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Let me introduce myself. My name is Mark Sisson. I’m 63 years young. I live and work in Malibu, California. In a past life I was a professional marathoner and triathlete. Now my life goal is to help 100 million people get healthy. I started this blog in 2006 to empower people to take full responsibility for their own health and enjoyment of life by investigating, discussing, and critically rethinking everything we’ve assumed to be true about health and wellness...

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April 23, 2014

7 Things You Had No Idea Gut Bacteria Could Do

By Mark Sisson
178 Comments

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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178 Comments on "7 Things You Had No Idea Gut Bacteria Could Do"

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NOLA Paleo (new orleans)
2 years 5 months ago

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.

SEModiste
SEModiste
2 years 5 months ago

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….

Wenchypoo
Wenchypoo
2 years 5 months ago

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

meg
2 years 5 months ago

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… :/

LCDR USN Ret
LCDR USN Ret
2 years 5 months ago

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!!

George
George
2 years 5 months ago
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… Read more »
Paleo Bon Rurgundy
2 years 5 months ago
“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… Read more »
Lara
Lara
2 years 5 months ago

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

Zach rusk
2 years 5 months ago

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?

Lucylu
Lucylu
2 years 5 months ago

Amen!

Jane P
Jane P
2 years 5 months ago

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.

Eva
Eva
2 years 5 months ago
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… Read more »
Geoff
Geoff
2 years 5 months ago
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… Read more »
Pip
Pip
2 years 5 months ago

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!

Roger Bird
Roger Bird
2 years 5 months ago

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.

Paul
Paul
2 years 5 months ago

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.

KariVery
KariVery
2 years 5 months ago

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!

Mike
Mike
2 years 5 months ago

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

Cori
2 years 5 months ago

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.

Colleen
Colleen
2 years 5 months ago

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

Westie
Westie
2 years 5 months ago
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… Read more »
cavenewt
cavenewt
2 years 2 months ago

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.

Smileyprimaljulie
Smileyprimaljulie
2 years 5 months ago

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!

Nocona
Nocona
2 years 5 months ago

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.

Yasmine
Yasmine
2 years 5 months ago

Ha!

Tom
Tom
2 years 5 months ago

It’ll take me a little time to digest that pun.

Sandeep
Sandeep
2 years 5 months ago

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.

C L Deards
2 years 5 months ago

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”?

Tim
Tim
2 years 5 months ago

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…

C L Deards
2 years 5 months ago

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.

Scott Finley
Scott Finley
2 years 5 months ago
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… Read more »
WalterB
WalterB
2 years 4 months ago

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.

Rob
2 years 5 months ago

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.

C L Deards
2 years 5 months ago

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.

Rob
2 years 5 months ago

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.

KariVery
KariVery
2 years 5 months ago

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

Eva
Eva
2 years 5 months ago

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.

Kelda
2 years 5 months ago

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!

Paul
Paul
2 years 5 months ago

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.

C L Deards
2 years 5 months ago

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

Jacob
Jacob
2 years 5 months ago

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….

Westie
Westie
2 years 5 months ago

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

Scott Finley
Scott Finley
2 years 5 months ago

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.

Cliff
Cliff
2 years 5 months ago

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

Eva
Eva
2 years 5 months ago

LMAO!

barb
barb
2 years 5 months ago

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

tx

Joyce
Joyce
2 years 5 months ago

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….

Ellen C
Ellen C
2 years 5 months ago

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

Joyce
Joyce
2 years 5 months ago

thanks; I wonder if the strain really makes a difference?

Paleo Sapien
Paleo Sapien
2 years 5 months ago

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

John D
John D
2 years 5 months ago

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.

Tom B-D
Tom B-D
2 years 5 months ago

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

John D
John D
2 years 5 months ago

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.

James
James
2 years 5 months ago

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

KK
KK
2 years 5 months ago

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.

Tom B-D
Tom B-D
2 years 5 months ago

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.

eatsleepswim
eatsleepswim
2 years 5 months ago

I add kefir everyday to my Primal Fuel smoothie.

Yasmine
Yasmine
2 years 5 months ago

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.

Beth
Beth
2 years 5 months ago

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.

Kelda
2 years 5 months ago

Ditto, potato starch twice a day has made a massive difference to me.

Joyce
Joyce
2 years 5 months ago

What is AOR? thanks!

Yasmine
Yasmine
2 years 5 months ago

Joyce,
http://freetheanimal.com/2013/12/resistant-primer-newbies.html
This is the article I was referring. AOR Probiotic 3 is one of three probiotics Richard (and Dr. Grace) recommends.

Yasmine
Yasmine
2 years 5 months ago

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.

Janet
Janet
2 years 5 months ago
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… Read more »
Lauren
2 years 5 months ago

This post is inspiring me to get a scoby and start up my kombucha factory again!

Dr. Anthony Gustin
2 years 5 months ago

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.

SumoFit
2 years 5 months ago
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… Read more »
sean
sean
2 years 5 months ago

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.

Debbie
Debbie
2 years 5 months ago

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.

Pip
Pip
2 years 5 months ago

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

victor
victor
2 years 5 months ago

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.

Scott Finley
Scott Finley
2 years 5 months ago
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.… Read more »
Michelle Choi
Michelle Choi
1 year 20 days ago

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.

Christine
Christine
2 years 5 months ago

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.

Helene de Winter
2 years 5 months ago

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?

Scott Finley
Scott Finley
2 years 5 months ago

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.

Dashui
Dashui
2 years 5 months ago

It took guts to write this!

John Campbell
John Campbell
2 years 5 months ago

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

Marilyn greenwold
Marilyn greenwold
4 months 7 days ago
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… Read more »
Tom
2 years 5 months ago

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.

Bear
Bear
2 years 5 months ago

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.

Pat
Pat
2 years 5 months ago

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.

Tanya
Tanya
2 years 5 months ago

Check out Chris Kresser’s article on what to do for your gut after taking antibiotics. http://chriskresser.com/what-to-do-if-you-need-to-take-antibiotics My family’s finding it useful even though it’s been a long time since any of us have had antibiotics.

framistat
framistat
2 years 5 months ago
Pat
Pat
2 years 5 months ago

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

jamie
2 years 5 months ago

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

Gym Queen
2 years 5 months ago

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.

2Rae
2Rae
2 years 5 months ago

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.

Cindy
2 years 5 months ago

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…

Cliff
Cliff
2 years 5 months ago

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.

jack lea mason
jack lea mason
2 years 5 months ago
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… Read more »
cavenewt
cavenewt
2 years 2 months ago

“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?”

Yes.

Luke
2 years 5 months ago

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?

http://www.marksdailyapple.com/gut-flora-healthy-immune-system/#axzz2zjGKC41u
http://www.marksdailyapple.com/prebiotics/#axzz2zjGKC41u

Perhaps a definitive guide is coming soon?

Wendy
Wendy
2 years 5 months ago
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… Read more »
Janet
Janet
2 years 5 months ago

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

tom LI
tom LI
2 years 5 months ago

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.

Nocona
Nocona
2 years 5 months ago

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

meepster
meepster
2 years 5 months ago

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.

Eva
Eva
2 years 5 months ago
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… Read more »
TJ
2 years 5 months ago

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!

Allison
Allison
2 years 5 months ago

Agreed!

Gitte
Gitte
2 years 5 months ago

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.

Richard Nikoley
2 years 5 months ago

Just fantastic.

Energy!
Energy!
2 years 5 months ago

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

2Rae
2Rae
2 years 5 months ago
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… Read more »
SumoFit
2 years 5 months ago

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.”

Allison
Allison
2 years 5 months ago

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?

Primal_alex
2 years 5 months ago

Time for a cup of that sauerkraut brine that is fermenting in the shelf downstairs 😛

Dr. Joseph DelGrosso
2 years 5 months ago

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.

NorfolkAndy
NorfolkAndy
2 years 5 months ago

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.

framistat
framistat
2 years 5 months ago

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.

NorfolkAndy
NorfolkAndy
2 years 5 months ago

Thanks!

Elizabeth
2 years 5 months ago
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! i.e.: http://en.wikipedia.org/wiki/Human_microbiome http://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… Read more »
Nathalie
Nathalie
2 years 5 months ago

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.

jack lea mason
jack lea mason
2 years 5 months ago

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.

Scott
Scott
2 years 5 months ago

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?

Energy!
Energy!
2 years 5 months ago

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

Simone
Simone
2 years 5 months ago
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… Read more »
Scott
Scott
2 years 5 months ago

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?

Simone
Simone
2 years 5 months ago

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.

Simone
Simone
2 years 5 months ago

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.

Scott
Scott
2 years 5 months ago

Simone , What would you do to get the good flora?

Simone
Simone
2 years 5 months ago
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… Read more »
Fredrick Hahn
2 years 5 months ago

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.

jack lea mason
jack lea mason
2 years 5 months ago

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.

Fredrick Hahn
2 years 5 months ago

Is there scientific evidence that sulfites kill gut bacteria?

Helene de Winter
2 years 5 months ago

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.

David
David
2 years 5 months ago

There are a few websites I follow daily. This one of course. This site and articles have me always wondering when I read of ailments if gut biology is involved. Another site I read daily posted this: http://www.lastwordonnothing.com/2014/04/23/guest-post-pt-1-why-are-doctors-skeptical-unhelpful-about-chronic-fatigue-syndrome/ . I wouldn’t be surprised if CFS doesn’t have a component associated to the patients intestinal biome.

Kristine
Kristine
2 years 5 months ago

What effect might a colonoscopy have on the gut flora?

Bear
Bear
2 years 5 months ago

I personally have believed there IS an impact, but the National Institutes of Health say there isn’t…take your pick:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641102/

Ellen C
Ellen C
2 years 5 months ago

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

Fredrick Hahn
2 years 5 months ago

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.

Ellen C
Ellen C
2 years 5 months ago

what?

Energy!
Energy!
2 years 5 months ago

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.

No Harmacy
No Harmacy
2 years 5 months ago
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 – http://www.gastroenterologyupdate.com.au/latest-news/fmt-may-induce-change-in-political-beliefs-study Patients who underwent a faecal… Read more »
Craig Johnson
Craig Johnson
2 years 5 months ago

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.

Ellen C
Ellen C
2 years 5 months ago

Are you taking a SBO (soil based organism) with the starch?

Storm
Storm
2 years 5 months ago

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.

Jason Caridi
Jason Caridi
2 years 5 months ago

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 🙂

framistat
framistat
2 years 5 months ago

There is a list of soil based probiotic supplements in one of the links I provided earlier… here it is again:

http://drbganimalpharm.blogspot.com/2013/11/how-to-cure-sibo-small-intestinal-bowel_16.html

Shawn
Shawn
2 years 5 months ago

So, the Bible could be a product of bacteria?

Mark S
Mark S
2 years 5 months ago

Huh?

Animanarchy
Animanarchy
2 years 3 months ago

Really? I guess it could.
Holy sh1t eh.

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