014
    • Very interesting questions… I’m thinking it takes a long time to change the guts biome system to this newer poisonous way of eating.

      Nocona wrote on April 23rd, 2014
    • 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.

      meepster wrote on April 23rd, 2014
    • 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.

      Eva wrote on April 23rd, 2014
  30. 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!

    TJ wrote on April 23rd, 2014
    • Agreed!

      Allison wrote on April 23rd, 2014
  31. 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.

    Gitte wrote on April 23rd, 2014
  32. Just fantastic.

    Richard Nikoley wrote on April 23rd, 2014
    • Seriously…thanks to you and Mark, TaterTot, et al, I’m a gut groupie!

      Energy! wrote on April 23rd, 2014
  33. 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!!!!

    2Rae wrote on April 23rd, 2014
  34. 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.”

    SumoFit wrote on April 23rd, 2014
  35. 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?

    Allison wrote on April 23rd, 2014
  36. Time for a cup of that sauerkraut brine that is fermenting in the shelf downstairs 😛

    Primal_alex wrote on April 23rd, 2014
  37. 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.

    Dr. Joseph DelGrosso wrote on April 23rd, 2014
  38. 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.

    NorfolkAndy wrote on April 23rd, 2014
    • 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.

      framistat wrote on April 23rd, 2014
      • Thanks!

        NorfolkAndy wrote on April 25th, 2014
  39. 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!
    “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.

    Elizabeth wrote on April 23rd, 2014
  40. 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.

    Nathalie wrote on April 23rd, 2014
    • 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.

      jack lea mason wrote on April 23rd, 2014

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