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 sapien? Pan 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