Friday, December 12, 2014
Gut Guardian Podcast: Episode 07 – Cracking Down on Candida
The yeast conversation continues as Matt asks Dr. Grace just how much truth is there to the candida epidemic. The symptoms are everywhere, but there is a bunch of skepticism along side the diagnosis of candida. Dr. Grace and Matt discuss how certain metals in the body can be detrimental in its harboring of candida. And for those who are having problems with candida, Dr. Grace offers her own experience and the methods she used to rid her problems. There is even more to be discussed on future episodes.
Show Notes:Dr. Grace’s N=1 Blog Post
Wednesday, December 10, 2014
PALEO MAG HOT TONY FEDERICO HAS THE ANCESTRAL CORE MICROBIOTA IN ABUNDANCE; Citizen Science; Cautions with RPS-RUMPS; High Dose RAW Starch Appears to Suppress Christensenella, Akkermansia, and B longum That Make Us LEAN (Part III)
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.
LEAN ANCESTRAL CORE
HEALTHY MEDITERR-ANEAN DIET
6ft, 190lbs, ~14% BF
--The best levels I’ve seen STELLAR
F. prausnitzii IV
--Mitochondria like gut flora
--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.
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
--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
LEAN, GUT LINING PROTECTIVE
4 TB RUMPS
Starches grains, yogurt
1 TB RUMPS in water + 1 TSP Psyllium husk
1 TB RUMPS in water
Closer to normal
5-fold below normal
11-fold below normal
24-fold below normal
(appears to drop 5-20% )
~3-fold below normal
(more tame --
~3-fold below normal
+ not part of the ancestral core top 7 category
LOSS AND DEPLETION OF CHRISTENSENELLA AND AKKERMANSIA WITH HIGH DOSAGE RUMPS/RS2?
Across the board among all three N=1s, Christensenella and Akkermansia diminished substantially, the one exception was psyllium may have raised Akk in Child 1 and buffered the RUMPS-induced reduction.
The losses of Christensenella and Akk may have consequences later. Low Akk is associated with higher intestinal permeability, leakage of bacterial LPS into the blood, inflammation, and metabolic disorders involving poor handling of dietary carbohydrates, diabetes, obesity, and fatty liver/NASH.
Is this a problem? With the potential loss or suppression of B longum growth (see below), I think so. These are collectively part of our vital gut guardians on the mucosal surface. The lack of these species is associated with disease gut fingerprint for the largest epidemic of times: obesity.
High dosage potato starch c*ck blocks fat loss? YES INDEEDY. It may usurp the leanness microbial fingerprint and promote a 'diabetic/obese/NASHy' intestinal flora profile. This is my biggest gripe lol. For this reason alone, I've taken a complete changed and altered approach to this prebiotic, and shoving it to the last step of gut recovery (version C, max dose 1 TSP of bionic fiber).
Many prebiotics and fiber remove and expel pathogens efficiently and well. This is not a surprise. In Child 1 psyllium is anti-pseudomonal and was associated with RUMPS in reducing Pseudomonas to below detectable levels. Child 1 also had a overgrowth of Sutterella which is associated with autism children with digestive issues; it appears neither psyllium or RUMPS improved this. After intervention, Sutterella appears 5-fold higher. For the 3 N=1, the remaining pathogens after RUMPS were a mix of similar organisms: Haemophilus, Serratia, Neisseria, Staphylococcus and Campylobacter. Allan's guts saw a wonderful reduction of some potential vipers which hopefully translated to better health outcomes later.
On the other hand, Inulin, FOS ,GOS and the bifidobacteria they induce may dramatically reduce pathogens like Pseudomonas, Salmonella, Serratia, Klebsiella, Proteus, beta hemolytic Strep and Staphylococcus in human and animal studies, At the same time these prebiotics will boost our leanness-inducing and anti-inflammatory gut flora like B longum, Akkermansia, Roseburia and clusters XIVa. RS2 or RUMPS has a vastly different spectrum for reducing pathogens.
LOSS AND DEPLETION OF B. LONGUM WITH HIGH DOSAGE RUMPS/RS2?
We are still waiting for the Bifido species separation and quantification. Allan has 6 datasets to acquire but I'm looking forward to see how the different prebiotics fare. Depletion of bifido occurs with chronic inflammatory diseases and as we age. Tachon et al state "At the genus level, depletion of specific beneficial gut bacteria such as Bifidobacterium and Akkermansia spp has been reported for elderly individuals."
In Nearly Every Disease of Western Civilization;
Every Disease Has A Gut Fingerprint
Bifidobacteria species varies in our guts. Some are naturally found in humans and others are from our food, dairy, supplement and environmental sources.
"Closer inspection of the Bifidobacterium 16S rRNA geneApparently no B longum was grown selectively on 18% or 36% high dosage RS2. B longum does not appear to ferment or cross feed off raw starch granules in other studies; its preferred food is oligosaccharides, FOS, GOS, inulin, and psyllium (arabinoxylan in seeds, grains), etc.
sequences showed that a diet containing 36% HAM-RS2
selected for specific members of the Bifidobacterium genus
(Fig. S3). Aged mice fed the Control diet or 18% HAMRS2
were predominantly colonized by close relatives of
Bifidobacterium pseudolongum subsp. pseudolongum and
globosum. In contrast, mice fed 36% RS were enriched
with Bifidobacterium most closely related to B. animalis,
including the subspecies animalis lactis."
The above highlighted strains are all strains that eat raw starch granules with fast fermentive speed and special adhesion properties for granules, that B longum lacks:
It appears that RS2 being a substrate is a special fuel for certain species according to this study and other fermentation studies. RS2 is different from RS3 and even RS3 is degraded by different or more varied gut flora than RS2.
Turroni et al examined the types of bifido found in healthy mucosa and fecal samples. His study is an epic review of where bifido is found, ecologically origins, how much and the difference between mucosa-associated bifido (aka, I call this 'MAB') and the fecal ones. The MAB ones are the ones we want; these provide barrier protection and SEAL THE AWESOME AMAZING GUT. So please keep this in mind and why such tremendous benefits for gut restoration are seen with anything that replenishes B. longum, the mucosal Superman. Matt Pepin and have done our best to discuss its role in health and how to boost it on our podcasts.
So fermented dairy and supps with B lactis are wonderful and work, but they are not the same as B longum and other MAB inhabitants. The authors note: "However, some bifidobacterial species, such as B. animalis subsp. lactis and B. dentium, appear to be more abundant or present only in stool samples, thus suggesting that these taxa do not represent a dominant component of the mucosa-associated bifidobacteria...A large proportion of the currently used bifidobacterial probiotic strains belong to the taxon B. animalis subsp. lactis (e.g., Bb12, DN-173, and HN019), which are considered to confer beneficial effects on the host through interactions with this host and with other components of the intestinal microbiota (39). However, in this ecological study, we found that this bifidobacterial species is only rarely found in intestinal biopsy samples whereas it is frequently detected in fecal samples, suggesting that this taxon may not be abundant among the intestine-adherent component of the human intestinal bifidobacteria. "
Fecal bifidobacteria (good representation of mucosal concentrations, except for B lactis, B dentium):
B longum 43.5%
B lactis 23%
B adolescentis 12%
B pseudocatenulatum 8%
B bifidum 6%
B breve 4%
B pseudolongum 2%
B dentium 1.5%
Mucosal Associated Bifidobacteria (MAB):
B longum 75%
B adolescentis 11%
B breve 5%
B pseudolongum 4%
B pseudocatenulatum 3%
B bifidum 1%
B lactis 1%
|Turroni et al 2009|
Tachon et al reports that in their study were high dosage HAM-RS2 were fed at 18% and 36% certain bifido strains were selected over others which lead to dominance of these populations. The starch eating strains overgrew (Fig S3). The non eating strains appeared to be suppressed: B breve, B bifidum, B longum, B adolescentis, and B. infantis. [B adolescentis and B breve actually can eat switch and ferment both inulin/FOS/GOS and cooked/raw starches].
Moreover, different Bifidobacterium species werefound in mice fed HAM-RS2. Bifidobacterium animaliswas specifically enriched in mice fed 36% HAM-RS2, andthis species was previously shown to degrade certain RSformulations with greater efficiencies than species pseudolongumand breve (Wronkowska et al., 2008).
Does this happen in real life? I believe so and we will learn much much more after Allan obtains the raw data. In 2 N=1, B longum was assessed after intervention with high dosage raw potato starch and the numbers were non-existent or extremely low. If RS2 reduces Akk and Christensenella by competitive selection as we see in the Allan's experiment, then the same loss of diversity of bifidobacteria may be observed in Tachon et al's study where a high degree of overselection of B animalis and other starch-eating Bifidobacteria occurred.
Degrading raw starches with oddly high efficiencies produces a gut flora that appears high in starch degraders and low in the non-starch degraders such as important B longum, B breve and B pseudocatenulatum. Their ecological niches cannot exist if it is overtaken by ultra fast starch degrading B animalis or other starch degraders like Bacteroides family or Ruminococcus, which are all enriched in raw potato starch reports.
3 N=1 B. LONGUM REPORTS
Lastly I think it is important hold off on raw potato starch until confirmation of the presence of B longum and Akkermansia can be made. B longum is very special. It is one of the ultimate gut guardians and is found elevated and in vast abundance in healthy subjects' guts. Out of the 66 phylogenetic core species that Tap et al in his research discovered in healthy subjects in Europe, B longum is #5 in abundance and enrichment in their fecal contents. I call B longum ancestral because the great majority of the top 7 species in Tap et al's core microbiota are also found in Hadza, Burkina Faso, Malawi and other ancestral cultures that practice HG or ancient living and cooking practices. Tap et al's work as been confirmed in 4 regions (France, EU, USA, China). Here is a list of the 66 core. B longum is dense and enriched in centenarians in two studies so far. It appears that we do not want to neglect this micro-organism.
As Tony discussed how important it is to enforce lifestyle practices that are ancestral and good for us, I believe that replicating and replenishing gut flora which follow an imprint that mimics ancestral patterns will improve not only gut health but overall longevity and leanness.
Below are 3 N=1 reports. We are going to be unscientific and again compare apples with oranges!
Report (a) is after high dosage raw potato starch. This individual probably started off with no B longum. Total bifido was 1/10th of normal.
Report (b) is after a long duration on high dosage raw potato starch. Bifido was extremely high but was it all likely B animalis and no B longum? Report (c) is the same person (Tim Steele) and shows the changes associated with discontinuing high dose RPS and starting real RS3-rich food (cooled tubers, beans, rice, grains).
Intrepid gut explorer. All the contents for this series and the past series (Parts 1-5) were approved by Tim to discuss several weeks. I brought up my observations and concerns very early on. He gave his approval to discuss all my concerns, precautions and problems for adverse effects generated by high dosage RS2 including concern for his liver, his high liver tests, SIBO/upper gut dysfunction, fatty liver/NASH, depletions of gut guardians including Akkermansia, and possible connections to the gut obesity fingerprint that is created with high dosage raw potato starch/RS2, the studies, the other N=1s, etc. He is an bold citizen of science and declined the three times that I asked him if he wanted me to omit his data. We've had ongoing discussions including on our comment sections of both of our blogs. In case you were not aware: "Grace has been privy to all of my gut tests, labs, and health concerns as a friend, not a doctor. I gave her express permission to discuss them how she sees fit. I think that this information needs to be shared freely. If I had a problem with any of this, Grace would be the first to know. I don't have a problem with her discussing me or my experiments. They are out there for everyone to see and interpret as they wish."
N=1 for 2 reports (b and c): What appeared to occur to the gut microbiota on switching from high dose RS2 to no RS2 (comparing, again, apples to oranges)?
- Akk was previously low 17-fold below normal and then almost doubled.
- Christensenella was undetectable earlier then increased and was more than half of normal of controls. RS3 (cooled-crystallized starches) and inulin 10g/day may have boosted this impressive and leanness-building gut flora. Stopping raw potato starch may be part of this successful equation.
- B. longum was nearly undetectable, 2000-fold below normal (but at least present! lol). We have no prior # to compare.
- B. animalis predominates at ~90% of all bifidobacteria detected in stools. Ancestral? Healthy?
x 1 month
x over 1 yr
NO RS2 [NO RAW STARCH]
x ~2 mos
CARBS 100-150 g
40g RS3 rich
HIGH DOSE RS2 MAY SUPPRESS 3 SPECIES
(psyllium, inulin, GOS, yacon eating)
2000-fold below normal
17-fold below normal
10-fold below normal
More than 10-fold below normal
2.5 fold below normal but improved on ZERO
RAW POTATO STARCH
HIGH DOSE RS2
OVERSELECTS SEVERAL SPECIES
Not ancestral or part of phylogenetic human core
CONCLUSION AND ACTIONS
Consider amplifying the gut guardian species associated with leanness and longevity for optimal health: B longum, Akkermansia, and Christensenella.
Temporarily stop high dosage raw potato starch to halt the growth suppression of vital barrier protective gut flora
Consider adding in foods and prebiotics that raise specifically B longum and Akkermansia
Try the 7 steps to optimize your digestion, leanness and longevity