Tuesday, November 25, 2014

HADZA GUTS HAVE THE ANCESTRAL CORE MICROBIOTA IN ABUNDANCE; High Dose RAW Starch Can Suppress Bifidobacteria, Roseburia, F. prausnitzii That Make Us Human (Part II)

Baobab Tree
Harvested by Hadza: fruit, seeds, honey, bark, etc


Let's neo-romanticize the Hadza hunter-gatherer studies for a moment. They eat a diet rich in starchy tubers, raw roots, chewing some of the tough, fibrous ones for several minutes, extracting as much starch, nutrients and energy as they can. The carbohydrate content varies from 27 to 70% of the tuber (see chart at end). Fiber varies from 3-35%. Cooking generally breaks tough fibers down. Stewing, boiling and roasting all make these more easily chewable and thus digestible.

Fermentation does as well. Paleophil has a short list of tubers that are fermented to process them into safe to eat starches (truly ancient 'safe starches' lol). Several varieties were put underground and allowed to pickle/ferment to remove toxins. The great majority of tubers on earth are toxic if raw. Nature provided underground protection for them. Potatoes contain trypsin and protease inhibitors (never fed raw to livestock or eaten by humans raw) and cassava, cyanide derivatives.  In Africa, co-evolution of consumption of toxic cassava may have actually conferred an advantage by improving sickle cell anemia. On the other hand, trypsin inhibitors in yams and potatoes are heat labile and easily deactivated by cooking. Heat rapidly degrades these toxins, making them safe for eating for everyone: small toddlers, children, elderly and adults.

In Africa and the tropics, extracts from toxic potatoes and yams can even be isolated for use in making poison arrows for hunting wild game.


Cooked starches with skins feed the great majority of our gut flora whereas raw, native starches feed only a few (but important few). From recent gut profiles from individuals who submitted samples to Genova, uBIOME and American Gut, a distinct pattern emerges if a high-dose raw resistant starch diet is implemented. Diversity is markedly low. The immunoprotective Roseburia/clostridia XIVa are missing. Is Roseburia important? I think so -- it is one of the strains that make us human, no hamsters or chimps. See prior post: Bifidobacteria longum, Roseburia, F. prausnitzii (and Akkermansia) Made Us Human (NONE OF THESE EAT RAW POTATO STARCH) (Part 1) NSFW


Here are 3 individuals (reports: a, b, c) who biohacked their guts and used high dose RS2 for a period of time before submitting stool samples to various testing groups: uBIOME, American Gut.

Bacteroidetes-Prevotella and Bacteroides overlap -- they both consume RS2 heartily and easily, as you can see below. On the other hand, the great majority of the core ancestral microbiota do not and with report c, one may observe that even consuming significant fiber as RS3, the Roseburia fails to 'bloom' in the gut. Normally RS3 (alone, sans RS2) feeds or cross-feeds Roseburia extensively based on Alan Walker et al research group. These 2 groups Prevotella and Bacteroides are big starch eaters of cooked digestible carbohydrates as well as resistant starch (cooked cooled, RS3). So they eat EVERYTHING. This is what I have an overgrowth of on/off the last few years of gut healing (and didn't realize). Prevotella is implicated in many cases of dysbiosis and uppergut overgrowths (SIBO/SIFO). Ck out pubmed: Prevotella/dysbiosis.
--T2 diabetes/Obesity
--colorectal cancer
--T1 diabetes
--IBD (Crohn's, UC)
--colorectal cancer
--HIV infection

When I saw the Prevotella on my stool reports I had previously (up until a few weeks) HEY THIS IS LIKE THE HEALTHY BURKINA FASO KIDS. I was totally wrong. My gut was like the dysbiotic HIV and other gut disrupted subjects actually.

I've had a lot of questions more than evolution lately:

What is the pattern that high dose RS2 exerts on the flora?
Does the resultant flora appear Bacteroides heavy and dominant? Why?
What is overgrown?
What is suppressed?
Does this have implications for the host?

Also if a gut is dysbiotic and we throw fire on the flame, will this cause dysbiotic-related metabolic changes? The research is inconsistent but I think the answer is, yes. It is entirely gut dependent. Many do great on raw potato starch and see gut healing. Others may run into obstacles like mine. Even testing for me didn't reveal the obstacles.

Dr Bill Lagakos reviews some studies where RPS or HAM-RS2 may worsen insulin by raising it and adversely effect blood sugars: here. It is not every study but appears to be seen in studies that are more recent IMHO and I suspect that the influence of livestock and human antibiotics adversely skewing our gut flora.

Journal club: new study in healthy pig gut flora, RS2 appears to raise insulin

Gut Microbe

Genus Level
N=1 (a)

20-40g RS2


N=1 (b)

10-20g RS2



uBiome Normal
N=1 (c)

20-40g RS2
10-20g RS3
PHD CARBS 100-150 g

F. prausnitzii
HIGHLIGHTED: suppressed immunoprotective and butyrate-producting gut flora


See below - this is comparing apples and oranges but let's do it for fun anyway. Comparing healthy (no inflammation or disease) Italians on the Mediterranean diet and Hadza guts, nearly every species of the 7 ancestral core microbiota of healthy humans (per Julien Tap et al research) are accounted for. They are similar or in higher abundance than USA ubiome healthy averages.

It is questionable whether or not the Hadza are truly 'missing' bifido or that lab errors in collection and subsequent bifido determination happened. Personally I think bifido are there!
“The conclusions about relative proportions of bacteria are likely not valid,” says Rob Knight, a microbiome scientist with expertise in technical issues. “Unfortunately there is no published reference for this yet; we’re working on one.” It’s not clear if this problem affects the study’s other conclusions, like the lack of Bifidobacteria. Source: NATGEO

For those on high dose raw starches -- you may observe vast differences.
  • the bifidobacteria are absent or nearly extinct (except for report c). 
  • F. prausnitizii which typically makes up 10-20% of healthy stool microbiota is only HALF OR LESS of 'normal' for either a hunter-gatherer Hadza or Western urbanite. 
  • Bacteroides appears overselected
  • low eubacteria 
  • no Roseburia/cluster XIVa

To me the most striking losses are bifido, F prausnitzii and Roseburia. These are hugely immunomodulating to the point where when these are used as probiotics in animal models, it is observed that disease and inflammation reverse. Bifidobacteria longum has been widely studied and since it is so easy to culture and grow, offered as a commercial probiotic for years.

Roseburia has recently been shown to reverse peanut allergies in a rodent model. In the gut, this is the superstar butyrate producer.  I think Roseburia/XIVa was key for me when I reversed gluten and dairy allergies after gut healing with eating soil probiotics, B longum probiotics (FloraMEND), steamed mountain white yams and purple potatoes (high RS3 diet) and consuming daily fermented root vegetables. Roseburia eats everything (except raw starches); its favorite foods are inulin, GOS (beans or supplements), chitin, beta glucan (grains, oats, mushrooms) and cooked starches (RS3). I talked about Roseburia HERE.


After hominids utilized fire as a routine tool to increase and unlock the energy content in USOs (underground storage organs), tubers, seeds and rhizomes, our gut flora of course adapted to this. I suspect that with routine employment of cooking, our human gut flora began to love RS3 and the additional fibers that came along it in roasted tubers, roots legumes and seeds.

Let's look at the Hadza. Their current diet is high in wild African, starchy tubers.  Both children and adults use sticks to forage these from the shallow ground in gallery forests and by vegetation near water sources. The amount of starch and RS is relatively lower than Western varieties though.  Contrary to what most people think, I think they eat a low net carb diet because their carb, fruit and berry sources are all extremely high in fiber. They do love their honey harvested from the hives in their native baobab trees. The fiber spectrum in their diets are not low but and I believe this is vastly reflected in the diversity which is almost double that of the healthy urban Italian cohort.

Below I compare their relative dominance in terms of the ancestral core human microbiota ( Nature).

Gut Microbe

Genus Level

20-60g RS3
African Tubers+

Italian Cohort

uBiome Normal
N=1 (c)
20-40g RS2
10-20g RS3
F. prausnitzii

(+ guesstimated)

Ancestral core species were sequenced and quantified in relative abundance. Hadza guts have a ton of diversity -- they are not short any of the immunoprotective or the bugs that produce buttloads of BUTYRATE:
  • F. prausnitzii
  • Roseburia
  • Eubacterium
What I observe is that with high dose RS2, an overselection of gut flora that specialize in raw starches and the de-selection (?suppression) of other species despite adequate consumption of other substrates (RS3). Losing diversity in the gut is the problem with aging/inflammaging, disease and debilitation in the Western world. What is ancestral? What is optimal for a diversified and robust gut?

I've polled a few gut researchers because I don't know sh*t about the gut microbiota. They say that it is highly plausible for overselection and competition of substrate media by a single group of gut flora, to the suppression or detriment of other gut flora.

If I neo-romanticize the Hadza, I would say keeping all fiber in context is helpful. Each person's ancestry play into this. Those who emerged from near the Fertile Crescent are likely to tolerate grains better. I'm Asian and I think we favor legumes, tubers and white rice and more net carbohydrates than  those of northern Europeans/Asians or aboriginal ancestry.

Hadza wild African cooked tuber
2 slices of one mak’alitako tuber (Emminia entennulifa)
Chewed for ~3min to extract carbs and nutrients
Spit out insoluble 'CUD'

Source: Nature
Hadza hunter forager diet


  1. "Detected SCFA values for each sample are reported in Supplementary Table 6. Principal component analysis of the SCFA relative abundance profiles shows a segregation between Hadza and Italians (P=0.02, permutation test with pseudo F-ratio; Fig. 7). The Italian samples are characterized by a significantly (P<0.01, the Mann–Whitney U-test) greater relative abundance of butyrate, while Hadza samples are enriched in propionate (P<0.01, the Mann–Whitney U-test). These differences may reflect dietary variation in both amount and type of fibre and carbohydrates consumed by Hadza and Italians, and the consequent relative depletion in butyrate producers belonging to the Clostridium cluster IV and XIVa in Hadza."


    1. Yes I don't know what the researchers meant by that. The relative percentages reported in the article are however relative to what uBIOME averages are. Hadza actually have far more than us. Urbanites have 1000 to 1500 unique OTUs and the Hadza 5 to 10 fold more > 10,000

      To me it seems this study brought up more questions than answers and a lot is related to the questionable collection methods which brought results that don't jive with other study data. Another thing species Akkermansia was not discriminated in the Hadza. Like bifido all animals on earth have Akk and so odd that scientists failed to detect. I asked a big Akk researcher and he said that it appeared the study did not extract to discern this gut flora.

  2. why can't you put a conclusion in the end with simple terms, ( in all of your articles ) that most people without phd's can understand. would be appreciated

    1. Of course John! Thx for your comment

      Consider a vast collection of dietary fiber to grow a diverse and disease free garden in the gut:
      --Small amounts of raw starch RS2 (if no vipers that eat RS2 in the upper gut, eg Klebsiella, Prevotella, Bacteroides, Fusobacteria etc)
      --cooked cooled/reheated starches (depending on ancestry)
      --high fiber plants (diverse and different colors, leaves, shoots, roots, etc)
      --fermented plants and roots

      Does that help?

    2. Thank you! (I'm not John)

  3. There are many probiotic supps with Bifido but what about Roseburia and F. prausnitzii? How can these be restored after being killed off?

    I tried PS for a while and at first it was good. Then after a while not so good. Now I mostly just try for RS3 from different sources and a little banana flour occasionally with meals.

    Thanks for your blog Dr. B G

    1. Yes we are limited in probiotics -- I like the soil probiotics that I list here below because they do supply the CAZy enzymes to degrade fiber that Roseburia, Akk, and F prausnitzii break down (inulin, oligo's, pectin, etc)

      Step #3 Soil and bifidobacteria probiotics:

  4. Hi Grace, Could you define what you mean by both 'High Dose' and 'Small Amounts' of RS2 please? Cheers, Adrian

    1. Adrian

      Each gut is different by when I see B longum 0.00037% on the raw taxonomy or 'yellow' zones on the Genova testing, I think high dosage is 'any' RS2, seriously. I can only hope the flora can be re-vitalized over time. B longum only consumes and crossfeeds from certain foods like inulin and GOS/oligosaccharides (beans, whole GF grains, Jarrow supplements, etc). Akkermansia feeds on the same -- inulin and GOS/oligos -- and it appears will be significantly suppressed as well.

      Personally I believe the best route for gut and metabolic health is to test the flora to know what your doing is on track. What to look for?
      --the 7 core ancestral microbiota
      --no pathogens, yeasts, protozoa, etc
      --diversity diversity diversity (no big gaping holes of Akkermansia, Roseburia, F prausnitzii and Bifidobacteria longum which is over half of the 7 ancestral core)

    2. How did you make the leap from Bifidobacteria to Bifidobacteria longum being ancestral core? Can't any scientific evidence saying that Bif. Long. is ancestral core over an above Bif generally?

  5. Pectin might help *restore* levels of f Prausnitzii at least. In the absence of starches that select for species that knock FP out of course!
    ...And of you'd need some to be in residence to start with. Where to get some if you're really at Zero count I'm not sure - fecal transplant? :)

    I'm wondering if anyone can help with this one. Do we keep a store of base commensal bacteria in our appendix - or is that just an old wives tale?

    1. Rosie

      'IN THE ABSENCE'~!!!!

      THAT IS THE KEY, perhaps ;)

      Yes they may be zero at the rate we are going. But we must have some if only 0.0021%, there is 'some' which hopefully if we carefully cultivate, nurture and spare their growth by (as you say) in the absence of raw starches that hyperpopulates their competition on the gut mucosa.

      The appendix does appear to store but I think it is naturally a two-way street.If we can consume organic soil covered tubers, beets, carrots, turnips, parnips, daikon, Swedes, etc I think we can replenish.

  6. This all confuses me. When I first saw the Hadza study, and they didn't have bifido, everyone was amazed. But then cooler heads prevailed and we all thought 'so what?' Maybe Hadza don't need bifido.

    Now I see they eat raw starch from raw tubers. Maybe that's why they don't have bifido. Maybe bifido only grows in our wimpy Western guts.

    So maybe eating RS2 and losing bifido is OK afterall.

    I look at those charts and I see lots of the ancestral core, who can say exactly what % we need? I am happy to see the names.

    It seems people are scrambling to make sense, but maybe the answer is there----just eat real foods and lots of cooked and lots of raw starches and let the chips fall where they may.

    1. Anon

      Thanks for your comment. I think when the native human gut flora is already amputated by modern living, high sugar/refined-carb diets, antibiotics and the deficiency of maternal tranmission, we need to carefully culture and protect the dwindling and 'endangered' so to speak species instead of pounding suddenly high non-ancestral dosages of white raw starch powder. The best way imho to kill off the last remaining species of the species that make us human (B longum, Roseburia and F praus) is to overpower the gut with skewed, massive dosages of one fiber like RPS (or even processed, synthesized RS3 powders) which starves these non-starch eating flora.

      I like banana flour -- it won't do this and it promotes fat loss because it has inulin which improves our metabolic profiles and feeds the entire gut.

      On the other hand, raw potato starch at high dosages does not allow fat loss. This is counter the rodent studies, which makes sense since raw starches is THEIR native diet, but not humans who mastered cooking. I concur with the first half of your statement: '-just eat real foods and lots of cooked'. I'd add eat plenty of raw and cooked inulin-oligosaccharide plant fibers from your individual and unique ancestral heritage to maintain a lean body and low inflammatory, disease-free status. Unlike starches, inulin-OS produce more butyrate gram for gram in every study that I've seen. Please refer to calories-proper blog by Dr Bill Lagakos -- he discusses extensively.

      Inulin-OS goes a long way -- don't need a lot.

      Have you done the cooked potato+skin 'reset'? This works because RS3 and the fiber/hemicelluloses in the skin feed bifido, Akk and Roseburia which each species help insulin sensitivity and produce leanness and body fat burning (after these gut flora are starved and outcompeted by raw starches without psyllium or other fiber sources to 'balance' out and selectively feed)

  7. i guess i'm lost, too, now.

    I quit eating anything raw because I was convinced it was not 'right' and now I see that the Hadza do indeed eat raw starches. Wazzup widdat? And I think they eat them just like Taterot and Richard said-cooked, raw, cooked and cooled. All three. Why do we avoid raw now? Is it just because of SIBO?

    Oh. Here is even better paper on Hazda tubers I found while Google searching for the tubers you mentioned.

    And I found this statement --

    While the women are digging, small tubers are commonly peeled and eaten. These are chewed for up to 3 min and a fibrous residue or quid is then spit out. The majority of the tubers, however, are collected over several hours of digging, then roasted for up to 30 min over an open fire, and allowed to cool briefly. Once cool, tubers are peeled, chewed, and a quid expectorated.

    This is exactlly like I would guess we have eaten forever, not cooking every single thing!

    that was from this link - http://www.anthro.ucsd.edu/faculty-staff/profiles/files/Marlett%20etal.2001.pdf


    1. Thanks Aaron -- I think for every gram of RS2 (raw starch) they get 5-10 grams of insoluble and soluble starch from the tuber and elsewhere in their diet. As you can see from their gut flora, RS2 doesn't impair the species that don't eat it and diversity in the Hadza guts is present (but not high dose raw starch n=1). Each tuber (100g serving) they masticate on only has 2-4 g RS2 and it's is mostly embedded in a thick, high insoluble fiber matrix. I believe they really need to work and chew to work these granules out, unlike our American spud (dried) which is 80% RS2 and 1-2g fiber. It is very different, which is the point of the post.

  8. wow this is getting too complicated for me to follow.
    Your answer to John helped a lot. Diversity is important obviously.

    You shlould indid try if you can to conclude your articles with actionable simply worded proposals/ideas.

    Thank you so much for your amazing insight.

    1. Thx AncientGreek -- hope it becomes more clear! Eat diversely, you'll get diverse gut flora (and they'll reward you well). Don't, won't imho.

  9. Hi Grace,

    Chris Kresser recently said on his podcast that he's lost trust in the Genova stool test. Do you share his concerns?

    This is from the transcript:

    "I used to run the Metametrix stool panel, but I’ve lost confidence in that after I read a study that didn’t mention Metametrix by name, but I think it was pretty clearly about Metametrix. After reading the study, which assessed the accuracy of the DNA PCR method that they were using, I lost confidence in it. Then Metametrix was purchased by Genova. A whole bunch of stuff happened there. So I’m currently using the Doctor’s Data Comprehensive Stool Analysis with three samples."



    1. Nate

      As far as I am aware, none of the companies have had published 3rd party testing (including the mentioned study). I'd love to see how CDSA and all the other companies fare, side by side, by an independent lab. Hasn't been done. Also I've seen stool testing with 2 companies run side by side and sometimes they are off and sometimes they are aligned, so hard for me to determine. Stool itself is heterogenous varying in microbiota content depending on where it is sampled (outer 'log' versus inner 'log' versus front versus backend lol).

      So personally I find all imperfect! With that said, it gives much more direction and guidance than let's say just shovelling in buckets of inulin or white powder.

  10. Hi Grace,

    Very cool breakdown. I especially appreciated how you expanded on the putative role of tubers and provided context: they're generally quite fibrous (i.e., calorie-poor in comparison to our average supermarket potato) & they're somewhere between medicine/food, in the sense that they primarily extensively modulate bacterial populations rather than simply serve as a predominant source of fuel for their human hosts.

    Please tell me the following description is a helpful way to look at what you're talking about (if it isn't, tear me down!):
    Julien Tap's work has identified an ancestral core of 7 enterotypes (I'm unfamiliar with the details atm) which need to be present in relatively similar amounts (no 1 kingpin, no low level workers). Beyond the ancestral 7 (itself a marker of diversity), it appears that strong competition (i.e. little predominance of 1 enterotype over the other) is more important than the extent of enterotypes present. So, you want a baseline diversity (ancestral 7) and also no MAJORLY dominant ones (ancestral 7 or other).

    In other words, I'm picturing this situation: a healthy gut is one where all the enterotypes are in a fierce competition. So fierce in fact, that none of them can afford to rely on the resources of their hosts (us) any more than the competition-derived homeostatic equilibirum already allows, as this strategy would put them at a disadvantage from the perspective of the host. Hence, the easiest way for our guts to maintain a favorable environment for us humans is to select for a mix of strains that can coexist in a manner that is not overly costly to us. This would eliminate any species who'd attempt to thrive by exploiting its host resources above and beyond the established 'average'.

    Have I lost you? :)

    TL;DR obsess about baseline variety & relatively homogenous distribution of enterotypes (i.e. competitive profile)

    1. Raphi

      Julien et al's work has been verified on different continents and geographical locales now.


  11. Hey Raphi

    Appreciate your deep thoughts!

    I couldn't find the total dietary fiber intake of the hadza. But I would not be surprised if it was 80-120 grams daily incl RS3. The baobab fruit and seeds are highly fibrous too.

    I'll post more later but I'm on the iPhone. Have you heard of the evolutionary strategies of the microbiota by a Dutch researher Van den Abbeele? Actually your discussion is aligned with his. I really like your idea about the competition-derived homeostatic equilibrium. I believe that you are absolutely correct that competition between the gut symbionts and pathogens have driven evolution of the microbiota for millennia-- they seek as you mentioned food, fuel, shelter, peace, partners and parasite (phage) avoidance just like US HUMANS.

    The interactions between the symbionts versus the non-collaborative opportunists are based on the symbionts practicing more team efforts (just like the Hadza working as one unit to hunt down prey) per Van den Abbeele like an elite and collaborative rugby or soccer team.

    I can't copy paste here but I'll put up Julien's links later

  12. A thought and a question.

    Nowhere do I see an account of the role of water in this process. Maybe it's not relevant; but I have noticed over the years that my digestion is influenced heavily at times by changes in water. Is it possible that water, and it's bacteria etc play a role in these samples?

    ...and the question: I notice you mention tubers with the skin on. I've started peeling it off yams and sweet potatoes and actually prefer it. Is there an advantage to the skin other than fiber?

    Thanks for your thoughts.


    1. tw,

      Skin has insoluble fiber but it's only 1-2 grams for tubers (except Hadza tubers) which I prefer to get from apple peels or beans/grains!

      If you are healing the gut, avoid diluting stomach acids, juice, enzymes excessively during meal times. Our bodies can only make so much and the function is to digest everything completely in the small intestines, and prevent putrification in the upper gut. With small intestinal overgrowths, food tends to ferment too early and this is called putrification. (this is what we can check on the urine organic acids tests, like Genova's ONE or Organix).

  13. According to my Anthropology course with Professor Schoeninger (she has done a lot of field work with the Hadza), tubers are a small part of the diet, not a large part. They mostly utilized for their water content and since they are high fibrous are not a significant source of carbohydrates. They are hardly cooked, mostly just to remove the skin since it is rather tough. The men often get most of their calories from honey (up to 4000 a day) and baobab nut for protein, infrequently meat if they are lucky. Their favorite foods are honey and meat.

    1. Samuel,

      Thx for your comments. Schoeninger sounds cool! I concur -- tubers seem a small part but I think it is seasonal as well as gender divided according to several gut researchers. The starches are very little (resistant starch) -- they are mostly water -- chewing on 1 kg of tubers is like 3-4 cups of water. Except for the low fiber sweet potato, panjuko, their tubers are similar in soluble and insoluble fiber, moisture, RS of our parsnips, turnips and carrots. Not sure I could gnaw on these all day for moisture but their berries I could!

      The honey contains 7 kinds of honeybee larvae which are rich in fat and protein (and vitamins A, B2 and C). AS WELL AS PROBIOTICS IN THEIR GUT. insects have fantastic microbes in their intestinal tracts and by eating these raw, supply awesome probiotics.

      I am surprised how their sweet potato has so much soluble sugar and pectin, it is almost like a fruit (panjuko, Ipomoea).

      Table 4 tuber composition of Hadza diet

  14. @ Nate, who gives a shit what Chris Kresser thinks about Genova stool testing.

  15. Dr Grace, I second John's request (which you have already kindly answered) -- I too would really appreciate an easy to comprehend summary in each of your articles. I'm not a scientist, and don't wish to delve into the detail, that others may find interesting, so something written more in layman's language would be helpful. And whilst your quick synopsis in response to John was great, something not quite so simple would be great. :-)
    Sorry if I'm being a pain, but basically something simple, but not overly simple, if at all humanly possible.

    1. I will try for both you and John -- will add an actionable summary in future posts.

  16. Anon,

    I'm concerned about the study Kresser cites (which I haven't been able to find yet).


  17. Hi Grace,

    What about H. pylori? Is it core? I recall reading that H. pylori does not cause stomach cancer (and some of the other symptoms) when having had it since being a child. Could it be beneficial?

    Cheers, Nils

    1. Nils,
      I think HP is core -- however it is hard to acquire the non-benign ancestral strains IMHO. It is transmitted via oral-fecal (you know ahaha family style). HP has been highly connected to protection against not just esophageal and stomach cancer (particularly the cagA+ strain) but also asthma.

  18. thank you very much, simple is great if you ever have time, if not I understand

  19. Hi Grace. Regarding a commenters question about how to repopulate with the ancestral core, it seems like in the recent past you said that animals have these and farmacy could help repopulate. Am I remembering correctly? If so, are you talking about mammals? So chickens would not work? If we keep a garden and put animal manures from local farms in it and then work in the garden and eat dirty carrots from it will this repopulate the ancestral core?


    1. If we take a clue from farmers who are impervious to nearly all western disease, I believe we will learn much. Many farmers use compost and manure from herbivores and other animals like bat guano. This is super nutritious for not only soil...but...! Yes all animals including bats have many of the ancestral core although the exact species are different. Yes the article says chickens have Akk too. This article is a MUST READ for all gut enthusiasts

      Microbes inside—from diversity to function: the case of Akkermansia

      Thank you so asking about the ancestral core and the missing ones with high dose RPS. The very profile that RPS creates is the diabetic one where fat burning is halted and blood glucoses rise and naturally IMHO it is related to a severed, hampered gut profile missing Roseburia, Akkermansia and the gut lining 'calvary' Bifidobacteria longum:
      http://www.ncbi.nlm.nih.gov/pubmed/24833634 [T2 diabetes lacks Roseburia, F prausnitzii, Akkermansia (and B longum)]

  20. someone asked about H. Pylori, this article is interesting.
    google NYtimes 'Some of my best friends are germs' by Michael Pollan.

    1. I love that article and Pollan's intrepid experimenting. Even he experienced quite a drop of gut symbionts and beneficial species after just one course of prophylactic dental antibiotics. No one is immune despite an awesome fermented diet and high fiber content. H pylori is a friend unless the gut (stomach and upper gut) lack acidity. H pylori loves acidity which is the natural ecology of where it naturally lives, in the stomach. Kombucha and lacto/bifido/soil probiotics all restored the upper gut's acidity so that H pylori stays 'friendly' and doesn't go mutant to protect its endangered ecological niche.

  21. Hi grace!!

    I'm a huge fan of u!! trust your word so much because its always backed by science and common sense.I have 1 question.. I had a sewage pipe instead of a gut.. nasty nasty stuff due to antibiotics and VLC :( so i started taking soil based probiotics along with potato starch 4 months ago.. do u think I might have killed off any residual good bugs, like bifido?? I took 2-3 tbs of ACV before this regimen and had horrible die off symptoms (or so I believe) like eye twitching and fatigue.. 1s I started SBO and potato starch I am much more eneretic and eye twitch has gone away.. but I am now worried about the potato starch ruining my gut further more.. Is there anyway of restoring AKKERMANSIA and rosberia..

    1. Hi Anon,

      Yes the few studies and case reports make it pretty clear to me that guts can lose vital gut species without realizing it and whether they can return or not is still questionable.

      SBOs are fed not only by potato starch but NEARLY ALL FIBER AND PREBIOTICS. I think the SBOs probiotics are wonderful and probably what helped with your symptoms, as they did mine (and I ate all RS3 rich tubers and yams, no raw starches at all).

      ACV is great to restore the terrain of the upper gut. It must be quite broken. Don't give up. Don't forget bile, bitters,, enzymes and exercise.

      I believe gut health and Roseburia/Akkermansia/B longum may be restored by
      (1) Stopping all raw starches temporarily (6-12 months? Gut and stool testing need to verify)
      (2) Version A and B of bionic fiber in place of any raw starches to rebuild these immunoprotective and fat burning gut species
      (3) Keep up what is tolerable on the 7 steps

      Please let me know how it works and obstacles. Would love to hear more about your continued progress on your sewage pipe ;)

  22. (2/2) Sorry. RS Alone So Far Has No Weight Loss Results in Human Studies

    These researchers Johnston et al found "Resistant starch consumption did not significantly affect body weight, fat storage in muscle, liver or visceral depots. There was also no change with resistant starch feeding on vascular function or markers of inflammation. However, in subjects randomized to consume the resistant starch, insulin sensitivity improved compared with the placebo group (P = 0.023)...Unlike in animal models, diabetes prevention does not appear to be directly related to changes in body adiposity, blood lipids or inflammatory markers. Further research to elucidate the mechanisms behind this change in insulin sensitivity in human subjects is required."

    Low (15g) and high dose (30g) RS2 for 4 weeks didn't induce fat loss either but improved insulin resistance in obese men, not women (Maki et al, 2012).

    Neither did 25 grams refined RS3 supplementation (Novelose330), but high-protein/40% carbs resulted in all body fat parameters pivoting: improved insulin sensitivity, body fat loss and weight loss in human subjects with metabolic syndrome (Lobley et al, 2013).

    Neither did 40 grams RS2 supplementation for 12 weeks in T2 diabetes (Bodinham et al, 2014). Strikingly, this study also showed that HAM-RS raised triglycerides in a statistically significant manner and failed to lower body fat, Hgba1c, blood glucoses or improve central insulin resistance at the liver.

    (However, a whole food supplement which contains a broad spectrum of microbial superfoods, native banana starch flour (NBS) 24 g/day induced 1.2 kg weight loss, improved waist-hip ratios and insulin sensitization in T2 diabetic, obese females after 4 weeks, contained only 8 grams RS2 (Ble-Castillo, 2010). Version B of BIONIC FIBER in the 7 steps. Green banana and plantains have been shown to heal ulcers and infectious colitis.)


  23. Dear Dr. B G,

    It is definitely gender divided in every way. Not the egalitarian structure I had imagined for such a hunter-gatherer community. The poor women hardly get any of the honey, which everyone there identifies as their absolute favorite foods (the men sneak a lot of it into their huts for themselves since it isn't obvious like meat).Looking at pics of the honey, there is definitely larvae burrowing throughout so it makes sense that men could go so long without meat. When the anthropologists wanted to go climb up the baobab trees for honey, it was blatantly frowned upon by the male Hadza.

    The most interesting observation and concern for me was the fact that the majority of their fat does not come from meat, but rather from the baobab nut, as has been the case for our ancestors back past australopoithecus (with other nuts). I looked up the composition of the baobab and it is around one third PUFA virtually all linoleic acid! These people, highly active, looking great into their 70s, if they make it their without infection. Begs the question as to the veracity of the malicious, relentless claims within the paleo community that it must be sugar and linoleic acid that are fundamentally at the heart of chronic disease today, rather than a question of degree.

    These men are getting most of their calories from sugar, and a balanced contribution from sfa, mufa, and linoleic acid.

  24. Samuel

    Thanks for your thoughts!

    Yes I've read other accounts of a less than egalitarian way of distributing meat as well

    There definitely might be gender effects of sugar and linoleic acid -- grrrrls might lay down fat faster than the gender that has high anabolic hormones which burn, not make fat.

    What do you think of the high fiber content of both the seed and the flesh of the fruit? Quite significant and definitely not a throwback food but as desirable the myriad of berries the Hadza also enjoy. THe berries are also high fiber and interestingly even some appear to have some protein I was surprised.

    What I suspect is that the men can have some 'inflammatory' type of foods (LA, sugar) because of counter balancing factors that are anti inflammatory
    --high fiber diet which leads to anti inflammatory gut flora profile
    --daily exercise (what's the average radius of range? 5 -10 miles?)
    --high threshold of microbial exposures and probiotics in water, soil, food, larvae bellies, hunted prey and their entrails (they even wash their hands in these good gut flora of their killed prey lol) etc
    --high polyphenols, anthocyanidins and antioxidants in berries and baobab seed and flesh as well as tubers and other untainted organic/heirloom harvests

    Our gut flora take linoleic acid and convert it into conjugated linoleic acid which is enormously anti-inflammatory (burns body fat and increases lean mass). Many of our gut flora do this -- those found in ruminates as well as bifido and lactobacilli and others.

    Smoking causes lung cancer? Only in the industrialized nations, hadza smoke filter less and no apparent risk of lung cancer. Genetic? I doubt it -- it's their fiber rich diet, gut flora, probiotic exposures and lack of gut disruption (antibiotics, vaccinations, C sections, formula, refrigeration etc).

    Smoking + sugar + linoleic acid = ur right, they should be dead lol!

  25. Hello Dr. Grace,

    What about adding some Baobab powder to your awesome bionic fiber drinks?


    Regards, Regina

  26. Hey Dr. B G!

    Funny you should link to that 2009 Julien Tap study. I picked it out from your 5-Part series on RS as well as the 2011 Nature paper (Enterotypes of the human gut microbiome PMID: 21508958). I've already gone through the Julien Tap et al. one but not the Nature one yet.

    I found it SUPER interesting for many reasons.

    [1] - Candidate species were those present in at least 50% of the 17-person sample [i.e. 50% threshold cut-off] & these accounted for only 2.1% of total sequences! WOW. To me this highlights 1) how precisely tuned our microbiome might need to be despite...2) how substantially its composition can change and remain (putatively) healthy...3) that this threshold is (AFAIK) neither 'incorrect' or 'correct' but is somewhat of a shot in dark (no wonder, we gotta to start somewhere). But > importantly it really highlights our current inability to understand how inter-individual phylogenetic variability should or does track with population variability. Maybe this goes some way to explain why probiotic recommendations really are in a stage of infancy (in terms of predictive outcomes). All the more reason to crack that nut! :)
    [2] - "These observations suggest that abundance [of OTUs] was not invariably related to frequency of observation" ==> this really complicates clinical recommendations seeking to increase/decrease specific strains because the abundance/absence seen in others isn't necessarily indicative of what a specific individual should be aiming for. Damn it!

  27. [3] - "when the diversity according to age, country of origin, diet was tested with AMOVA, the individual variability, which could be partly random, explained most of the difference […]” ==> from this & other parts of the paper, the omnivorous/vegetarian diets appeared to impact the gut quasi insignificantly. I don’t know that I buy that quite honestly. I think we don’t yet know what to look for &/or our mix of stats & PCR/pyrosequencing methods have big limitations we'll need to overcome. [see this for an e.g. https://www.ncbi.nlm.nih.gov/pubmed/19725865]
    [3] - "Whether the core OTUs represent a set of species sufficient for anaerobic degradation of dietary fibres remains to be determined” ==> that’s a BIG hole we need to fill. I think this suggests caution in strong general recommendations about specific strains (even Class!). I’m sure progress has been made in answering that question that I’m unaware of.
    [4] - Similarly...“From these data, however, the diversity structure appeared to interestingly depend on the genus considered. Furthermore, the diversity structure at different taxonomic levels can indeed be seen as a way to investigate the impact of host on community composition.” ==> I read that as saying ‘our struggle to characterize gut profiles is partly based on how we choose to divide the bacteria up & better profiles required smaller CIs & greater accuracy/threshold consensus in terms of sequence similarity that we currently posess’. Is that a reasonable interpretation?
    [5] - We need a better, > complete picture before picking at the details (e.g. individual strains) "Future studies on larger individual cohorts will enable to explore the link between gene redundancy and the prevalence of members of the putative phylogenetic core. Statistical models, as developed in this study, are also required in a broader perspective, to estimate sampling depth and number of individuals needed to characterize the ‘full’ human microbiome”.

    I feel like I’m missing the obvious (maybe fumbling with my taxonomical hierarchy?) asking you how does the 'Ancestral 7 Phyla' emerge from "a set of approximately 50 bacterial species may represent part of the healthy human phylogenetic core.”?

    Thanks for alerting me to that paper. It was very helpful. Onto the Nature one.

    PS: A major point that seems lost in a lot of microbiome discussions is the crazy capacity of horizontal gene transfer between bacteria, making speciation very difficult but also contributing to bacterial redundancy, just to make things a little more complex for us. Meaning, different strains have many of the same functions and thus profiling guts by “good strains/bad strains” may be overly simplistic. The question is, if not that, then with what? Functional sequences? Culture-based functional testing?..

  28. Raphi~

    The phylogenetic core emerges from actually 66 species that have been validated in healthy subjects in studies now from the USA, France, EU and China -- they are the most prevalent and dominant 2.1% of OTUs which are stable and conserved. Some species like Ruminococcus bromii (the keystone species that degrades RS2 and RS3 is missing in over 25% of healthy controls from studies now and even ~20 years ago -- this is abnormal imho). So some of the ancestral 7 are in 16 or 17 of all subjects but some only 8 or more and I think this is a result of the last 50 years of gut disruption.

    See fig 3 -- this is where AHS14 slides are based. Apparently per the authors, these are stable and fixed irregardless of gender, geography, enterotypes or diet. For me, they provided a framework to work from just as all of our organs are fixed. Our livers have 3 lobes, but if we are missing all 3 we are kinda screwed. If missing only 1-2, can survive and even live long but might be highly susceptible to liver toxins and liver damaging factors. The gut is not unlike the liver imho -- some of the ancestral core may be missing but it's not ideal. The missing strains actually create the fingerprint that is seen every western disease. For T2 diabetes, this fingerprint is so distinct that in 3 studies, the researchers can reliably with 80% or more sensitivity and specificity identify a subject with T2 diabetes from a healthy control. The fingerprint can be very distinct -- can tell who is human and who is Vibrio!

    The authors: "A few species are altogether more prevalent (conserved between individuals) and more represented, constituting a phylogenetic core"

    This is the PDF that goes into detail of the 66 and several of the other studies the data is validated:

    Actually I've not 'created' anything LOL (not a genius like YOU) -- it's pulled and extracted all from the gut research. However I've run my conclusions by several prominent gut researchers and been lucky to receive resounding approval including Julien. The key next step (which Julien and his team have done) is looking at the metaproteome (microbial proteins) and metabolomics (microbial metabolites) to see what is spewing from the pre-existing gut microbiome and how it disrupts the host causing disease. His latest study looks at the switch in metabolic pathways in colorectal cancer -- there is a distinct switch: less fiber degradation, invasion of fecal opportunistic pathogens and actually increased mucin degradation.

    "Potential of fecal microbiota for early‐stage detection of colorectal cancer" Tap et al http://bit.ly/crcmicrob

    [1] Concur -- very exciting. The 7 (or 8) core are in 14 to 17 of each healthy Euro subject in the Tap et al study. Looking at many disease states, each of these core are missing, depending on the disease state. Roseburia/XIVa is one of the key missing ones, as it is the superstar butyrate producer, not shocking. Bifido longum is one of the key guards of the mucosa lining -- again not neuroscience to realize when this is missing, diseases as diverse as heart disease to celiac or NASH/fatty liver are all related and may be associated to the reduced lactate and acidity in the upper gut as well as the way B longum interfaces with immunity to control Th1 v Th2 v TH17 arms of our delicate immune systems.

    [2] No I'd disagree -- this is the goal of prebiotics/fiber and probiotics. To shift from dysbiosis and pathogens to a pathogen-free status and 'eubiosis'

    Read this: pg 92 to 114 (recent microbiome workshop -- it's already outdated lol but has good basic 101 reviews)

  29. (cont)
    [3] Yeah the plant-based diet is good for the gut but certain genotypes require vitamins and nutrients that can only be animal-sourced (methylated B vitamins, retinol, omega-3 to name just 2 vital brain and eye nutrients which cause disease if deficient in fetuses, babies, toddlers and adults). What may have merit is that if the vegetarians gut is quite robust, the gut flora produce some of these nutrients: B12, methylated Bs, folates.

    Thx for the link on pyrosequencing errors -- yes data may not always be sound (which all have limits).

    [4] I think your take is right on. I think the gut researchers have conflicts with OTUs and the functional enzymes. Researchers have said that 60% of all DNA is variable -- from the environment, biofilms, community, phages, etc. You said ‘our struggle to characterize gut profiles is partly based on how we choose to divide the bacteria up & better profiles required smaller CIs & greater accuracy/threshold consensus in terms of sequence similarity that we currently posess’

    For sequence similarity of different pathways and carbohydrate degradation pathways (CAZy), again I think they will eventually go toward the 'functional genome' not the strict DNA and categorical species taxonomy (but I'm not certain -- you would know better!!).

    Love HGT! Our best is our endosymbionts: mitochondria (plants: chloroplasts)!

    Have you seen this one? Scorpions and other animals have bacteria-donated antibiotic genes in their genomes (hat tip D'adamo):

    [5] Nahhh... this is the best time in the world to start picking at individual species, the very species and genus that make us human not vibrio or gerbils ;) The data is here. We are at the crossroads to shift and optimize gut function with the knowledge (reversing diabetes, obesity, autism or anxiety/depression). Joel Dore is the best spokesperson; he's on Julien's team. "We have characterized a phylogenetic core within
    the human intestinal microbiota, in terms of composition; i.e. a set of conserved species that could be responsible for major conserved functionalities. " It's a very narrow range and only healthy subjects have them; diseased guts don't and display low gut flora diversity. Many of these ancestral 7 have been used in clinical studies in animal models as probiotics and guess what? THEY WORK; they're anti-inflammatory and work to reverse diseases of industrialization and supersanitation:

    autism: Bacteroides fragilis (sim to B vulgatus)
    peanut allergies: Roseburia etc/XIVa
    colitis: F. prausnitzii
    obesity, NASH/fatty liver: Akkermansia

    EVERYTHING! (celiac, gluten intolerance, anxiety, fatty liver/NASH, obesity, high cholesterol, high triglycerides, etc): Bifidobacteria longum

  30. http://www.old-herborn-university.de/literature/books/OHUni_book_23_article_3.pdf



  31. Regina!

    Thanks GUT GODDESS~!! Yes I love all the wild Hadza ethnobotanical herbs, seeds and fruit. I know several people who have added baobab fruit powder (similar to the high ORAC greens or reds in bionic fiber). It has substantial ORAC 15,000 apparently per 2 TBS, phenols and excellent antioxidants. The phenolics are gut healing and sealing. Baobab is high in soluble fibers as well containing the whole fiber spectrum. What's not to like?

    Here one study "Adansonia digitata (BAOBAB fruit) had the highest antioxidant capacity (IC50 values of 8.15μg/mL and 9.16μg/mL in the DPPH and ABTS assays respectively; TEAC of 0.75 in the FRAP assay) along with the highest amount of total phenolics (237.68mg GAE/g) and total flavonoids (16.14mg E/g). There were good correlations between DPPH and ABTS values (R2 0.98) and between total phenolics and total flavonoids (R2 0.94)."

  32. Are you seeing any studies on what people have been doing to specifically fix a gut that was skewed by RPS? It sounds like the best approach is RS3 cooked&cooled and inulin raw&cooked.

    "Have you done the cooked potato+skin 'reset'? This works because RS3 and the fiber/hemicelluloses in the skin feed bifido, Akk and Roseburia"

    Cooked potato skin "reset"? Is this the recommendation for RPS recovery?

  33. Anon,

    YOu are close. Potato skin is great (if no solanine) -- it binds fecal carcinogens, produces great butyrate and increases beneficial gut flora and lowers pathogens.

    Each gut is individual -- if the pre-existing gut is missing bifido, Akk and Roseburia, then yes whole RS3-rich foods (GF grains, legumes and tubers) will improve these numbers immediately.

    Akk is a little more special. To me from the few studies and our special cases of n=1, RPS completely knocks Akk down and out to extinction. The longer someone appears to be on high dose raw potato starch/HAM, it appears the lower the Akkermansia. Please see report (c) where duration of high dose RS2 was > 1 year.

    Most diseases of industrialization show low Akkermansia as well (diabetes, obesity, NASH/fatty liver, UC, crohn's, everything).

    To bring Akk up, I would consider
    --stopping all raw starches
    --adding if tolerated inulin- and GOS-rich foods (beans, onions, leeks, sunchokes, green veggies, asparagus) or supplements
    --basically all 7 steps (RS3-rich foods, exercise, probiotics, etc)

    I love RPS as it is in version C; but, I would verify first on gut testing that Akk, B longum and Roseburia are all replenished before adding in (Bionic fiber, version C)

    FYI I believe and suspect that B longum is its BFF on the mucosa lining! Invariably both are missing together.

    Did you see the Akkk and Roseburia posts?



  34. Hi Grace,

    You said:

    "If I neo-romanticize the Hadza, I would say keeping all fiber in context is helpful. Each person's ancestry play into this. Those who emerged from near the Fertile Crescent are likely to tolerate grains better. I'm Asian and I think we favor legumes, tubers and white rice and more net carbohydrates than those of northern Europeans/Asians or aboriginal ancestry."

    Can you comment on what food/fibers are ancestral to northern Europeans? I am confused by the last bit of your above statement. Are northern Europeans usually not able to handle as many net carbs?

    Also wanted to ask: Are you still doing consultations? I have emailed you a few times over the past several months to inquire and I never get a response.


    1. Diane

      I think the northern Euro and Asians who did not adapt and change to higher grain diets near the Fertile Crescent are more accustomed to tubers and lower (net) carb diets. The fiber (including RS3 -- this very special 'fiber' in starchy plants/seeds --- may have been higher actually because the resource allocation from the plants just didn't have easily accessible carbs, unlike milled grains like oats and spelt and ancient grains.

      Before the agarian heavy farmers moved north to Ireland and other parts and introduced grains and decimated forests, HGs were the dominant lifestyle and culture. The shoreline diet was high in omega-3s, magnesium and diverse nutrients and minerals. I believe the Irish potato had not been carried over yet. So I believe there were genetic adaptations (like hemachromatosis) but more recently in the neolithic. Also we are such a mix of genetics now so this obviously has 50 million shades of grey. Add to that our industrial toxins, pollutants, PCBs, and heavy metal poisoning which make many of us carb intolerant, despite wonderful genetics sometimes.

      Replied -- thank you for your patience Diane!

  35. Finally found a probiotic with sufficient amounts of B. Longum (1.5 x 10^7). However.. it is sweetened with Sucralose. Will the net benefits still be good?


  36. Grace what do you think of using humid/ fulvic acid (in the form of shilajit or zeolite) as gut fertilizer? In animal studies it seems to improve villi height in the gut. http://www.ncbi.nlm.nih.gov/pubmed/15379912

  37. Palva

    A friend sent me this -- no sucralose

    The artificial sweeteners appear to lower the good gut flora. I dunno about sucralose.

    Please send me another note. I'm sorry, I missed them.

    Yes the further away we appear to get from the equator (high fruit) and fertile crescent (high grain based diets) where agriculture bloomed, there appears less high starch diets and genetic variants that show sensitivity to refined carbohydrates and sugar:
    apo E4
    low copy AMY1 (amylase) (< 4 copies)
    other carb metabolism gene variants


    Also the more industrial and healthcare 'toxins', the more insulin resistant we may be. PCBs, estrogen-like plasticizers, and mercury toxicity all induce insulin resistance as well as hypothyroidism and affect poor T4 to T3 conversion.

    All kinds of plant fiber help us to bind and remove these toxins out of the body. The gut is like the ultimate exchanger of health!

  38. Thanks for the tip Grace, sadly I'm not US based.

    I suppose a tiny bit of sucralose won't be that detrimental,


  39. Hey anon. Sucralose definitely has an effect on gut flora. See this (rat) study:


  40. Anon--
    thx for sucralose link

    Would love to hear what works!

    For lisao on berberine (HT Isadora)

    Berberine boosts brown fat (by increasing our gut guardian B longum???! and lowering yeasts and opportunistic pathogens?) Berberine has multiple mechanisms including as an AMPK agonist to improve insulin sensitivity (like bio-curcumin and grapeseed extract)

    1. Wow! Really cool. Thanks for info. Also love curcumin/turmeric. Any whole food ways to get compounds in grape seed extract?

  41. Hi Grace. What about the Irish of yore and their mostly potato diet? Descriptions of them from that time are that they were fine pecimens, very healthy and robust. Also scientists studying ancient people from all over Europe and the Americas find a variety of grains and tubers that they were eating as well as legumes. There is ted talk by a woman about the paleo diet sans grains legumes tubers being unscientific. Can't remember the exact title. Have you seen it?

    Is it possible that the idea that people in more northern latitudes do not do well with higher carbs is as unsubstantiated as the idea that Paleolithic people didn't eat grains, tubers and legumes?

    What is the evidence that these foods did not make up a substantial percentage of the diets of Northern Europeans/people of northern latitudes diets? Or that they didn't tolerate them well?


  42. http://www.paleoterran.com/journal/2012/8/11/new-hypothesis-acellular-carbohydrates-promote-obesity.html

    What do you think of this hypothesis?

    Are they saying that all grains whole unground or ground into flour are acellular?

    Should I give up my gluten free multigrain bread to lose weight? Don't eat a lot of it but like some for breakfast sometimes or an occasional sandwich.

    Here is another article explaining cellular vs acellular carbs. You probably already know all about them but others might not.


  43. Hi Dr. Grace!!

    What is your take on fructose now? On fruits like apple and figs?? Would love to know what u think


  44. Hi Grace. I am reporting on differences I've noted between Heathers acacia gum and Frontier herb co. Organic acacia. It seems that Heathers is much more processed. It instantly dissolves is tasteless. Very different that frontier brand. That brand is gummy in water sticks to teeth. Frontier produces a serious thermogenic effect, heathers is very weak by comparison. It seems that the prebiotic quality and effect of the more processed heathers is poor in comparison, or do you think I'm wrong in judging it based on the above observations?

  45. Berberine has many beneficial effects, so I'm not sure how much of the positive changes people experience when using it we can actually attribute to flora changes. It does affect a lot of other things: http://examine.com/supplements/Berberine/
    Still a great supplement.

    I've gotten the impression that the majority of Europeans are actually farmer stock, based on genetic studies. They mixed with, but also out-competed the hunter-gatherers. Is that right?

    Refined carbs aren't particularly great for anyone, but AMY1 copy number does seem to reflect ancestral starch consumption: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377015/
    But check the supplementary table: file:///C:/Users/Cat/Downloads/NIHMS44514-supplement-Supplementary_.pdf
    You can see that equatorial populations weren't necessarily high starch, and thus have low copy number. There's also lots of variability in copy number for European and Asian samples . . I think it's best to just get a genetic test and find out individual susceptibility, rather than guessing whether your ancestors skewed high or low starch. I don't think geographical location of ancestors is that great of an indicator(?). I dunno. There are numerous studies by now, so I'm sure there's a good review somewhere.

  46. Hey Grace,

    Noticed you mention methylated b-vitamins and wondering you're take on the best way to supplement b-vitamins when healing the gut? I've been using dessicated liver caps and daily egg yolks, but realizing supplementation may be needed. Maxbnd from premier research labs is the most bioavailable product I've found, but says Sac Cervaise was included in fermentation.

  47. Anon,

    Are you hypersensitive to mycotoxins or fungi right now?

    The one I almost exclusively use is fungi and yeast free

    Please let me know how it works for you. Most people notice energy in 3-5 days that they were lacking previously. The food sources are wonderful you mentioned! I think our demands go up with depletion and central inflammation (like gut related ones). Also absorption is compromised until the gut barrier is restored (probiotics, removing vipers/yeast, balh blah blah).

  48. Anon

    'They mixed with, but also out-competed the hunter-gatherers.' YES. I believe the herders and those with fermented milk/raw milk sources had certain advantages (products of fermentation -- high protein and better gut resilience). True for not just northern Euro, Russia, etc but upper Asia, Mongolia etc. Many of these were able to grow millet and buckwheat, so I don't think grains are per se 'bad', especially if prepared ancestrally (soaked, fermented, eaten whole, no pesticides/herbicides, no GMO, etc).

    Cat? I like the supp table -- it is true genetics is one thing, and I believe our gut flora provide the enzymes to do things that we as hosts we fail to have the genetics for, eg making methylated folates, B vitamins, absorbing minerals, fermenting RS1234, and fiber, etc. The gut flora actually have alpha-amylases to break down cooked starches. So it is not inconceivable to me that obesity is not a problem for those with low copy AMY1, just as lactose intol isn't a problem for those with gut flora that contain the lactase enzyme!

    The industrialized world has really affected our native gut flora so it doesn't do what it has the potential to do (like digest small amounts of gluten -- which I was able to do after soil probiotics; Matt Pepin, after soil + bifido).

    Do you know where to find the AMY1 data on the 23andme? That would be interesting to see.

    From the GUardian: "The researchers went on to estimate the precise copy numbers of the amylase gene in the DNA of a further 481 Swedish subjects, 1,479 subjects from TwinsUK and 2,137 subjects from the DESIR project. They found that the number of copies of the AMY1 gene was consistently linked to obesity. Further analysis in French and Chinese patients with and without obesity showed the same patterns.

    "A lower estimated AMY1 copy-number showed a significantly increased risk of obesity in all samples and this translated to an approximate eightfold difference in the risk of obesity between those subjects with the highest number of copies of the gene and those with the lowest," said the study."


  49. lisao,

    I think tubers are paleo. Thank you for your thoughts!

    Also legumes as well. Botanically they precede C4 plants and indeed been with us for millenia but perhaps humans did not likely figure out how to process/soak/cook the antinutrients out until the last few thousands of years of the paleolithic. Also it is hard to find plant evidence, though it exists. Wrangtham from Harvard has written about it (see post). Also small seed grains (including rye barley and ancient wheat) have evidence of being used by Neanderthals in some regions

    Personally when I eat roasted tubers, I find hardly any calories or carbs for me, eg boiling makes more digestible carbs as per RS studies and glycemic index calculations. Warmed and hot work better for me for energy. However the RS3 worked the best for my gut from all the tubers in China -- white mt yam, purple heirloom potatoes, taro, sw potato/yam, etc. What are your thoughts on whole tubers and iRNA? These genetic elements in whole foods produces effects that we underestimate I believe. There was a study called the FUNGENUT that evaluated the genetic expression of whole foods v modern, refined. I'm not promoting oodles of rye but the whole grain rye products had effects that were pronounced and anti-inflammatory (and gut, IMHO):

    When did potatoes make it to Ireland? What do you think of Irish oats? I wonder if there was any Irish tradition to ferment the oats after cooking, preserving them longer and making them more nutritious, less phytic acid? I think the Viking travels and conquering really affected Irish and northern Euro diets. I've read that Ireland had a strong fish and marine based diet earlier. Hemachromatosis didn't appear to show up until the Vikings and introduction of heavy grain based diets.

    To me the carbs in tubers are not the same as the gluten grains from the Fertile Crescent -- but both of course have value and advantages for the gut.

    I think the northern Euro and Asia regions started use of buckwheat and millet, but I haven't found evidence of when this started pre neolithic or paleo? If you find anything, would love to hear about!

    Those adapted to heavy agriculture and dramatic reductions in animal based fats, collagen, bone marrow and other brain/organ-specific nutrients) had to change and some of these changes were related to less toxicity from hyperglycemia: apoE2, higher AMY1, higher carb metabolizing pathways (PPAR variants, etc).

  50. Anon

    I love fruit but I think everyone has different tolerances. For insoluble fiber and pectin, I love the winter oranges and a couple of tart green small apples or small organic gala or Fuji ones! (I can go thru 2 kg bag in 2 days; very convenient for me).

    For some a lot of fruit is like nature's candy. Our modern 'version' that is added to packages of fruit boxes for kiddies and adult 'crack' drinks is HFCS. High fructose corn syrup is worse than crack for teeth and metabolism! Addictive and highly inflammatory (it caused me 50 lbs of fat gain in the form of Starbuck 5 pump-HCFS mochas and Snapple lemon tea from Costco!)

    Berries and low sugar fruits are awesome and have much higher ORAC, antioxidants and polyphenols than the modern fruit at the supermarkets. If insulin resistance is low, the range of fruits can be much wider and really not problematic at all.

    The super fat burning combo (version B) improves insulin resistance if that is a current obstacle.

  51. Re: the comments on Hadza smoking with little consequence... Could a healthier gut be the REAL French paradox?? In addition, I'd think, to higher volume of nutrient dense and traditionally prepared foods

    1. YESSSS~!!! lol I LOVE THAT! the Hadza PARADOX

      Attribute it the giraffe poop in their water and bacterially dense food!

  52. Cat

    Thanks again for the supp table with the Hadza and other HG AMY1. I've been so lame and couldn't locate!! UR BRILLIANT


    UR an amazing, gorgeous gut goddess~!! Being on the front lines gives an edge and understanding that few I suspect will appreciate. Maybe everything depends on the status of the pre-existing gut, it's diversity and composition? I think there is a huge spectrum.

    Would a robust gut that is characterized by deep richness like the Hadza gut be able to consume acellular grains?

    On Cat's supp table, the petite Mbuti are listed. The are still rainforest HGs but they started to trade maize and grains with neighboring agarian cultures for their meat and tubers. M. McEwen writes excellently about them. Have they adapted? Are there any consequences to their health to introduce this carb source?

    I read the acellular article years ago when it came out but WAPF might be a better framework than such a restricted and tight view. Personally I find the genetic adaptation that have occurred the last 10 to 25k years are important for us. They forged our genetic capabilities to do what we do best now -- bigger brains, use of carbs for brain and muscle energy and empathy/cognition that no animal on earth can rival.

    What I love about the robust gut is that it should be able to do things for us whether it's digesting minute amounts of soaked/fermented gluten or helping us to maintain longevity. For me I think I was able to do fine again with gluten and dairy when the ancestral 7 core microbiota were replenished. These are the same core found in 'recovered' C difficile patients after FMT: high butyrate producing Roseburia + XIVa, etc. Their growth are sustained by all things found in ancestral diets: high fiber, lignin, hemicelluloses, pectin, glucomannan, xylans, beta glucan, arabinoxylan, FODMAPs/oligosaccharides, in other words, wide spectrum of fiber and RS3.

    The acellular theory also doesn't address fermented foods or beverages or dirrty soil exposures.... The influx of probiotics from soil, root vegetables, fermented vegetables and beverages can offset many gut losses. The GF bread we eat isn't ideal or WAPF -- it's not soaked/fermented or sprouted! I don't eat a lot either like you. For some, if the gut is permeable, this kind of bread and the phytic acid might cause gut problems and mineral leaching.

  53. lisao

    Melissa McEwen is awesome -- from Leach "In a series of elegant studies, Cani and colleagues ( 2-4) have shown that holding calories constant and varying macro levels of fat can induce low-grade metabolic endotoxemia which can lead to complications associated with cardiovascular health. As fat intake, so do serum levels of LPS and associated biomarkers. However, in high-fat diets with prebiotic oligosaccharides added (derived from chicory roots), serum levels of LPS drop, as do the metabolic markers of inflammation."

    Her conclusion which I concur: "So it is also possible that prebiotics in indigenous diets also have a protective effect. So we shouldn't look so much perhaps at dividing carbohydrates into two categories, but tracing each type of carbohydrate to the type of bacterial environment it promotes."

    The bacterial environment I'd strive for optimal longevity is one that mimics one's own ancestors (not gerbils) and in that equation are so many missing characters secondary to antibiotics and lack of exposures to farming/soil/gardens/outdoors and animals and healthy livestock. My sister is getting a coop of chickens soon! I'll be playing with her poopy chickens shortly lol

  54. What are high amylose producers to do to take care of their microbiota, adrenals and weight too?

    Low amount of digestible starch? What to eat and avoid or minimize?

    1. lisao --

      I think low digestible starches are advisable until the gut can handle -- this is where paleo, SCD, GAPS, Gotschall, VLC, etc can be helpful short term. Too long, it impairs the gut lining and compromises the ecosystem at the expense of attempting to 'starve' the vipers. Works for some, but not others.

      Once the gut is healed, the bionic fiber version B supercharges IS -- INSULIN SENSITIVITY -- by boosting the lean microbiota core (which need for longevity too!! centenarians have this).

      HT D'adamo -- new article. Vrieze is a F*KCING SUPERSTAR. The environment within: how gut microbiota may influence metabolism and body composition

      Don't forget the drool-inducing national Irish RUGBY HAWWT TEAM and their brilliant gut gardens -- no vipers, no inflammation, lots of Akkermansia and LEAN CORE MICROBIOTA

  55. Yes, the gluten free bread isn't soaked or fermented but what I buy is made from brown rice and potato. Nourishing traditions says it isn't absolutely necessary to to soak rice. Maybe that opinion is debatable though. I used to make soaked and fermented bread from freshly ground organic hard winter wheat. It made me itch. Mostly I made pancakes with it as that is so easy. Soaked and fermented the batter for 24 hrs

    When I switched to gluten free no more itching

    1. I didn't say that the itching from the wheat was at the beginning if my gut healing a couple of years ago. It was in the first few weeks of berberine use when I went from being able to eat no starches was on gaps like diet to eating any and everything with normal formed poops. The only repercussion from eating wheat was a bit of itching nasal and places not mentionable. Within a couple months I gave up the wheat. So this was before I added the bifido probios and sbos and learned about resistant starch and all the prebiotic fibers. Things might be different now. I think gluten free might still be better. I just bought some organic buckwheat to try.

  56. lisao

    I think things might be different now! I sure hope so.

    What did you mean by high amylose producers? You mean high copy AMY1 carriers?

    Berberine is really something!

    Grape seed extract I believe has similar properties. Other foods with similar OPCs and polyphenols might be cranberries and other seeds (carrot seed, red raspberry seed, pomegranate seeds). Hard to source tho.

    Brown rice can have antinutrients in the outer grain. Much of the rice grown globally have arsenic. Soaking 1-2 times can help reduce. White rice has it too and some pediatricians are now warning to limit children to only 1 serving max per week (much like ahi tuna and fish precautions).

    1. Meant amylase. Was I misunderstanding? Thought I understood that study was saying obesity is linked to producing a lot of amylase, starch digesting enzyme, causing much more starch to be digested absorbed. Might have read too quickly

    2. That is so sad! Are the pediatricians telling them to avoid wheat cause it is soaked in round up right before it's harvested? There is so much bad stuff in and on just about everything. I've read that chemicals are found in the snow and ice at the poles. There is no where to go to escape. It seems that there won't be anything left to eat that isn't contaminated before long. I knew about the arsenic thing. For that reason I've mostly stuck to white basmati rice from India which is supposedly lower. Also I rinse it very thoroughly to remove the starch on it which lowers some too. I haven't really rationed it. I got kind of tired of being afraid of everything I put in my mouth. It seems like you really could be afraid of everything and wear yourself to a nub financially, emotionally and mentally trying to avoid all the alleged poisons and problems eating completely organic etc. I think the fear and stress can be as damaging as the things being avoided.

      Maybe we should all be chelating and detoxing almost continually with EDTA and charcoal etc

    3. I totally concur!! It's good to be 'aware' not fearful... Solutions abound. We chelate on/off and do lots of fiber to bind the metals and toxins. But my kids can't stand fiber, so we do what we can ;)

  57. http://www.livestrong.com/article/337525-weight-loss-with-acacia-rigidula/#page=7

    Apparently the effects of acacia on metabolism, weight, fullness, the thermogenic effect are not just from its prebiotic fiber. The above article lists substances which have these effects that are in acacia. Page 7 states that beta3-adrenergic compounds boost body temp and tryptomine increases metabolism also. Lots of interesting things in this plant with cool effects.

    Differing growing conditions and processing would explain why some acacia gums would produce much greater thermogenic and metobolic effects than others. The places and conditions of growth and processing would make large differences in the amount of these compounds.

    If you want to heat up like a furnace, frontier herb co acacia is for you!

    1. Lisao
      Ur an absolute botanical beauty!!!

      I've not heard of that acacia. I tried only two brands -- NOW and Heathers but the initial heat kinda ended quick. Also I didn't push the dosage until later for the fat burning formula and the heat didn return. But as you noticed the the Heathers brand dissolves very easily. The Now brand gums up mildly and tastes like licking the resin like for bows (violin)! Yum!

      I'll ck out. The beta-3 effects are curious. Reminds me of yohimbime. That has potential sexual priapic effects if so FYI lol

      Do you have any Italian or Mediterranean background? Have you heard of mastic gum? I was trying to mimic this for gut effects and acacia is the closest and ancestral

    2. I tried mastic a bit for the gut. I can't remember exactly what all it does. I think it is antimicrobial. It's interesting how the body responds to different thermogenic substances. A few years ago I got that from coconut oil and it eventually stopped. I got it from rps back when I was doing it and it didn't stop but didn't do it for very long. The frontier herb co stuff I just finished a pound bag. It was the first acacia I've tried. Only took a total tbsp divided into 2 doses. I just finished it and started on a bag of heathers and can tell a marked difference in thermogenic effect. I wonder why thermogenic effects can disappear. Maybe if it is caused by substances that are having a adrenergic effect maybe it stops because of adaptation. Maybe down regulation happens.

    3. I do have Mediterranean ancestry. Southern France. My grandmother was French American. I think it was her grandmother that traveled to the US. Both of my grandmothers parents were of French ancestry. But I'm a mutt. English, Scottish Irish, Cherokee, and some African from what I'm told by my mom who has done geneology. My great, great grandmother was full blood Cherokee.

  58. Hello Lisao,

    Acacia! I need the heat here in Chicago! Acacia fibers have been a wonderful add-on for me.

    My journey to this place began with insane night-time itching but it took me a very long time to figure out the problem. It was over two years ago. I kept trying different laundry detergents. No help. New pajamas. New sheets. Kept buying more and more natural household cleaners. (But still eating like Homer Simpson). Then people started talking about gluten. I was like "wheat??!?" Eventually I tried not eating wheat. BINGO!! Eureka! That was it. I felt the best I'd felt ever really. I haven't looked back.
    Recently, I began some gentle weeding and I got night-time itching again for a few days but it resolved.
    Regards, Regina

    1. Regina,

      Glad you got the itching! Otherwise you may never have figured out the connection with gluten! I hope you can have minimal exposures again without problems later in the future. Soil probiotics and B longum are particularly good weapons for gliadin degradation in the gut to prevent these reactions.

      Literally I believe celiac/gluten intol = Bifidobacteria longum/soil deficiencies

      Please read and let me know your brilliant brilliant brilliant thoughts, ~R!!

  59. That's great Regina! Maybe later after improving gut you'll be able to tolerate it some. Sometimes, rarely, I have a bit of bread or a piece of pie with wheat crust and I'm ok. White flour seems to not bother me much. But it's only an occasional treat. You are about six hours north of me in Chicago. It sure gets cold there! I flew up there and down to Dallas to my parents once. It was in fall. I couldn't believe the difference in temp. I only had a light jacket thought I would freeze.

  60. What are Berberine and what forms do they come in and does bio -curcumin have something to do whith it?

    1. Berberine is an alkaloid found in a few different herbs: barberry root, goldenseal, Oregon grape root, coptis. Barberry and coptis were used in Chinese medicine for dysentery and intestinal infections for thousands of years. It has been discovered that berberine works in Vivo more like an adaptogen of the mucous membrane gut lining that a direct antimicrobial. It heals leaky gut, normalizes mucus secretion and immune function and affects immunoglobulin production and phagocyte functioning. It lowers inflammation in the gut.
      I used some goldenseal and barberry as well as isolated berberine and love those herbs. Curcumin is a chemical in turmeric and has different effects. It is not a mucous membrane alterative/tonic/adaptogen.

      Good info on berberine at Paul Bergners medherb website.

    2. Luv ur botanical brilliance~!!! Thank you for your thoughts. Definitely I will be studying Bergners!

      You are the first to discuss any adaptogenic effect on the gut, but since the gut is the second brain, this makes immaculate sense. The nerves in our gut are equal in density and # to our spinal cord and its connections peripherally.

      In the gut, viruses abound (by 10:1 to bacteria lol -- wow eh?). Many viruses are or become vipers (esp the live vaccines given to dysbiotic children/adults). Berberine like many of our favorite botanicals it is antifungal AND antiviral.

  61. Oops, yes, that anonymous was me. You have a good eye for writing style, Dr. BG!

    Completely agree with you on all points.

    I think the post-Paleolithic period did indeed cause enough shifts in allele frequencies and what-have-you, so that it wouldn't make much sense to ignore. As far as I can tell, Poland, and probably other nearby European countries, had pretty grain-rich (and legume) diets. Personally, I can eat as much gluten as I want, never had an issue. Instead, I have to be careful of rice intake, because if I eat it too frequently I get some TMI problems . . safe starches are different for everyone, apparently.

    I think Asians already ate wild grains during the late Paleolithic?
    "A broad-spectrum subsistence strategy was already practiced by people at Shizitan during the LGM. The intensive exploitation of Paniceae grasses and tubers for more than 10 millennia before the Neolithic would have helped people to develop necessary knowledge about the properties of those plants, which eventually led to millet’s domestication and medicinal uses of tubers."
    Of course, wild plants are different from domesticated . . have you seen the book Eating on the Wild Side? It goes into this issue for fruits and veg. Interestingly, heritage varieties are not better across the board, because newer varieties may have been bred to include more antioxidants . . gotta look at it case-by-case.

    Reduction in meat intake did not necessarily occur alongside agriculture though . . Poland is heavily forested and game was eaten a lot + livestock too. Forests are bountiful!

    Hmm, I thought there would be some AMY1 copy number tests by this point, but I guess not. 23andme doesn't do it. It does seem a bit counter-intuitive that being better at digesting starch (more copies) would lead to less obesity, doesn't it? Since that means you're better at extracting glucose. Evolutionarily, it makes sense, but what is the mechanism for reduced obesity supposed to be? Linkage disequilibrium with genes for better glucose disposal?

    1. Cat,

      No -- ahah lol. I suspected but your name was on one of the links!

      You're like one of my best pals -- she gets TMI with rice and she's CHINESE. I think there is dysbiosis and a bloom of methanogens with rice. I think you are probably low on sulfur and SRBs. Methanogens are shifted DOWN by sulfur -- how do you do with more sulfur rich vegetables or Opti-MSM? Brassica family -- kale, cauli, brocc and Brussel sprouts? Quinoa? Garlic? Onions? All the things that promote glutathione endogenous production!

      Ye s-- thx I've seen! Definitely -- we are so grain adapted it's not even funny.

      Starch will putrify if not digested. If the disaccharidases and other carb 'cutters' (enzymes) are insufficient, you get a lame Coors factory set up in the uppergut ( our cheapest, mass produced canned beer in the USA).

      The higher AMY1 is proposed by Perry et al to improve outcomes from gastroenteritis, a big mortality hit in the olden days. By failing to digest food faster during times of acute GI stress probably was the deal breaker for the babies and toddlers. Yes -- glucose disposal for immunity. Have you heard the old saying 'feed a fever, starve a cold.' Maybe that is related? Infectious disease clearly impacts our genetics. Evolution of our genetics is shaped by 3 main factors imho: pathogens, parity/partners and predator avoidance.

  62. Hi Cat. So I misunderstood breezing quickly through that study it appears. Being better able to digest starch makes less prone to obesity? I thought it was other way around. That is weird. I'm not very patient reading all the technical lingo. Going to have to force myself to slow down. Wonder if there is anything can be done to compensate for being less able to digest starch?

    1. Yes, 8-fold more obesity. It would be so neat to see these genetics.

  63. Maybe taking enzymes could compensate. Could it be that having more digestible starch escape digestion and go into the colon affects the microbiota adversely, explaining the increase in obesity?

    1. It would be a broadspectrum collection of enzymes -- my dish washer has amylases LOL. Not hard to get. We need the other carb cutters too for full digestion and prevent putrification, NASH, overgrowths of ethanol-producers (yeasts, E coli, etc) and the central inflammation at the liver which leads to cancer, diabetes and heart disease/strokes.

      Acid, bile, bitters -- all helpful too. SIBO knocks them all out temporarily until the organs recover -- pancreas, GB, liver, stomach glands, etc.

  64. @Lisao Do you have a specific brand you could recommend for berberine?

    1. Matt

      These are all wonderful!

  65. Love this blog, please keep it up!

    I have a lot of the Bobs Red Mill raw potato starch... can it be cooked and cooled to retrograde the R2 into R3?

    1. I would think if you made baked goods with it and then cooled you would get rs3. The question is how much. I have a recipe for copying betty crocker gf bisquick the ingredients are rice flour I use white basmati, potato starch and guar gum aluminum free baking powder salt and unrefined sugar just a smidgen for flavor and browning. You could really up the fiber in it by adding flax meal. I have a grinder and grind my rice and fresh grind flax in coffe mill. I don't eat this stuff very much but it makes pretty good pizza crusts, pies, pancakes etc now and then when u want more of a white flour like thing to eat. Of course you can leave out flax if your really craving that.

      I don't know that testing has been done that would give accurate rs3 numbers for baking and cooling potato starch products.

    2. Recyclable plastic can be made from commercial potato starch! My daughter and her friends did it for a science experiment (was too brittle -- they didn't do quite right).

      Other uses: gravy, gluten free baking

      Or after confirming your gut has decent abundance and diversity for B longum, Akkermansia, other lean microbiota -- then use for low dosage in version C of bionic fiber = acacia, psyllium, inulin, etc (add whatever glucomannan, pectins, MCP, citrus peel, amla, bao bab, banana flour, etc)

  66. How about this one Matthew:


    Regards, Regina

  67. @Regina

    I like that one, looks really potent.

    1. Hi Matt. I just used swansonvitamins.coms berberine. It is 400 mg capsules. I think 100 or 120 per bottle for like 10$ last I purchased. They were the best deal and worked great. Other ingredients: brown rice flour gelatin cap, may contain mag stearate and silica. I know some people want to avoid mag Stearate but I've never noticed any difference in ways I could feel between with or without so I don't care about it. I'm a tightwad and won't spend two or three times the price for something based on what seem to me to most often be marketing ploys based on questionable info

  68. I must be an anomaly but I tried both Swanson's berberine an then Candibactin BR. They both caused nausea and vomiting, the latter violently so. I first tried the Swanson's because I read that it is supposed to improve blood sugars and I didn't really make the connection that it was making me sick - I thought I had the stomach flu. Then when I tried the Candibactin-BR I wasn't sure either until it happened twice within a couple hours of taking it - it was unmistakable. I wish I could take it for all of it's virtues and maybe I am just experiencing die-off.

    Grace - I tried emailing you again - did you get it this time?


    1. Diane,

      That is quite a reaction. It sounds like something was shifting (and releasing their cell wall endotoxins and innards).

      Yes -- thx for your patience. Looking forward to meeting you soon.

  69. Diane, you're not the only one who got horribly sick right away from berberine. Hopefully when I try it I don't get sick.

  70. Hi Dr Gracie
    what brands of Acacia, Inulin and Green banana flour do you use for your Verson B? I'm having trouble locating them.

    1. GBF is from Australia/NZ -- Mt Uncle -- and in USA sourced from WeDo's online or at Whole Foods. I'm sure there are other purveyors now. If you find a good brand, please let me know. These make great RS3 in baked forms -- ~18 grams RS3 in baked goods according to Mt Uncle's sources and testing. GBF tastes just like spelt to me -- great cakes or savory scones, etc.

  71. I got my organic acid and stool test results:

    abnormal organic acid results
    -high pyruvate
    -high l-lactate
    -high methylmalonate
    -high 5-hydroxyindoleacetate
    -high pyroglutamate

    abnormally high
    -bacteriodes-prevotella group
    -bacteriodes vulgatus
    -odoribacter spp
    -prevotella spp
    -faecalibacterium prausnitzii
    -pseudoflavonifractor spp
    -roseburia spp (guess I'm not low on this)
    -oxalobacter formigenes
    -fusobacterium spp

    -enterobacter cloacae 4+
    -candida parapsilosis 2+

    borderline low
    -products of protein breakdown
    -fecal fats
    -long chain fatty acids
    -n-butyrate concentration
    -n-butyrate %
    -butryivibrio crossotus
    -firmicutes/bacteroidetes ratio

    borderline high
    -acetate %
    -barnesiella spp

    Overall, it said my diversity was in the red circle zone on the graphic. It was about 20% above the bottom of the graph.

    What does the overgrowth of all these commensals mean? Is it because my diversity is so low? How do I get these overgrowths under control?

    Do I treat the candida parapsilosis like candida albicanas?

    Thanks for any suggestions you can offer.

    1. Did you have antibiotics growing up? Mom had dysbiosis/IBS, etc?

      Yes -- I would target the fungi overgrowths first. Avoid any raw starches (forever?) because of high Prevotella and other RS2 superfeeders.

      You want to aim for boosting all the gut symbionts

      Roseburia consumes inulin -- so any fermentable fiber is best to minimize until the clearance of the uppergut is better (or symptomatic). Shouldn't take long! Support your gut -- step #7 -- acid, bitter, bile, digestive enzymes, mild exercise, etc


  72. Hey Aaron,

    Can you elaborate about what causes berberine to make some people sick? Is it die-off?


  73. @Lisao

    Does barberry have the same effect as berberine? Weaker/stronger?

  74. lisao

    Thanks for the reply.

    I was actually thinking of cooking the raw potato starch with just enough water to evenly distribute the heat and then cooling it in the fridge. Unless there's something I'm missing it should retrograde overnight.

    1. The % of retrogradation depends on how long the starch is cooked. Too long -- less RS3. Too short -- less RS3. I don't know what would guarantee enough RS3. FOod is best! Roasted potatoes is like nearly all RS3 after cooling in fridge 24hrs: 16-19 grams per 100g serving.


  75. https://www.bulletproofexec.com/dr-grace-liu-fixing-the-gut-microbiome-with-resistant-starch-and-probiotics-177/

    Thank You

    1. Thanks - just put up the post announcement with some fun studies! http://drbganimalpharm.blogspot.com/2014/12/new-bulletproof-podcast-with-dave.html

  76. Dr. Grace,

    Thank you so much for the fabulous research studies. You are my Angel!! How fortunate I am to have found my way here. Like a beagle, I kept sniffing and found the right place.
    No surprise that I have zero bifido and severe glutamine deficiency as well as HLA-DQ8. The GAG research also corroborating with the NAG feeding b. longum. These papers refer to bifido longum CECT 7347. I can only find BB536. Is it so strain specific?

    More dot connecting is even milk-fed (I wasn't) infants with HLA-DQ genotype have deficient b. longum: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030791

    Thank you!!!

    1. Regina/Goddess~!

      I think it is altogether possible to eat gluten again if the ancestral core microbiota can be replenished (and look like the ancestral or rural guts like Malawi, Amerindians and spectacular Hadza).

      NAG may also feed or crossfeed other symbionts as part of its spectrum of beneficial effects I think. Often probiotics are strain specific, but I've noted all the B longum seem to share overlapping benefits. BB536 is the most studied, that I've found.

      The big celiac epidemic in Sweden coincided with a drastic drop in formula use and decrease in natural lactation. Awesome study, THX! Formula may have n6 PUFA which may be particularly gut destructive for certain genetic types, maybe? The oxidized milk fats and lack of oligosaccharides (HMOs) which are protective and propel those pathogens that authors list. Breastmilk contains over > 200 different oligosaccharides which protect the baby that lacks immunity. In studies, oligos are shown to be anti-pathogenic, anti-pseudomonal, and anti-salmonella.

      Our plant foods (evolution's beautiful 'plant babies!!') contain these:
      beans -- GOS
      raw dairy -- GOS and other oligos
      whole GF grains -- oligos, FOS, AXOS
      low carb tubers -- FOS, inulin, XOS, etc

  77. Hi Grace,

    This is just an amazing thread. My question: Is there a CDSA test which by chance test for the seven ancestral core? I know the Genova GI Effects 2200 picks up three I believe (B Longum, Roseburia, Akkermansia). Any other CDSA tests that you kno of accessible to the layman pick up any of the others?

    1. Ubiome has the raw taxonomy and get the breakdown of the bifidos including B longum (I've found it extinct or nearly extinct in nearly every ubiome I've seen already except one dude who eats an inulin-rich diet and NEVER TOO RAW POTATO STARCH lol ahah)

  78. I just found an old bottle of 100% essential neem oil. It dawned on me, to wonder what neem kills vs. what triphala kills, and even better what in the Hazda diet is analogous to neem and triphala?

    1. Thx Samuel! Plus any clay or charcoal they may purposely or inadvertently ingest. These are antifungal and antiparasitic as well as a bit of biofilm busting agents

      In Asia konjac and kudzu roots are ancient and medicinal. These have glucomannan and other insulin sensitizing prebiotics. The glucomannan oligosaccharides are powerful anti-pathogen agents for the gut epithelium.

      Certainly if neem isnt used in Africa, something analogous is taken advantage of! The gums (like acacia) are antimicrobialowned antipest to protect the trees from pests and infestations

  79. Hey Grace,

    Any input on possible issues of food combining when dealing with dysbiosis and high fungal loads? For instance some say not to consume fats with starches. However, consuming the two together is supposed to help with insulin resistance.

    Additionally, any thoughts on implementation of starches and RS throughout the day when dealing with insulin issues? I usually start with fat and protein meal and bring in starches during the mid-day and evening meal.

    1. Anon, I don't know much about food combining but I've heard it has great merit. For better adrenals, I recommend some starches matched with both fat and protein at 4 small meals per day. Usually with severe dysbiosis, this helps but starch tolerance has to be present. What ways have you tried to lower fungal load and improve digestive support?

  80. Anon

    Studies show it -- B longum is the superstar on human gut mucosa for healthy folks and centenarians. Sick people don't have it (and those on high dose #hamsterfood)

  81. Anyone know where Akkermansia exists in nature? Is it a soil bacteria, thus picked up by gardening?

  82. Dear Dr. B G:

    So glad I found you!! So easy to get led astray and only find the RS2 Paleos. I am reading and listening to everything I can find that you have done.

    I have dysbiosis, however, I do have a good amount of B. longnum, a tiny amount of Akk, but no F.P. (Hope the 1 week of RS2 didn't hurt too much. Once I found you, and threw it out.)

    My question is how do you get rid of really high prevotella? I noticed in a previous comment you said it eats everything. If I do one of your Bionic Fiber versions, and avoid all raw starches will this help the ancestral species out compete prevotella?

    Or in the alternative, if I take some herbal antimicrobials to knock everything back, do you think supplementing heavy with the prebiotics the ancestrals like would help them out compete the prevotella when things grow back?

    Any thoughts?

    Thanks Darcie

  83. Darcie,

    Thanks for your kind thoughts! Glad you discovered the potential, inherent problems before more issues occurred.

    What your initial gut composition is, diversity and baseline level of 'good flora' will probably determine how well you do with prebiotics. Sounds like you've done testing and are making informed decisions! Good for you! Ur a super bright chica. Thanks for finding the blog.

    For Prevotella, its populations can be lowered by avoiding starch and prebiotics that feed it temporarily (psyllium) and by increasing probiotics that live in the upper gut:
    --soil probiotics
    --bifido longum (no starch eaters -- void B animalis, B adolescentis and B breve)

    See step #3 for list of probx to replenish

    For prebiotics, again it depends on ur current gut composition. For me what worked (I don't have Kleb -- inulin feeds certain Kleb so need to avoid if this is the case) was the bionic fiber minus psyllium the first month.

    Br J Nutr. 2007 Sep;98(3):540-9. Epub 2007 Apr 20.
    Jerusalem artichoke and chicory inulin in bakery products affect faecal microbiota of healthy volunteers.
    Kleessen B1, Schwarz S, Boehm A, Fuhrmann H, Richter A, Henle T, Krueger M.
    Author information
    A study was conducted to test the effects of Jerusalem artichoke inulin (JA) or chicory inulin (CH) in snack bars on composition of faecal microbiota, concentration of faecal SCFA, bowel habit and gastrointestinal symptoms. Forty-five volunteers participated in a double-blind, randomized, placebo-controlled, parallel-group study. At the end of a 7 d run-in period, subjects were randomly assigned to three groups of fifteen subjects each, consuming either snack bars with CH or JA, or snack bars without fructans (placebo); for 7 d (adaptation period), they ingested one snack bar per day (7.7 g fructan/d) and continued for 14 d with two snack bars per day. The composition of the microbiota was monitored weekly. The consumption of CH or JA increased counts of bifidobacteria (+1.2 log10 in 21 d) and reduced Bacteroides/Prevotella in number and the Clostridium histolyticum/C. lituseburense group in frequency at the end of intervention (P < 0.05). No changes in concentration of faecal SCFA were observed. Consumption of snack bars resulted in a slight increase in stool frequency. Stool consistency was slightly affected in subjects consuming two snack bars containing CH or JA per day (P < 0.05). Consumption of CH or JA resulted in mild and sometimes moderate flatulence in a few subjects compared to placebo (P < 0.05). No structural differences were detected between CH and JA before and after processing. In conclusion, adaptation on increased doses of CH or JA in bakery products stimulates the growth of bifidobacteria and may contribute to the suppression of potential pathogenic bacteria.

  84. (2/2) cont

    Br J Nutr. 2010 Oct;104(7):1007-17. doi: 10.1017/S0007114510001571. Epub 2010 Jul 1.

    A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects.
    Costabile A1, Kolida S, Klinder A, Gietl E, Bäuerlein M, Frohberg C, Landschütze V, Gibson GR.
    Author information
    There is growing interest in the use of inulins as substrates for the selective growth of beneficial gut bacteria such as bifidobacteria and lactobacilli because recent studies have established that their prebiotic effect is linked to several health benefits. In the present study, the impact of a very-long-chain inulin (VLCI), derived from globe artichoke (Cynara scolymus), on the human intestinal microbiota compared with maltodextrin was determined. A double-blind, cross-over study was carried out in thirty-two healthy adults who were randomised into two groups and consumed 10 g/d of either VLCI or maltodextrin, for two 3-week study periods, separated by a 3-week washout period. Numbers of faecal bifidobacteria and lactobacilli were significantly higher upon VLCI ingestion compared with the placebo. Additionally, levels of Atopobium group significantly increased, while Bacteroides-Prevotella numbers were significantly reduced. No significant changes in faecal SCFA concentrations were observed. There were no adverse gastrointestinal symptoms apart from a significant increase in mild and moderate bloating upon VLCI ingestion. These observations were also confirmed by in vitro gas production measurements. In conclusion, daily consumption of VLCI extracted from globe artichoke exerted a pronounced prebiotic effect on the human faecal microbiota composition and was well tolerated by all volunteers.