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

COOKING BROADENED HUMAN UTILIZATION AND FORAGING OF WILD AND TOXIC PLANTS

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.




RS3 AND RS2 FEED DIFFERENT FLORA IN THE GUT

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



N=1, THREE HIGH-DOSE RS2 INTREPID SELF-EXPERIMENTERS

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)
--IBS-C IBS-D
--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
ANCESTRAL
CORE
N=1 (a)

20-40g RS2

VLC

UBIOME
N=1 (b)

10-20g RS2

VLC

UBIOME




uBiome Normal
Avg
N=1 (c)

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

AMGUT
Akkermansia
3.52
undetect
1.2%
0.07
F. prausnitzii
8.56
3.58
9.3%
4.8
Roseburia
0.601
0.166
3.4%
0.4
Eubacterium
0.0591
0.00310
0.9%
0.1
HIGH DOSE RS2 APPEARS TO
OVERSELECT
Bacteroides
(+B-Prevotella)
28.0
(+undetect)
0.617
(+77.4)
9.4%
(+7.36%)
46.2
(+undetect)
Bifidobacteria
undetect
0.0311
0.88%
11.32
Ruminococcus
2.21
0.292
6.06%
13.0
HIGHLIGHTED: suppressed immunoprotective and butyrate-producting gut flora



HADZA GUTS (AND HEALTHY MEDITERRANEAN) HAVE NEARLY ALL THE ANCESTRAL CORE MICROBIOTA

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 

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 gallergy forests and by vegetation near water sources. The amount of soluble 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 sources are 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 belive this is vastly reflected in the diversity which is almost double that of the Italian cohort in this comparison below ( Nature).


Gut Microbe




Genus Level
ANCESTRAL
CORE
HADZA
BETTER
GUT DIVERSITY

20-60g RS3
African Tubers
MEDITERR-
ANEAN
DIET


Italian Cohort




uBiome Normal
Avg
N=1 (c)

WHOLE FOOD
20-40g RS2
10-20g RS3
F. prausnitzii
11.8
18.5
9.3%
4.8
Roseburia
3.9
7.7
3.4%
0.4
Eubacterium
2.2
1.4
0.9%
0.1
Bacteroides
B-Prevotella
0.2
6.2
7.1
0.4
9.4%
7.36
46.2
(na)
Bifidobacteria
0.02
8.1
0.88%
11.32
Ruminococcus
2.1
8.6
6.06%
13.0



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.

Thoughts?
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

Monday, November 17, 2014

New GG Podcast: EPISODE 06 WEED THY GUT

Gut Guardian Podcast: Episode 06 – Understanding Yeasts and Skin Flora

Yeasts, they are in our breads, beers, and in and on our body. Matt asks Dr. Grace how to deal with lingering skin issues that he attributes to yeasts. Dr. Grace explains tips on how to distinguish if skin issues are caused by a topical problem or a deeper issue residing in our guts. And just when you thought probiotics would only work for your gut, there is a formula for your skin flora!

Enjoy the episode!



Show Notes

Information on Yeasts

Dr. Graces Recommended Hair Treatment 

Another Skin Flora Helper (Apply to Skin/Scalp before bed and wash in morning)

AOBiome




00:00
00:00

Sunday, November 9, 2014

Bifidobacteria longum, Roseburia, F. prausnitzii (and Akkermansia) Made Us Human (NONE OF THESE EAT RAW POTATO STARCH) (Part 1) NSFW




Journal Club today:

Moeller et al PNAS 2014 'Rapid changes in the gut microbiome during human evolution'




Fig 1. Compositional changes in the gut microbiome during African ape diversification. Shifts in relative abundances of microbial genera within the gut microbiome were inferred for each branch of the host phylogeny. Genera whose relative abundances increased or decreased are listed above or below each branch within blue-shaded or yellow-shaded boxes, respectively.
Moeller et al PNAS 2014
Ancestral Core:
Roseburia, F. prausnitzii, BIFIDOBACTERIA,
Bacteroides, Clostridium


Highlights:

Ancestral Core:
Roseburia, F. prausnitzii, BIFIDOBACTERIA, Bacteroides, Clostridium

The ancestral core made us human. These are enriched 2 to 5-fold in humans through deep evolutionary time compared to our wild African chimp and ape cousins. These gut flora eat a range of plant polysaccharides but the more immunoprotective, the more they are likely to consume breastmilk-like oligosaccharides (inulin type fructans, GOS, raffinose family oligosaccharides) and inulin. Roseburia, F. prausnitzii, BIFIDOBACTERIA and Clostridium thrive and crossfeed on RS3 and inulin/oligosaccharides, but not raw starches/RS2.

"Changes in the composition of the microbiome accrued steadily as African apes diversified, but human microbiomes have diverged at an accelerated pace ow- ing to a dramatic loss of ancestral microbial diversity. These results suggest that the human microbiome has undergone a substantial transformation since the human–chimpanzee split."

"For instance, the relative abundances of Prevotella and Bacteriodes were negatively correlated within each host population."  Prevotella are high grain-eaters, seen high in Burkina Faso children and those consuming whole-grain-based diets. Bacteroides are versatile -- they consume everything: carbs/grains, fats,  andmeat/protein.

"Relative abundances of Bacteroides were always positively correlated with those of Ruminococcus and Parabacteroides."  Bacteroides again are big meat-and-potatoes fans. 

"We identified 35 instances in which the relative abundance of a microbial taxon shifted since the divergences of the extant species of African ape (Fig. 1), 17 of which occurred in humans since the divergence of Homo and Pan. Several of these changes in the composition of the human microbiome have functional implications for host nutrition." The introduction of diverse, high-fiber, high-RS3 cooked starches changed many things for humans including the evolution of their gut flora: seeds (lotus, quinoa, fenugreek, buckwheat, etc), legumes, lentils, roasted tubers-rhizomes, whole soaked nuts, ground nut flours (tigernut 'cakes', acorn 'pancakes'), maize (porridges, tortilla), whole grains (oats, millet, maize, sorghum, teff, amaranth, black/red/brown/purple rices), etc.





Humans Expanded Their Food and Ecological Niches By Taming Fire




Whole Real Food

100g = ~ ½ cup

Inulin-Oligosaccharide Content

RS3 Content
Chicory root
100g
41g  
0
Jerusalem artichoke
100g
18g  
0
Dandelion greens
100g
13g  
0
Onion (raw or cooked)
100g
4g    
0
Garlic (raw or cooked)
25g
3g  
0
Cowpea, White Lupin
100g
5g
4g
Lentils, Chickpeas, Hummus
100g
4g
2-4g
Pinto Beans (cooked/cooled)
100g
3g  
10g
Purple Potato (roasted/cooled)
100g
na
15-19g
Yams (boiled/cooled)
100g
na
6-8g
Potato (boiled/cooled)
100g
na
3-7g
Rice (cooked/cooled)
100g
na
1-2g
Long grain Rice (cooked/cool)
100g
na
2-3g
Sushi Rice (cooked/cool)
100g
na
3-4g





Other Highlights

"The relative abundance of Bacteroides, which has been positively associated with diets rich in animal fat and protein (9), has increased in relative abundance more than fivefold in humans. Conversely, the archaeon Methanobrevibacter, which promotes the degradation of complex plant polysaccharides by using the end products of fermentation for methanogenesis (10), has undergone a more than fivefold reduction within humans."

"Fossil and genetic evidence in- dicate that the divergence times for African apes range from 5 to 13 mya for the chimpanzee–human split and from 8 to 16 mya for the human–gorilla split (12, 13)."

"Despite the clock-like nature of microbiome diversification in African apes, the gut microbiomes of US humans have undergone an accelerated rate of change and are more different from those of each wild ape population than expected based on the evolutionary time separating Homo from Pan and Gorilla. Based on genus-level BCD, the microbiomes of US humans are more different from those of Malawi humans than the gut microbiomes of Malawi humans are from those of bonobos." We started cooking and routine control of fire. Hunting, fishing and broad spectrum foraging allowed us to travel and massively change our diets and ecosystem roles and niches. As apex predators, we took over the globe.



Men's Health 2014 (current issue)
Sexxxy Guts for a special EvMed reader
Hamster? Homo sapienPan GUTS???


NUTRIGENOMICS AND DIET

Even Neanderthals harvested small seed grains and used fire routinely to cook on hearths. I suspect however they didn't adapt to the gluten ones well and may have had genetics like HLA DQ2.2, DQ2/8 that are related to higher gluten damage and gut devastation with raw or unfermented gluten grains (eg sourdough, lacto fermented porridges, etc). Neanderthals reigned for tens of thousands of years but with agrarian dominance and reliance on gluten containing spelt, emmer, barley and rye, I believe it took a toll on Neanderthal guts. Their numbers gradually dwindled from 50,000 years to 25-40 thousand years ago. Modern humans may be seeing similar gut devastation: slow disease and debilitation; epidemic infertility; mental illness and cognitive decline. Modern skeletons are shrinking, craniums de-evolving.

One thing in common tubers, roots, seeds, nuts, grains and legumes have are the fact that they are all 'plant babies' and thus share many common nutrients - protein, storage carbohydrates and protection from cold/frost/mechanical stressors. These translate to better nutrients for those that consume them as well if the anti-nutrients don't get them first. Resistant starch, inulin and oligosaccharides are the signaling molecules which buffer and aid plants to survive the rough elements from weather or wind.

Not everyone can consume grains which are high carb and gluten-damaging. Most can eat high fiber, heirloom potatoes and yams which are how many current ancestral societies still thrive. Legumes and non-gluten grains (millet, maize, rice, teff, oats) which are low glycemic index (not impact blood sugars) are also typically well tolerated. Notable cultures that follow traditions ferment, soak and cook these as their staples.

Copies of AMY1, Apo E2, FUT2 secretor status, and non-MTHFR genes may regulate who CAN versus who CANNOT tolerate the abundance from the fertile crescent and heavy agrarian societies.

Adaptive Drool in the Gene Pool: AMY1
Novembre et al Nature 2007
Low AMY1 Copy (High Starch Intolerant) v. High AMY1 Copy




TUBERS ROOTS SEEDS NUTS GRAINS AND LEGUMES

Bernstein et al (Nutrients 2013) examined the fiber spectrum in whole seeds and grains -- certain populations on earth get a lot of variety of fiber and RS from whole grains, including inulin, inulin-type fructans (ITF; short ones = oligosaccharides), gums, arabinoxylan (like psyllium), glucomannan, beta-glucan, hemicellulose, lignins and cellulose. For our ancestors who consumed these foods, their guts likely became adapted and diversified to an enormous range of gut flora that would breakdown and make useful such an assortment of soluble and insoluble fiber/RS3.

Beans and lentils look a lot like below too. These are seeds of legumes. They are rich in GOS (galactooligosaccharides) which specifically feeds our omnipotent Bifidobacteria longum, as well as nearly every character in the ancestral core. GOS is like breastmilk -- immunoprotective and pushes stubborn pathogens off epithelial sites. GOS are also known as RFOs, raffinose family oligosaccharides.

Oligosaccharides and inulin type fructans behave like anti-freeze, protecting Evolution's plant babies from the intermittent Ice Ages, frosty seasons and deep aridity of desert storms. They are widespread on earth -- the second most abundant plant carbohydrate in existence. Your gut flora love them! Please don't starve and torture them.

Non-bean/grain OS and inulin rich foods: artichokes, asparagus, dandelion roots, chicory roots, sunchoke/Jerusalem artichokes, Dandy drink, onions, leeks, garlic, chives, cactus, etc (YES THESE ARE FODMAPS: alert).

ALL the gut species that make us human as discussed in the Journal Club eat inulin and oligos.
  • B longum and all the bifidobacteria
  • Roseburia
  • F. prausnitizii
  • Akkermansia
  • Bacteroides
  • Clostridium



Dr. Bill Lagakos PhD writes often about GOS and B longum, one of his FAVORITE gut creatures: Calories Proper, Guts 'n GOS, Opus 142



Bernstein with Dr M. Roizen/OZ TEAM et al