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In the human gut and mouth, two other domains of microbial life are involved in human physiology.   Archaea and Eukaryotic fungi and possibly protozoa, likely play an as-yet-undetermined role in optimal health maintenance. The human mouth and gut are a teeming microbial cauldron of life, which covers such intimate vital tissues, like our teeth and gut that remain exposed to our current environment.  No longer can a human being be viewed as simply an individual produced from a diploid genome  from its parents germ cells (Mom and Dad).  Throughout the last 15 years, paradigm-shifting studies have shown the how gut microbial metabolism can truly alter human health and disease states.  Today we will discuss how pregnancy and obesity are very closely related but yet different because of the hormone surges that each present with in humans.  That hormone difference is all that separates a normal physiologic state (pregnancy) from a neolithic disease state (obesity). Because of this new knowledge, I now recognize that modern man is a cyborg like “superorganism” colonized with a huge variety of microbial life that can positively and negatively alter the course of health and well-being.  Understanding the anatomy or the physiology in textbooks often just falls short of the entire story of human metabolism.  It is complex and is tied to modern epigenetics, and this ultimately determines “our look and body composition.”


Many of you know I believe obesity if an inflammatory disease of the brain.  Where this disease begins may surprise some of you.  It begins in our eyes and gut flora.  How does this happen?  Read this link!  Sub optimal bacteria which contain bacterial toxins called lipopolysaccharides (LPS) which are found in bacterial cell membranes. As gut LPS rises, it has been shown to cause a rise in serum leptin levels.  Once leptin levels are raised high enough it stimulates SOCS 3 signaling in the hypothalamus to cause LR.  The overweight seem to physiologically ‘guard’ their elevated weight once it has transpired. In many mammal models of diet-induced obesity, leptin resistance is seen initially at and within the signaling though the vagal afferents into the area postrema.  This blunts the actions of satiety incretin hormones centrally, and causes low brain dopamine levels.  These things, along with the gastrointestinal bacterial-triggered SOCS3 signaling, are all implicated in the etiology of human obesity. In humans, dietary fat and fructose elevate systemic lipopolysaccharide, while dietary glucose also strongly activates SOCS3 signaling.  Protein seems immune to this signaling of SOCS3 and it is why protein and AM light exposure of the eye are keys to reversal in my Leptin Rx.

This information implies that the gut flora can directly induce leptin resistance and be a cause of obesity. Gut bacterial LPS also raises blood levels of triglycerides as do simply refined dietary sugars and industrial seed oils found in most western diets.  Both of these things are the modern principal causes of leptin resistance at the blood-brain barrier near the hypothalamus.  It is also clearly established that eating a diet high in refined carbohydrates with or without a combo of industrial seed oils “simplifies the gut flora” in both species and in shear numbers, and these changes selects out for bacteria that cause inflammation at the blood brain barrier by increasing SOCS3 signaling.

NON GEEKS: Low numbers and amounts of bacteria happen to people who eat lots of processed foods and industrial seed oils.   This leads to constipation and hard stools like we see in grade 1 and 2 of the Bristol Stool Chart.

So far in the Brain Gut series we have focused mostly on the brain side of this equation.  Today we begin to work a bit on the other side of the equation were the gut is located.  We are going to talk about the gut microflora.  The key frontier questions now for scientists and clinicians are to figure out what is the purpose of the gut microflora?  In Brain Gut one and two, I make the case, that the gut microflora is our casino dealer who shuffles the deck of genes that we collect from viruses.  It also appears that the gut microflora helps in presenting these viral components to the immune system and they are neutralized and made less virulent so that we can carry their spare parts in our genome to use at a later date when we see fit based upon our genomic and epigenomic needs.

These viral genes are ‘humans junk yard’ for new gene creation.  We learned from Barbara McClintock’s work that these collected genes are then purposefully and systematically inserted into parts of genome where we have the most genomic or epigenomic needs based upon the stresses the organism faces in its current environment.  The human body is roughly made up of one trillion cells.  The latest number science gives us about the numbers of bacteria in our gut now is close to 100 trillion! Just a few years ago we thought this number was ten trillion cells. This means we have 100 times as many bacteria in our own guts that we do in our body.  What might this imply?  When you are on a process of discovery you always want to ask really good questions and try to avoid old answers with dead ends.  So todays blog asks this question, “What is the purpose of the gut microflora in humans?”  It is a loaded question for sure, but let us explore it.

When we consider the non-digestive microbiota benefits, they can be broadly segregated into two large areas:

1. gut homeostasis

2. immune system education.

What is becoming clear to clinicians and scientist alike now, is that human beings are truly a cyborg like creatures.  Our genome and things that make us humans unique are made up from large amounts of retrotransposons from viruses and the bacteria in our gut truly take this concept to a new level as we explored in Brain Gut 2.  We technically are “super-organisms.”  As a result of this co-evolution, our guts shortened in length from our immediate ancestors, and our gut bacteria ecology became quite complex, to offset the change in length to facilitate the dietary changes we saw in the East Rift zone to make a human brain. These evolutionary moves also dramatically also improved our immune system’s ability to present antigens to our cellular immunity arm to better protect us from the ecology that the transitional apes found themselves in.  We explored this in Brain Gut 5 in some detail.  The immune system had to undergo great expansion because of how we evolved using viruses and bacteria as our path to our humanness.  By once again harnessing the power of diversity of bacteria from our vertebrate ancestors with in our own guts,  it allowed us to digest more new food sources that we used to fuel the blueprint to build a human brain.  This diet is called the Epi paleo Rx.

While 99{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of the adult gut microbiota is dominated by two bacterial phyla Bacteroides and Firmicutes, a full-term infant who is breast-fed,  has a radically different gut microbiota from adults which is dominated by Bifidobacterium species along with Lactobacillus species for the first few months of post natal life.  This persists until solid food ingestion begins and a transition to a normal adult microbiota occurs.  Moreover, the human microbiota also evolves as we age as well.

Recent studies have shown that delivery type (Cesarean versus vaginal), birth weight, breast feeding, and diet all influence which gut microbes colonize the sterile newborn gut.  This implies that the early colonization window of an infant is environment-dependent (epigenetic) rather than host-dependent action in humans.

Moreover, this gut microbial plasticity is quite temporary because shortly after birth, at approximately 100-300 days,  most of the infant’s gut microbiota transforms to a more adult-like composition mentioned above.


All along the gastrointestinal tract, there is a distinct gradient of immune tissue type, chemical acidity, and a specific rate of transit that controls the microbiota composition. I consider the GI tract as a “monopoly board” where some places are very different like the Boardwalk and Oriental Avenue properties found in the board game.  I have recently began to mention this in many of my educational consults I have done recently.  For example, in the stomach, Proteobacteria dominate, but in the distal gut (colon), Firmicutes and Bacteroides, which are barely detectable in the upper GI tract, become the dominant super organisms in a normal gut. This transition is very likely epigenetically and host-mediated (by antimicrobial peptide production).  The precise physiologic and immunologic mechanisms which control these compositional changes have not yet been delineated by modern science, but we now know this happens in health and in disease states.

The microbiota composition, in the distal gut at least, is probably evolutionarily ancient,  given the dominance of Bacteroides and Firmicutes amongst all mammals studied so far to date by science.  This implies it is a highly conserved finding in the mammalian clade for an evolutionary reason.  The parasympathetic nervous system controls the connections between the gut and the brain in humans.  On each end of this conduit are two specialized membranes to control the optimal health milieu of both the gut and the brain at all times.  The policeman of this system is the vagus nerve.  In humans, the distal gut is also not innervated by the vagus nerve which is the tenth cranial nerve.  The remainder of the gut is innervated by this nerve.  This means the distal gut has no direct conduit to the brain.  This is why most neolithic disease happens in this area.  This is a direct connection of the gut to the brain in 90{a7b724a0454d92c70890dedf5ec22a026af4df067c7b55aa6009b4d34d5da3c6} of its length.  The fact that most neolithic diseases occur in this uncovered gut real estate by this cranial nerve seems to imply that the brain directly is involved with monitoring the gut microbiotic mix in health.

I mentioned earlier in this series that I believe their has been a massive co-evolution of the gut microbiota with the host immune system.  I believe this arrangement has allowed the host physiology to become optimized for survival of some bacterial lineages over others, but no direct scientific evidence for this effect has yet been presented as far as I know of today.  The findings we have found today in the lab in humans are now strongly pointing in this direction.

Microbiota and Progesterone:

The bacterial survival issue also appears to be carried directly over to reproductive fitness too in humans.  Women’s gut microbe populations change as pregnancy advances, becoming more like those of people who might develop diabetes.  It now appears there is a special microbiota for pregnant women that develops during the first 5 months of pregnancy to allow them to put on massive amounts of weight without developing diabetes in a normal pregnancy.  The reason they do not appear to develop diabetes is because during pregnancy their progesterone levels are massively raised (by their placenta if it is functioning well)  while their cortisol levels stay flat to decreased.  This is true of most normal pregnancies, but today in the modern world due to the older age of women at conception,  now infertility issues and obesity are skyrocketing and as a result those switches no longer work well.  Many obese, infertile, and older women have low progesterone and high cortisol’s before they get pregnant and this radically alters the gut flora to favor an obeseogenic status as their pregnancy progresses.  This is why we often see gestational diabetes develop in these women with low progesterone levels as their fetus gets larger.

Morevover, if you go back and re read point 12 in Brain Gut 5 you will see another hormone, called E3 or estriol, has a massive affect on the gut microbiota. This diminishes the risk or cancer development both to the fetus and to the mother’s breast.  This is precisely how epigenetics has direct actions on a fetus and mom.


In pregnant women overall, the diversity of their gut bacteria declines between the first and third trimesters.  Simultaneously there is a massive change in species.   Certain types, such as the Proteobacteria and Actinobacteria, are increased dramatically from pre-pregnancy to pregnancy states.   The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera.  Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic.

These species, ironically,  are also more common in people who are obese or have metabolic syndrome associated with T2D. Proteobacteria in particular are often the bad guys in research studies checking stool samples of pregnant women. They are associated with inflammation, elevated cytokines and lowering of DHEA and progesterone further.  They also are implicated in causing leptin resistance.  This also allows for even higher cortisol levels to develop quickly.  Remember what I told you in the Hormone 101 blog post about high cortisol levels?  A high cortisol level can not be sustained forever and eventually adrenal fatigue is the end result.  Go re-read the blog to understand what is happening both in a suboptimal pregnancy and in obesity.

Dr. Kjersti Aagaard, an OB/GYN from Baylor University, published some data comparing vaginal microbiomes in pregnant and non-pregnant women; those in the pregnant women were dominated by Lactobacillus species, which are thought to prevent the growth of harmful bacteria and help aid human digestion.  Many probiotics are loaded with these bacteria but in too few a dose to make a ton of immediate help in a diseased state without the help of higher progesterone and lower cortisol levels.  The ideal way to have both of these situations is to have an optimal hormone panel that pays strict attention to circadian light and dietary signals.

Furthermore the research also shows that the process is reversible after birth.  It appears the shifts in microbial diversity did not affect mothers’ health during pregnancy.  What it did show is that their stools  (PCR analysis) collected during the third trimester contained more inflammatory markers than those collected during the first trimester.
These trends held firm thoughout whether or not the women were of normal weight or overweight before falling pregnant, had actually developed diabetes, or had taken antibiotics or probiotics (supplements taken to provide or boost populations of ‘healthy’ bacteria) during pregnancy. Meanwhile, after birth, the children’s microbiota’s resembled those of the mothers’ first trimester samples.  This implies the status of mom’s gut health and pre pregnancy and her hormone panels are of primary importance to the developing fetal brain.  In my opinion, this link best explains why we are seeing record increases in autism and spectrum disorders today.  I don’t believe that vaccines are the major issue in spectrum disorders as some do.  I believe hormone changes in the mother prenatally are to blame.  This is due to sub optimal circadian biology  (artificial light, EMF’s, and diet) which cause subsequent changes to the gut microflora pre-pregnancy are of primary importance in these epigenetic diseases.  This also implies it is reversible and can be made optimal before a child is conceived if the mother decides to become proactive and understands how much power her decisions truly yield in forming an optimal brain for her child.

When researchers transplanted gut bacteria from stool samples into mice that had been raised under sterile conditions, they found that mice receiving microbiota from third-trimester samples became fatter and insulin resistant than mice that were given first-trimester samples.  This was not a surprising result to me because there is quite a bit of information in the literature today that obesity has its own inherent gut microbiota that is highly inflammatory and blocks normal gut signals and eventually leptin at the blood brain barrier.

The reality appears today that that the microbiome is a contributing factor to this change.  Some of us believe that it maybe the driving force behind it completely.  It may be that obesity is due to a change in signaling between the gut microbiome and the leptin receptor in the brain.  The link is both ingenious and fascinating and of course how it ties the hormone panels together is something that modern medicine remains quite blind too.  You no longer should be blind to this link.  It maybe the critical first link in reducing your risk for obesity.  CT helps destroy inflammation while increasing energy expenditure and it too changes your gut flora.

It appears in pregnancy direct hormone surges dramatically alter the gut microbiota, and these changes give you the changes in metabolism to foster massive growth of the body and brain of a fetus.  This implies that food and hormones are cut from the same cloth with regards to physiology.  This eerily sounds like the quote I made in Brain Gut 5.  It said, “Think of food as hormone information, not as a metabolic fuel. Think of the Epi-paleo template as human jet fuel for the human nervous system.”

Here is another piece of the QUILT in how the gut and brain are married and dance a beautiful dance together when circadian biology is optimally matched.

You should mind your gut health and it might help you repair your hormones and all this can help heal an adult ‘bad brain’ or one that is forming your own uterus right now!




1. Nonaka et al. Effects of LPS on leptin transport across the BBB. Brain Res. 2010 July 1016 (1):58-65







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  1. shilohman August 5, 2012 at 3:59 pm - Reply

    Dr K, thanks for this enlightening blog. This explains why after increasing my fish consumption of raw fish I 1) became constipated for two days 2) after eating my stomach/digestive track just felt different. Is there any way to quantify this improved gut flora from the Epi-paleo diet? Obviously hormone panels should be improved after a while, but other than observational results are there any tests that can show an improvement in the gut flora?

  2. John Sorrentino August 5, 2012 at 4:04 pm - Reply

    These links aren’t embedded, Jack.
    Here is another link in how the gut and brain are married and dance a beautiful dance together when circadian biology is optimally matched.

    You should mind your gut health and it might help you repair your hormones and all this can help heal an adult ‘bad brain’ or one that is forming your own uterus right now!

  3. Jack August 5, 2012 at 4:05 pm - Reply

    @shilohman There are……hormone panels are one way but doing a metametrix PCR array is another on the gut flora. There are now several companies offering PCR arrays of stool…….to see what the clinical affect is. The implications of my blog today are that if the gut really has a sectional microflora……doing a stool sample PCR may not be a great actionable test clinically. I personally think this will be the biggest area of medicine and labs transformation in the next 25 yrs. The technology has to improve to catch up with our knowledge.

  4. Jack August 5, 2012 at 4:07 pm - Reply

    @JS it was not meant to be linked……the word link was used in it correct sense. I changed the phrasing to make it clear.

  5. Lee August 5, 2012 at 4:14 pm - Reply

    I feel like this was written just for me. I weighed 95 lbs when I got pregnant the second time. Circadian wasn’t allowed to exist. Ironically, I stepped on the scales after delivery and I weighed my normal 119. We have a condition that needs treated like diabetes. Low blood sugar all the time is a mandate. Its nice to know that it may be possible to recreate a better gut flora. It would be nice to lose the bad guys.

    • Jack August 5, 2012 at 4:22 pm - Reply

      @Lee this is now an epidemic problem for pregnant women because women born post 1977 are now having kids. This is when artificial light and a modern diet collided in unison……and when all neolithic disease generation just explode in a few decades. The reason is simple. The fix is more complex as modern man is finding out now 40 yrs later.

  6. Kristin Graffin August 5, 2012 at 5:29 pm - Reply

    Would it be accurate to say then that the use of antibiotics has a direct effect on cortisol levels because they destroy the gut flora balance? Even in a non-obese, non-T2D individual? Would the antibiotics used for SIBO have the same effect? In the case of SIBO, would eating the Epi-Paleo RX provide for a quicker recovery from the antibiotic use?

    • Jack August 5, 2012 at 5:34 pm - Reply

      @Kristin ABx have massive effects on microflora. Some can last months.

  7. Kristin Graffin August 5, 2012 at 5:54 pm - Reply

    What is the best way to recover the microflora after treating SIBO with antibiotics?

  8. Jack August 5, 2012 at 6:17 pm - Reply

    @Kristin depends upon many factors and honestly this is the kind of loaded question we face in educational consults.

  9. Jack August 5, 2012 at 6:17 pm - Reply

    @Jimbo Regarding your autism question on BG 5 and BG 7. Read this:

  10. will boyden August 5, 2012 at 7:02 pm - Reply

    Jack, Just what the doctor ordered.I had some digestive issues, but I think eating the epipaleo diet was improving it. I don’t think digestive enzymes are the answer. Your media interview with Kim Greenwood was superb , a little pre epi-paleo but it did capture the essence of your ideas, including the natural circadian life-style. Will

  11. Melinda Fairchild August 5, 2012 at 9:06 pm - Reply

    My husband is having a minor break in his ankle scoped and repaired tomorrow. I noticed they plan on giving him antibiotics before hand…I think that is standard practice…is that how you still roll? The lower shelf in my refrig is loaded with home fermented veggies, I hope to rebuild his gut flora asap.

    • Jack August 6, 2012 at 6:05 am - Reply

      @Melinda I would have done somethings differently if I was your hubby ten days prior to surgery to avoid the Abx. Now the only thing he can do is CT. Post op he needs to consider increasing his vitamin D3, CT, and use Kevita probiotic drinks daily and use a good probiotic for 8 weeks post op.

  12. chewingthefat August 5, 2012 at 10:09 pm - Reply

    Might it be wise to pay more attention to the strains of bacteria in our probiotics during different stages in our lives, as opposed to mindlessly popping the generic probiotic? Do we do more harm than good with some strains?

    • Jack August 6, 2012 at 6:06 am - Reply

      @Chewingthefat we are not sure yet but based upon what we know today it appears you might be correct.

  13. coldbren August 5, 2012 at 10:48 pm - Reply

    Thank you so much for another incredible blog post. I have been buying GT’s Organic Kombucha lately and I really like it. Is there any problem with drinking LOTS of this?

    • Jack August 6, 2012 at 6:06 am - Reply

      @Cold bren no there is not.

  14. Jonathan Swaringen August 5, 2012 at 11:50 pm - Reply

    @Melinda I’m guessing Jack would use CT instead….just a guess though.

  15. Vicky Melissas August 6, 2012 at 12:11 am - Reply

    Thanks for the post Doctor!

  16. JanSz August 6, 2012 at 7:47 am - Reply

    Might it be wise to pay more attention to the strains of bacteria in our probiotics during different stages in our lives,
    as opposed to mindlessly popping the generic probiotic? Do we do more harm than good with some strains?
    we are not sure yet but based upon what we know today it appears you might be correct.
    When we are restoring our hormones, the goal often is to aim at the desirable levels of 20yo Adonis or Aphrodite.
    When I (72yo man) come across Adonis, should not I think in terms of fecal transplant possibility?
    How to asses if the contemplated donor is suitable?
    Him/her following epi-paleo diet and life style, would be on the list. What else?
    Are there male/female diferences to be considered, what kind?


    • Jack August 6, 2012 at 8:05 am - Reply

      @Jansz we already know that fecal transplant is the gold standard in c. dif refractory cases. I have my own hunch the indications will grow. I think we will find out there is a microbiota that is sexually dimorphic because the two major whole body energy receptors are also sexually dimorphic, that being leptin and adiponectin.

  17. wally courie August 6, 2012 at 7:54 am - Reply

    dagnabit Jack, u r supposed 2 b on vacation, b/ thanks for another informative post!

    Everybody thinks the Caucus mountain people live long lives b/c of the yogurt/yoghurt they culture, b/ actually it is KEFIR. Kefir is more complicated than yogurt involving a yeast complex as well as bacteria. Have read somewhere that whereas yogurt repopulates gut bacteria, kefir actually colonizes the gut.

    I was making a ton of kefir during the winter, straining it thru coffe filters to make kefir cream cheese, then drinking the kefir whey. then i learned about the A1/A2 milk casein stuff and cut back the dairy.

    One a sidenote, i wish i could get my wife to give up splenda sweetened crap. i understand gut bacteria take up splenda thinking it’s good food, they can’t digest it, and there’s a massive die off. I guess they come back- b/ it certainly can’t be good 4 u.

    Thanks again- now get back in the water.

  18. MJ August 6, 2012 at 8:03 am - Reply

    Wow this really puts the responsibility on the moms…all young pregnant women should be aware of the role their diet and sleep patterns play in the development of their newborns! Good thing I didn’t own a computer or cell phone during my pregnancies! For people who are not fully epi-paleo, or at all, do they need to be taking a probiotic daily?

    • Jack August 6, 2012 at 8:07 am - Reply

      @MJ it depends upon their pre natal state of health or their state of health now. Most people in the western world have a poor gut flora because their epigenetics is terrible. If that is bad their gut flora is also sub optimal. This leads to a poor hormone panel. If your hormone panel is off you can bet your behind your gut flora is bad too. It is the giant circle of life.

  19. will boyden August 6, 2012 at 8:08 am - Reply

    Jack, 15 years should be at least doubled. Listen to what they call music. It’s mindless tuneless dribble (including churchiana) that could only be enjoyed by a brain that does not appreciate beauty. I wouldn’t mind that much but they are imposing it on me. Name me a popular modern song! The same applies to TV. there is very little worth watching for a reasonable brain..Will

  20. MJ August 6, 2012 at 8:25 am - Reply

    Makes sense…and ok, if mine come out bad, we fix one thing at a time!

  21. jonny h August 6, 2012 at 8:52 am - Reply

    Hi, I can get raw milk from a local farm that has a Guernsey herd, so I assume it is A2 milk from what I’ve read.
    If it is A2 milk, would that be ok to use for making kefir?

    • Jack August 6, 2012 at 9:29 am - Reply

      @Jonnyh your call……Me……I follow what is in Brain Gut 6.

  22. Jonathan Swaringen August 6, 2012 at 9:21 am - Reply

    @jonny h The only way you can know for sure is if they test…I think. I’m not sure if all Guernseys are A2….but I’ve heard most are.

    I think it should be ok…It would help if you normally have issues with milk to test…if you normally have issues and drink it and it doesn’t cause issues I would think that means its different.

  23. Jonathan Swaringen August 6, 2012 at 9:38 am - Reply

    So Kevita is water kefir…I was thinking this but after looking at their page its definitely water kefir.

    They are saying that they use their own proprietary culture basically which may have a different combination of bacteria and yeasts than the kefir grains I have.

    I wonder what the differences are…if I were to guess my kefir grains are different than other peoples kefir grains too…I’m curious if mine are actually inferior to the ones the company uses or not.

    Its interesting to say the least though. I’ll probably drink some Kevita too as they have flavors..and I haven’t gotten making flavors I like down yet.

    Are there any Kevita flavors we should stay away from due to too much sugar? Or should we just make sure to drink it with a meal?

  24. wally courie August 6, 2012 at 9:42 am - Reply

    i guess the cheapest A2 test is how your body’s rxn 2 it per jonathan’s comment above. i guess A1 cassein raises your inflammation levels- i can’t remember right now- and that would be measured subjectivly by how u feel and objectively by a c reactive protein test? i gotta get one done, they’re only $45 or so.

  25. Jonathan Swaringen August 6, 2012 at 9:43 am - Reply

    @jonny h
    2. All US dairy (including raw US dairy) because of the A1 casein problem and its tie to BCM-7 and its massive link to Hashimoto’s and disease. Hashimoto’s in not a static disease but a dynamic one. This means you must pay attention to your thyroid panels and AB’s as you evolve through your life too. One can use French or New Zealand dairy products if you can source them.

    So if your labs tell you its effecting you negatively don’t continue drinking…my thoughts. If everything feels fine and labs don’t seem to be a problem than it should be good.

  26. klellja August 6, 2012 at 9:49 am - Reply

    Is it possible to restore a “friendly” gut flora (I mean bacteria that promote good health) in someone with flora damaged EARLY in life? Like babies acquiring bad flora from their parents or taking lots of ABx or being operated -everything that destroys gut flora

    I see people dealing with candida and other stuffs like this -all tied to a bad flora status- for years and it seems to be an endless fight. It’s depressing.

    • Jack August 6, 2012 at 10:06 am - Reply

      @Klellja I believe so.

  27. jonny h August 6, 2012 at 10:16 am - Reply

    Thanks for replies regarding the milk, I’ve never had any issues with milk, my latest blood test for CRP was below 1.
    I’m from the UK, I have emailed the farm to ask wether they have tested their herd/milk.
    Thanks again.

  28. Chris M. August 6, 2012 at 10:53 am - Reply

    @ Dr. Kruse — you say “and use a good probiotic for 8 weeks…” — any brand or strain which you prefer above the rest?



  29. SCRN2007 August 6, 2012 at 12:05 pm - Reply

    Thank you Dr. Kruse! Your “inflammatory brain condition” phrase is much more clear now. I feel like this was written for me, but I know better. No doubt thousands of us female 30-somethings are now seeing the results of our light-cycle abuse (and ensuing cortisol issues), antibiotic use, and carb addiction in ourselves and our children. I have long thought it obvious that the vaccines are not the immediate cause of the autism spectrum disorders (if they were, then all kids would develop ASDs from vaccines); rather, it seems that vaccines are a “last straw” or at least a “big straw” for some kids who where teetering on the edge of a cliff due to horrific gut dysbiosis passed on to them by their light-cycle abusing, antibiotic using, carb-addict, hormonally deranged moms. At least this seems to fit what has happened with my child and to also explain why GAPS helped so much.

    However, I do think your answer is superior to GAPS. I have seen resolution of nagging neurological problems in my child by removing fermented dairy, legumes, nightshades, and eggs from my child’s GAPS fare. Who would have though that green beans could make a child stutter and speak as though they had a stroke, or have balance and coordination issues? Who would have thought that removing eggs would give the child the social empathy they seemed to lack in 4 days time(!)? Thank you for pointing me to the Paleo Answer and Cordain’s work on foods and autoimmunity! Thank you for this site! You have no doubt saved my child’s brain from further attack and helped me put my child on a path to further healing.

    Is there anything to be said about why particular parts of the brain seem to be more suceptible to this sort of damage than others in some children? For example, if my child were full-blown autistic, a savant label definitely would have applied, even on the worst day–my child, at age 2.5, can sit down and accurately read my medical textbooks (and your blog) aloud, sounding out the 4+ syllable words, and has a photographic and audiographic memory. Even before GAPS, when there was lots of stimming, tantrums, extremely poor coordination, and hyperactivity, my child could read well and remember.

    Is the GI Affects test appropriate for such children, or is it normed to adults (based upon your comment about normal flora changing through the life cycle)?

    Am I incorrect in assuming that goitrogens would be a bad choice for such children to eat, given that Cordain says that folks with an HLA/autoimmune genotype are those most likely to develop autoimmune diseases as a result of their exposed and therefore extra promiscuous human epithelial growth factor receptors? I assume the inference as to genotype would be safe to make in the case of a child in whom green beans cause serious neurological symptoms? If I am correct to assume that goitrogens would not be a good choice for such children, where would one draw the line? Eliminate all goitrogens; monitor intake of goitrogens (i.e., x times per week) and boil and drain before eating; cut out or limit the lactofermented sauerkraut which is supposed to be so healing to normal folk (Masterjohn says that the fermentation makes the cabbage more goitrogenic); or so forth? I just wonder how far it should be taken, especially in light of how well Dr. Wahl’s diet worked for the autoimmune disease MS, even though it seemed to include lots of raw broccoli and kale (gasp!). Are some of the goitrogens (as identified by Braverman and others) worse than others?

    • Jack August 6, 2012 at 12:25 pm - Reply

      @SCRN I thought you’d like this before you consult…… has huge implications for you. I would avoid all goitrogens if I were you. Terry AI disease has unique features……..and there is a very specific reason the raw stuff worked for her.

      This is not the first time I have used this term……..look at the pic in this link from my TEDx talk:

  30. Caroline Cooper August 6, 2012 at 1:44 pm - Reply

    Hi Dr Kruse,

    From your clinical work, how does cold thermogenesis change gut flora?

    • Jack August 6, 2012 at 3:02 pm - Reply

      @Caroline……it reduced the inflammatory species in my own stool samples. This signified to me a more diverse and complex flora. If you read the cites on PCR analysis on this blog you might understand how it works.

  31. golooraam August 6, 2012 at 11:47 pm - Reply

    hmm, combining this with what I learned in your last blog post – going to add fermented food to my meals

    dinner tomorrow of mussels will included a probiotic dill pickle 🙂

    • Jack August 7, 2012 at 6:31 am - Reply

      @Golooram that would be wise.

  32. Glamazon August 7, 2012 at 6:14 am - Reply
    • Jack August 7, 2012 at 6:35 am - Reply

      @Glamazon all that matters is that we get the message out.

  33. Marijke August 7, 2012 at 6:25 am - Reply

    In the second alinea on gut real estate: “In humans, the distal gut is also not innervated by the vagus nerve which is the tenth cranial nerve.”

    Is the word not intended here?

    • Jack August 7, 2012 at 6:38 am - Reply

      @Marijke no, the paragraph is correct.

  34. Marijke August 7, 2012 at 7:25 am - Reply

    I see. So I must take special care of my colon.

  35. Jack August 7, 2012 at 7:54 am - Reply

    @Maijke yes indeed. This is why colon cancer rose from 1900 being the 37th cause of cancer to number 2 in 2012. That is an amazing rise in 112 yrs all due to modern life and diets.

  36. Jack August 7, 2012 at 7:56 am - Reply

    @Vickie: Adiposity Index of you microbiota can be tested in a GI test:
    Firmicutes should be < = 80 Bacteroidetes >= 20
    The Adiposity Index is derived by using DNA probes (PCR) that detect multiple genera of the phyla Firmicutes and Bacteroidetes. Abnormalities of these phyla may be associated
    with increased caloric extraction from food and cause us to gain weight. This is just another reason a Calorie in never equals a calorie out.

  37. Zorica Vuletic August 7, 2012 at 10:50 am - Reply

    Is being able to eat less (but epi-paleo foods) and feeling full a sign of good nutrient absorption? This is in the presence of taking a pro-biotic with bifido bacteria and acidophilus (24 million straing) that also has FOS in ingredients, in addition with the myco(sp?) boulardi and bovine colostrum?

    I feel that I get full faster now…so don’t know if it’s the seafood/fish, the pro-biotic and/or the colostrum? I’m really hoping this means my gut is being repaired! 🙂

    I use bacon, eggs, fish of all types (skin and bones), scallops (raw and cooked), oysters (raw and smoked), etc. Olive oil, coconut oil, butter…but just all way less quantities now.

    • Jack August 7, 2012 at 11:25 am - Reply

      @Zorica 1. It is a good sign…..but not a perfect indicator. 24 million in a flora of 100 trillion is what I call tinkling in the lake………and saying you raise the level of the lake……not likely a big effect.

  38. Zorica Vuletic August 7, 2012 at 10:54 am - Reply

    I also wonder about basal temperature. Mine is on average around 36.2-3. Sometimes that seems ‘low’ or ‘slow metabolism’? But I wonder if it might mean metabolic efficiency since I don’t feel ‘cold’. I will see through out the month on this to see if I am better on the Optimal track.

    I also notice that sometimes people with higher basal temperature can still feel cold even if they’re warmer in body temp….also sometimes I see this precedes a person gaining weight and/or hormonal difficulties.

    The reason why I’m confused is b/c ‘they’ say about average temp being 37’C and/or 98.6’F.

    Thanks again!

    • Jack August 7, 2012 at 11:26 am - Reply

      @Zorica Sign of a low T3 level or an elevated RT3. Consider testing.

  39. Zorica Vuletic August 7, 2012 at 11:26 am - Reply

    …and the standard veggies (was implied).

  40. Zorica Vuletic August 7, 2012 at 11:27 am - Reply

    OK thanks. Damn. Thought I was making progress…sigh. My skin seems so smooth and glowing and redness in face gone…

  41. Zorica Vuletic August 7, 2012 at 11:33 am - Reply

    Can I double up on the pro-biotic for now until it runs out and I will get a stronger straing next time? If it’s a low amount…will taking more capsules equal a higher billion strain? Does it work like that? A week or so ago, I took like 8 capsules of the 24 billion strain, hoping it would be more ‘boosting’ mega dose.

    • Jack August 7, 2012 at 11:47 am - Reply

      @Zorica 48 million to 100 trillion? Do the math………50 billion is low…….low is low. Consider eating real organic foods with dirt upon them…….way better choice.

  42. Zorica Vuletic August 7, 2012 at 11:48 am - Reply

    Oops sorry. Read the trillion wrong. OK. Will do. Thanks.

  43. Zorica Vuletic August 7, 2012 at 12:13 pm - Reply

    I’m not sure the difference getting tested would be, since the interventions would likely be the same: higher pro-biotic strain intake, organic food w/ dirt, seafood etc. I suppose this way is more shooting in the dark…but if the intervention remains the same in both cases…and maybe over time would self-correct.

    I wouldn’t be surprised if it’s somehow auto-immune based on other life patterns/symptoms. I am pretty sure I lost some hearing from some kind of infection I had last Fall. I let it slide, didn’t do anything about it…DUMB! (My body temp was sure higher then ‘not from measuring, but sweating etc. was indicator…and for a time ears were on fire’ etc.). I did not know of this website at that time though.

    Sorry…I just really thought I was making a good progress!! I am silly sometimes about health even though I say I’m serious about health…I make little sense sometimes. *slaps face*

  44. Dali Dula August 8, 2012 at 7:43 am - Reply

    During my consult you suggested I get a Dexascan. You must have seen something in my labs that was a red flag. I got the scan yesterday. I have osteopenia of the spine. You are scary good at this Jack. The forearm and the hip were fine, but the value on the spine are L1 -1.8, L2 -1.5, L3 -1.6,L4 -1.4 Is this a condition that may improve with wellness? What else does this tell you? Thanks again.

    • Jack August 8, 2012 at 7:49 am - Reply

      @Dali Dula depends upon the context… could but it may take some time……if your patient and continue to eat like a champ OK. If you want a reversal of fortune there are things one can do.

  45. Dali Dula August 8, 2012 at 11:49 am - Reply

    Thanks Jack, we’ll tackle that at next consult with fresh labs.

  46. Susan Moles August 8, 2012 at 5:44 pm - Reply


    I am on a very limited income and am doing everything I can to combat my osteopenia. I have been eating a LC/Primal diet the past 3 1/2 years, and I have recently foregone dairy. I walk regularly for 2-4 miles on flats and hills. Recently picked up some kettle bells, and I take all the recommended supplements (including bumped up K2 to 15 mg a day, and I am not sure that is enough to really help but it is all I can afford). My question is about coffee. Does caffeine really effect bone terribly if I only have a couple of 10 oz. cups a day? I don’t really mind being thought of as the “fanatical health nut” in my neighborhood, but I do like to enjoy coffee now and again when I do get the chance to be neighborly (actually I really like coffee anytime!).

    Thanks in advance if you should reply 🙂

    Susan M.

    • Jack August 8, 2012 at 8:09 pm - Reply

      @Susan Moles I would drop the coffee then.

  47. Lauren August 9, 2012 at 1:47 pm - Reply

    Dr K, when my husband was a teenager he had emergency surgery for a burst appendix. During that surgery they did a bowel resection. How does this sort of bowel surgery affect gut flora? Thanks.

    • Jack August 9, 2012 at 2:09 pm - Reply

      @Lauren it sure does.

  48. Andre van Staveren August 10, 2012 at 1:20 pm - Reply

    Dr Kruse,

    Could there be an evolutionary benefit to having a part of the colon not ‘monitored’ by the brain? Seems like everything has a reason.

    • Jack August 10, 2012 at 3:01 pm - Reply

      @ Andre I think you might be right.

  49. Jack August 11, 2012 at 7:51 am - Reply

    @Sandi I would disregard what you heard on the twitter feed about IBD/UC from AHS12. I don’t believe in calling out my patients with that disease by calling them “JERKS” for how they eat. Sometimes years of not knowing (often because the doctors never told them) what was wrong causes a change in gut flora and in the hormone response. Blaming a patient for not knowing this is a very “Ivory Tower” thing for a person to do.

  50. Zorica Vuletic August 11, 2012 at 8:05 am - Reply

    Good words, Jack! That is the mentality today. Here’s another annoying mentality.

    So people will then try to ‘brag’ about having ‘good genes’ where they can ‘eat whatever they want’ and not be sick, or fat. They brag and brag…these are the same people that end up blaming those for being sick…frustrating. But they also are like, “Ew, glad I’m not like THAT person…o thank GOD…”. This is because they know of the judgement. This is deranged mentality, something I am far from now.

    I think epi-paleo is the best solution ever!! It’s much better than regular Paleo because it provides that extra ‘mile’ that even Paleo couldn’t solve.

    Always, thanks!

    • Jack August 11, 2012 at 10:51 am - Reply

      @Zorica This sounds like the crowd mentality of some faction of this community. They seem to think if you eat Paleo that is all it takes……..Epic Wrong idea.

      Here is my FB wall Quote from today from one of my good friends who is at AHS 2012.

      Many people, especially the ignorant ones, want to punish you for speaking the truth for being correct, for being who you are. Never apologize for being who you are, for being light years ahead of your time. If you are right and you know it, speak your mind. Even if you are a minority of one, the truth remains the truth. Mahatma Ghandhi

      The people who heard Terry Wahl’s, and Dr. Kuiper’s lectures at AHS 2012 best pay attention. They talked about Homo’s Sapiens solution……not a book Rx for the SAD.

  51. Lee August 11, 2012 at 1:03 pm - Reply

    @69 maybe its a standby uterus

  52. wally courie August 15, 2012 at 6:39 pm - Reply

    i want to sure i got it nailed. It is ok to eat moderate fruit & sweet potaters in North Carolina or TN b/n april 15 and sep 15?

    yesterday was a weird day. i started mixing my metformin. Regular and Extended release to let one act as a bolus and the other as a basal. i usually take two 500 mg metformins in the morning w/ a smidgen (a very tiny amount) of glipizide. i take the glip to stay under a 100. i may just cut it out entirely. Anyway the regular metformin pill is round and so is the glipize. i must have taken a 10mg glip by mistake. i went hypoglycemic 3 separate times in one day. i was on the road and ate 10 banans, 4 cholcolate bars, a package of fresh raspberries. i was soaking wet and trembling. bad hypo. i used to carry a box of raisins and keep a few glucose pills in the car b/ i got out of the habit.

    def not paleo or epi-paleo yesterday. i hadn’t had a banana or bar of chocolate (even tho i put dark choc powder in my coffee w/ coconut oil) in over a year.
    “Metformin has an oral bioavailability of 50–60% under fasting conditions, and is absorbed slowly.[82][99] Peak plasma concentrations (Cmax) are reached within one to three hours of taking immediate-release metformin and four to eight hours with extended-release formulations.[”

  53. Kami August 21, 2012 at 8:36 am - Reply

    1. Will fixing gut and hormones fix the glucose response?

    2. Or would cycloset help get the job done faster?

    • Jack August 21, 2012 at 11:37 am - Reply

      @Kami 1. maybe
      2. maybe…….discuss it with your doctor.

  54. Souldanzer August 22, 2012 at 10:09 pm - Reply

    “Think of food as hormone information, not as a metabolic fuel. Think of the Epi-paleo template as human jet fuel for the human nervous system.”

    That quote just keeps reverberating in my mind ever since the first time I heard it in BG 5. Every time I eat, every time I shop for food, every time I work in my garden it comes into my mind. It makes some choices very simple. It wiped out a whole lot of AN infected thinking at once. It really changed my world somehow. A new purpose to the thing I feared the most for a very long time.

  55. Souldanzer August 22, 2012 at 10:33 pm - Reply

    “Consider eating real organic foods with dirt upon them…….way better choice.”

    As a general rule, most vegetables, organic or not, have already been washed at the farm right after harvesting. All vegetables are dunked in ice cold water at the least to remove the “field heat” which would cause them to wilt before they’d ever reach the consumer. Sturdier vegetables (like roots) are washed with a pressurized water stream. Customers don’t like dirt in their vegetables, so this is something that is paid attention to before the veggie goes to the farm stand or store.

    I’d say that the washing at home makes little difference unless, of course, one goes overboard with veggie washes, soap, or, (to my horror) bleach. You’d probably have to grow your own if you really want to get the dirty goodness from your veggies. We used to joke about our consumption of dirt while harvesting (and tasting along… gotta taste what you sell)…. must be something good in all that dirt!

    • Jack August 23, 2012 at 6:42 am - Reply

      @Souldanzer……not if you buy them at the Farm or grow them your self! Thanks for the nice words about BG 5. That is a vital cog in the Quilt.

  56. […] about what I have just showed you earlier, in the brain gut 7, about how obesity and metabolic syndrome have their own particular gut flora associated with […]

  57. Mamagrok September 26, 2012 at 2:39 pm - Reply

    Mind-blowing theory of GD.

    So what are the implications for pregnancy termination? I know earlier studies showed that induced abortion increased breast cancer risk in ways that pregnancy continued to birth did not, seemingly because pregnancy caused changes in breast tissue that made it more susceptible to cancer, but that birth reversed those changes and took them even further, so that after birth you were less likely to have breast cancer than before conception. (Strangely, the increased risk did not apply to spontaneous abortion, probably b/c such an event was the result of processes leading toward it, and not an abrupt change that the body wasn’t prepared for.)

    I have to ask if there are similar implications in the changes in gut flora, or if perhaps the changes in gut flora and changes in breast tissue might be so interrelated that they are actually the same thing going on?

    • Jack September 26, 2012 at 5:22 pm - Reply

      @MamaGork the research is so new and fresh a clear picture is not present……but what it is leading to is us asking better questions. That is precisely what I am doing.

  58. Cognitive Ability. – Thoasp July 12, 2018 at 10:58 am - Reply

    […] Macronutrients, micronutrients and gut bacteria, oh my! Don’t forget that there are good and bad sugars, carbohydrates, fats and proteins. […]

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