Paleo Mag
Tony Federico
Author of Paleo Grilling
BEAUTIFUL GUTS, BEAUTIFUL MINDS
Matt Pepin and I had the pleasure of having Tony on the show recently for the Gut Guardians podcast. Look out soon for it. We explored all sorts of paleo and ancestral themes particularlyTony's take on how we are so plugged in yet not getting the ancestral hits of oxytocin from face-to-face, voice or real contact. We also had the chance to review his uBIOME from earlier this year and why he felt that raw resistant starch was not ancestral, thus never partook. His bold piece on Resistant Starch (RS) was one of the first on the 'RS Cautions and Concerns', which also includes my early (unevolved) thoughts at the time.
New evidence has presented, namely studies and citizen science (N=1, AMGut, uBIOME, Genova Diagnostic 2200 results) that use 16S rRNA analysis to detail and drill down what is occurring in the gut microbiota with RS2, raw starches, as a fiber and prebiotic and downstream effects.
In the podcast we discuss more in depth revelations on this and why I think caution should be considered for situations when high dosage RS2 (raw starches) should be avoided, why, how, and what might be considered ancestral.
He gave me permission to use his uBIOME and give my thoughts on his N=1. Luv citizen science.
Currently I am preferring uBIOME over AmGut for mainly 2 reasons: (1) easy access to the detailed raw taxonomy to view down to species and genus depth, (2) turn around is fast. Like all testing, it's imperfect. Accuracy and sensitivity are likely limited like all testing by 20-30% if we are lucky. Comparisons between testing methods also restrict what conclusions we can make, and additional testing contaminants and other lab obstacles still clearly exist. Now onward and let's do the unscientific thing and compare apples with oranges!
Placing Tony's 'Paleo Diet' column against the Hadza, healthy Mediterranean diet and the % of relative abundance in the healthy cohort reported by uBIOME, we can see how his gut size up, knowing this is provisional and only gives us 'patterns'. Functional medicine practitioners like myself compare gut species and phyla. With the upgraded Genova Diagnostic 2200 Stool GI Function testing it is possible to tie suboptimal health with the gut microbiota 'fingerprint'. By altering the 'fingerprint', better digestion, better health and performance can be obtained. Gut testing and knowing your gut 'fingerprint' is the future of all medicine because all health begins in the gut (Hippocrates).
Here is a great manual, interpretative guide, see pg 21-25 to review Tony's data along with me. I would place 'green' as the above average measurements and 'red/yellow' as below average depending on the magnitude (eg 10-fold v. 0.2-fold reductions). Microbes magnify their populations by log scales, so below the representations are by 'fold' or 'times' expression.
Tony's diet and lifestyle: no grains, no dairy, lots of non-starchy vegetables, fermented foods, meat, fat. He is also a personal coach and works out nearly daily with a lean BF of 14% and high muscle mass.
Gut Microbe
LEAN ANCESTRAL CORE
ANCESTRAL
GUT DIVERSITY?
20-60g RS3
Hadza Tubers
HEALTHY MEDITERR-ANEAN DIET
Italian Cohort
uBiome Normal
Avg
PALEO DIET
uBiome
Non-starchy vegetables
6ft, 190lbs, ~14% BF
Active physical
Fermented Foods
Christensenellaceae
Christensella
--
--
0.844
0.0120
4.35 5X
--ROCKSTAR
0.0224 2X
--The best levels I’ve seen STELLAR
Akkermansia
--
--
1.22
0.0488
Bifidobacteria
0.02
8.1
0.894%
0.0010
B.longum
B.catenulatum
--
--
?
?
0.4-0.5%
--
None
0.0010
Roseburia XIVa
3.9
7.7
3.46%
1.27
Eubacterium XIVa
2.2
1.4
0.912%
5.97 6X
Blautia XIVa
3.5
9.5
7.63%
12.9
F. prausnitzii IV
11.8
18.5
9.48%
11.8
RuminococcusIV
2.1
8.6
5.96%
6.27
Alistipes
--
0.9
1.39%
2.13 0.5X
Bacteroides
0.2
7.1
9.66%
2.49
Rikenellaceae
--
--
1.43%
2.15 0.5X
--Mitochondria like gut flora
PATHOGENS
Pseudomonas
Haemophilus
Enterobacter
Staphylococcus
0.0583%
0.0689%
0.2600%
0.6010%
ALL NEGLIGIB
0.0007
0.0047
0.0043
0.0094
--No neisseria, serratia, morganella, fusobacteria, klebsiella, etc
TONY'S HAWWWT MICROBIOME: LEANNESS ADVANTAGES
CHRISTENSENELLA: One thing that really struck me first about Tony and his gut microbiota is the richness and abundance of an up and coming new potential probiotic and gut flora known as Christensenella minuta, Tony's shows double the normal values reported in healthy controls from uBiome. Unfortunately I could not locate the Hadza or Mediterranean cohort data. For the phyla that C minuta belongs to, Christensenellaceae, Tony's gut values were OFF THE CHART, 4.35-fold above normal. This is impressive to me because I look at a lot of testing and never seen any numbers even close. We will go over others -- because RS2, raw potato starch -- appears to lower it significantly in every record I've observed.
Ruth Ley and her group reported first on Christensenella minuta. It is quite the bug. When obese rats are implanted with viable, live probiotics, they were leaner than controls and did not gain fat as easily on fat-inducing diets (high sucrose, high fat rat chow). Like Tony, C minuta is found in higher concentrations in lean people. (And high dosage raw potato starch ingesters have hardly any.) The genus C minuta is in only two species that I'm aware of so hopefully the numbers listed are a good proxy for C minuta.
Recently Ed Yong wrote about this special leanness probiotic: "The team confirmed this by deliberately adding Christensenella to a stool sample before transplanting it into germ-free mice. Without the microbe, the mice put on 15 percent more weight and had 25 percent body fat. With it, they put on just 10 percent more weight, and had just 21 percent body fat. For comparison, that’s the equivalent of a 70 kilogram person putting on seven extra kilograms rather than ten." NatGeo.
Source
BUTYRATE-PRODUCING XIVa/IV CLUSTERS: Eubacteria, Roseburia, Blautia, Ruminococcus and F. prausnitzii were all extremely robust. These are versatile eaters of RS3 (cooked-cooled starches, which Tony eats little, it appears) and the entire fiber spectrum. I can tell from these #s that Tony's diet is a true smorgasbord of rainbow colored vegetables, fruits and seeds. Beyond butyrate, cluster XIVa has been shown to very important for sealing the gut barriers and reversing immuno reactive conditions such as peanut allergies in animal models.
Alistipes is one of the leanness building microbiota and part of the ancestral core. Tony's appears 50% higher than normal.
OTHER LEANNESS ALTERING MICROBES AKKERMANSIA, B LONGUM: BELOW AVERAGE
Akkermansia is another leanness building microbe. Scientists give it to fat mice and it alters their body fat composition, decreases body fat, improves blood sugars, lowers LPS and endotoxemia, reduces several inflammatory markers, decreases liver function tests, fixes faulty intestinal permeability, increases HDL cholesterol, decreases TGs, and even improves the signs and symptoms of fatty liver/NASH (non-alcoholic steatosis hepatitis). Like Christensenella it is find in abundance in lean, non-diabetic subjects. Those with diabetes have low amounts. Weight loss and administration of the insulin sensitizing drug metformin appears to raise Akkermansia. Elite rugby players on the Irish national team who eat a 'clean', whole food, high protein diet have elevated levels of Akk. Cranberry extract which is high in polyphenols raise it. Factors that raise bifidobacteria, also will raise Akk (I suspect it crossfeeds from them too).
"Akkermansia and Bifidobacterium proportions werealso correlated with the level of expression of proglucagon,the precursor of the potent anorexigenic peptideGLP-1 (Moss et al., 2012), which is associated with theimprovement of glycemic and insulin responses andreductions in fat mass of mice fed prebiotics (Delzenneet al., 2011). One possible mechanism to explain theseeffects is that Akkermansia fermentation of mucin resultsin the production of propionate (Derrien, 2004), a SCFAknown to stimulate the production of GLP-1 in rodents(Zhou et al., 2008). Generally, Akkermansia is increasinglyassociated with improved gut health and ameliorations inbody weight disorders (Zhang et al., 2009; Png et al.,2010; Santacruz et al., 2010; Delzenne et al., 2011)."Tachon et al
The prebiotics associated with increased Akk are: GOS/oligosaccharides (beans, whole grains), inulin, FOS, yacon root, yacon syrup and inulin-type-fructan-rich foods (onions, leeks, garlic, sunchokes, green vegetables, cactus, etc). Not hard to get but the tubers like yacon or sunchokes may be more challenging than eating a lot of onions daily. Obese humans benefit from these prebiotics and foods and experience the same metabolic improvements and fat reduction because both Bifidobacteria longum and Akk increases substantially HERE (personal communication -- Akk incr; Salazar et al 2014). I made some suggestions to Tony because achieving Akk is a 'tool' to sustain not only better gut health but to supercharge performance. It it appears to be highly associated with better sports performance (elite Irish rugby players), fat burning and overall energy partitioning between our brains, fat, and muscles.
Paleo foods are not honed in yet on obtaining the prebiotics that support good Akk or B longum -- inulin rich sweet tasting, non-starchy roots, onions, leeks, sunchokes, chicory, rhizomes, and tubers.
Akkermansia is a very special microbe which will be a superstar probiotic in a few years like Christensenella, I predict!
B longum was low for Tony's gut. Not shocking. Everyone's is low or extinct secondary to antibiotics. Tony reports he has not had a single course of antibiotics for the last 10 years.
So despite low Akk and B longum, I believe the Christensenella and perhaps other factors that we cannot grasp or understand at this time with the lack of research can explain a lot of what can be observed with limited data. I think in the future we shall hear a lot about Tony's guts -- full of Christensenella and big butyrate factories that protect against disease, obesity and inflammation.
A PATHOGEN-FREE GUT IS A DISEASE-FREE GUT
The standard opportunistic bacteria and invading oral/skin biome that enter the gut were all super low for Tony's guts. I was really happy to see this, as much as the high Christensenella. Having a low burden of pathogens is the hallmark of a gut with longevity and health. When pathogens are present, yeasts typically are as well. I can presume Tony's yeasts are minimal or non-existent by the pattern here (organic acid urine testing is best to confirm). Stool testing like this will not reveal the giardia/protozoa, yeasts or helminths/worms, so other testing is needed to confirm if interested.
As we age, two things are observed in humans and animal models
--higher pathogens
--depletion of bifidobacteria and other symbionts (ancestral core)
How do we combat this? Are there ways to achieve longevity, leanness and healthy via our gut microbiota? I take Tony's guts as a standing example of being successful with lifestyles and diet that promote the most optimal, diverse, and balanced gut devoid of dysbiosis and pathogens. His diet is rich in plant polysaccharides and fiber, few gut disruptors (gluten, n6 PUFA, etc) and appears to feed a myriad of gut flora that make us into lean phenotypes (butyrate producers and Christensenella).
CITIZEN SCIENCE: ALLAN FOLZ'S FAMILY RUMPS EXPERIMENT
Allan and his family received 3 out of 4 of their final results from AmGut recently. Please ck it out. We will talk more about these reports in the next 1-2wks but here are some of my initial thoughts that I shared with Allan. Drilling down was fun and we can see a neat view of a several cases and 2 prebiotic results (psyllium, raw potato starch).
Allan had reported he felt wired and not the same on RUMPS, which required changing the dosage from 4 TBS at bedtime to splitting it 2 TBS twice daily. He recorded the blood sugar readings pre- and post challenge.
RUMPS = raw unmodified potato starch (RS2)
The most outstanding changes were, I noted:
Drastic drop in Christensenella for 2 (the third, Child2, had no detectable Christensenella to begin with)
Significant drop ~15-fold and 50% of original Akkermansia (Allan, Child 1 respectively). No change/mild increase where psyllium was used (increased Akk in Child 1; appears the depletion is buffered with additional insoluble/viscous/soluble fiber)
Significant increases in total bifido of 5 to 20-fold magnitude; B longum data is pending
Decrease in diversity (number of species detected) but some pathogens reduced and some new pathogens emerged or increased (Suterella, Staph, Campylobacter).
Slightly higher blood sugar readings afterwards for 3 (except Child 1 who was on psyllium+RUMPs; psyllium is associated with lower and better controlled blood sugars and weight loss). Goal BG less than 84 (normal/optimal).
No weight loss reported by either Allan or Adult 2
Gut Microbe
ANCESTRAL
CORE--
LEAN, GUT LINING PROTECTIVE
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