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)

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
MICROBIOTA



uBiome Normal
Avg
Allan pre

low-mod
LC paleo
RS3-GOS
beans daily
Allan post

4 TB RUMPS

RS3-diet
Child1 pre


Starches grains, yogurt
semi-
paleo
Child1 post

1 TB RUMPS in water + 1 TSP Psyllium husk
Child2 pre
Child2  post

1 TB RUMPS in water
B longum
(inulin/GOS/
psyllium eating)
0.4-
0.5*
---
pending
--
---
--
--
--
Christensenella


Christensenellaceae
0.012


0.844
0.010
good

0.23
below detection

0.37
0.010 good

0.04
below detection

0.01
below detection

0.03
below detection

0.02
Akkermansia
1.2%
16.93
Over
growth?
1.45
Closer to normal
0.24
5-fold below normal
0.26
psyllium
buffered?
Little change
0.11
11-fold below normal
0.05
24-fold below normal
Diversity
Species#
0.001+%
(appears to drop 5-20% )
102
81
93
87
smallest drop-PSY
95
84
Bifidobacteria




B.animalis
B.adolescentis
(RS2 eating)
0.88%
0.95
good
4.99




? unknwn
0.33
~3-fold below normal
1.48
(more tame --
psyllium?)



?unknown
0.27
~3-fold below normal
6.23




??unknwn
Potential pathogens

staph
haemoph
enterobac
fuso
neisseria
serratia
campylo
haemoph
neisseria
serratia
sutterella 0.05
pseudom
staph
sutterella 0.26
campylo
neisseria
haemophil
staph
campylo
haemop
staph
campylo
haemoph
staph

+  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).




PATHOGENS

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."
Bifidobacteria Depleted
In Nearly Every Disease of Western Civilization;
Every Disease Has A Gut Fingerprint
AHS14

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 gene
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."  
Apparently 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.

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:
B animalis
B lactis
B pseudolongum
B globosum

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?




ANCESTRAL
CORE
N=1 (a)
20-40g RS2
x 1 month

N=1 (b)
20-40g RS2
10-20g RS3
x over 1 yr
N=1 (c)
NO RS2 [NO RAW STARCH]
x ~2 mos
Human Phylogenetic
Core Species
VLC DIET

UBIOME

uBiome Normal
Avg
PHD
CARBS 100-150 g

AMGUT
10g inulin
40g RS3 rich
REAL FOOD

uBiome
HIGH DOSE RS2 MAY SUPPRESS 3 SPECIES

B longum
(psyllium, inulin, GOS, yacon eating)


undetect
below 0.0001
below
normal


0.4-0.5*


[low?]   


0.0021
2000-fold below normal
Akkermansia
3.52
above
normal
1.2%
0.07  
17-fold below normal
0.12
10-fold below normal
+Christensenella
0.0076
below normal
0.0120
Undetect
below 0.001
More than 10-fold below normal
0.0048
2.5 fold below normal but improved on ZERO
RAW POTATO STARCH
HIGH DOSE RS2
OVERSELECTS SEVERAL SPECIES




Bifidobacteria

+B.animalis
(starch eating)
0.0712


None
0.88%
11.32

unknown
8.81

7.90
Not ancestral or part of phylogenetic human core
Replaces
B longum?


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

73 comments:

Anonymous said...

Hi Grace, For now, and possibly for ever, you've convinced me it's best to remove the Potato Starch from the equation. I have to admit that when you first started raising this issue, or when I started taking notice, I was seething furious that I had been taking 3 to 4 Tbs a day for about a year, and that I might have been taking my, and my kid's, digestive health in the wrong direction. Undirected fury but fury none the less. I have been backwards and forwards a few times since with yours and others opinions. I am somewhat mollified by the fact that we have been taking probiotics (Bio-Kult,Prescript Assist, AOR P-3), fermented vegies, yoghurt, keffir, and kombucha all along, as well as having cooked and cooled potatoes and white rice daily, as well as multi coloured vegies/salads, including onions, asparagus, and carrots. We are now supplementing with inulin and pyshillium as well - in our morning banana, yoghurt, cinnamon,and dessicated coconut mix. Personally I would like to take the time to thank you for courageously and passionately going deeper and deeper, and continuing to search for the truth, which I acknowledge is bound to continue evolving. Warm Regards, Adrian

Anonymous said...

Ahh Dr. Grace,

I am smiling ear to ear.
You've done it again Gut Goddess!
Spectacular post.

Brava!!
Thank you so much for your amazing dedication.

Regina

Dr. B G said...

Adrian

You can't be more mollified than me. You're not allowed ok? I've administered retractions and refinements where I can. If you heard the Bulletproof podcast, that was the height of my clarity.

Have you done gut testing? Test don't guess because your gut is probably fine

Actually you are far ahead of the curve with your awesome diet, probiotics and prebiotics. Bio kult is wonderful and contains the range of bifido, b longum and l plantarum. I suspect your gut will be fine so test don't guess. Our guts are quite resilient. We are lucky to see so many citizen gut testing particularly the PRE- and post-interventions because they shed a lot of light on what researchers take years to obtain. There is a lot of inter-individual variability so again this is pseudo science or even unscientific by some. (yet others rely very heavily on touting their test results). We can see from Tony's that two species may not tell enough (low Akk and extinct B longum) but when we are able to observe 5 or 8 then a story unfolds.

RPS is great because it got people into gut health. See? That worked. Fiber is not sexxxy or cool. Poop isn't really either. Im very grateful for that

So many people have dysbiosis or are missing huge swaths of gut microbes. As long as someone is consuming a wide range of ancestral levels of microbes, fermented foods, RS3, viscous, insoluble and soluble fiber and inulin, I believe diversity will be optimal. Skipping any of these appears to lead to reduced diversity which our guts already appear to suffer from. Please read Raphi's comment on the hadza post. He's a microbe researcher. Competition and collaboration/crossfeeding are the rules of the gut.

Going VLC, gluten free or Paleo actually leads to loss of diversity in studies so no matter what, if we have been down these roads, what we can benefit from consuming the entire spectrum of what evolution shaped for our guts.

Matt Pepin jokes with me that he wishes he had his PRE-Paleo or PRE-VLC gut flora! I concur!! I had better gut diversity back then!!

Dr. B G said...

Sweet and Brilliant Regina~

Thank you for all of your kick assed and aikido-powered comments and generous insights !!

G

Christopher said...

So....persuading Richard to bury the whole thing makes it no less egregious. I'm quite sure Bea would agree. Oh, but wives don't really factor into all this 'ancestral' stuff. I forgot... Richard put it all out there - the only way you can make it go away is to come clean.

Or post one of those infamous pics. ; )

Dr. B G said...

Christopher,

Thanks for your kind comment. I left the circus of broken hearts a while ago.

Anonymous said...

Hi Grace,

Thanks for keeping on posting stuff. Raw PS has indeed been a catalyst for a lot of interest from an army of anonymous people who want to take their health in their own hands. I personally became so much more knowledgeable about nutrition and overall health issues. But the irony is that my diet (whole foods, emphasis on prebiotic ones) and lifestyle (good sleep, low stress, a lot of various physical activities) are actually very simple and pretty similar to what it used to be before I started to know about paleo :D Funny, isn't it ?!
So these days, I tend to forget paleo / primal / VLC ON PURPOSE :D
But it was a good journey for I learned a lot (and to be honest, I never believed much of all that - all I had to do was to look back at my close ancestors and emulate what they were doing to some extent). So life is good :)

PS: about the "circus", I guess nobody cares really. I am not sure why RN has to make all this stuff public but after reading his post, I can't help thinking that all this sounds a lot like high-school stuff - it's irrelevant, and it is so North-American. As a European of latin ancestry, all this flirty under-the-belt private chit-chat is perfectly normal, there is absolutely no need to bring that out or even brew some sort of guilt for it. We are sexual animals after all, so what is all this fuss about ?? :D

Dr. B G said...

Adrian,

When and if you receive any gut testing results I'd love to see what is in your black box given the commendable gut improvements you've done already. I don't know what 'recovers' the suppression induced by high dose RPS or what buffers. For child 1 I see some buffering but not for Akk, Christensenella and (i predict) B longum since people appear depleted already for these vital gut guardians.

Dr. B G said...

Anon

We are probably kindred spirits -- and reverting to just ancestral ways without processed food or white powder! Thank you for sharing your thoughts and wisedom

Anonymous said...

Another great post Grace. I had a question about Jerusalem artichokes, do you advise them as a B. Longum supporting food? Would it be better to cook them or can they be eaten raw? Thanks for all you do.

Dr. B G said...

Anon

Raw jerusalem artichokes are awesome -- really crispy, crunchy and mildly sweet. We are able to get from our local Sprouts and I heard the farm home deliveries have them through the winter. My kids however enjoy them more in soups -- somehow they are delighted to find them when I put them in!

Whole foods are awesome. They contain iRNA, interference RNA which shuts off many detrimental and inflammatory pathways in our bodies. Scientists are just finding out how important and aligned our body is to whole, real food and all of its contents (and exteriors like SOIL PROBIOTICS lol)

Sid Dishes said...

Hi Dr BG,

The increase in Allan's Proteobacteria is interesting. Are species-level pre and post data available? I don't think we can draw conclusions about a prebiotic being "good" or "bad" on the basis of phylum-level data. Some are pathogens, some are good.

I agree that psyllium is a good prebiotic that mitigates against some of the negative inflammatory effects of RS2 in those who are immune compromised. I've experienced this first hand. I think psyllium might actually be a good starter fibre for people who are just getting into this.

I agree that RPS is not optimal but I hesitate to diss it because I still think it's a very cheap and useful tool for getting people to think about the stuff that really matters (metabolic endotoxemia) instead of chasing down downstream endocrine sequelae like insulin and leptin. I also think it's useful, at least initially, for those who find themselves on a VLC/grain-free/paleo induced death spiral.

Dr. B G said...

Hey Sid

Thank you for your thoughts -- I don't know what to make of some the pathogens. I concur. The lack of pathogens with Tony's high plant fiber Paleo diet is very impressive to me. It reminds me of Wahl's gut successes and MS recovery.

I had GERD/reflux and I've never had it before. I was losing oodles of body fat and gaining lean mass, then a re-trial of the RPS high dose halted all of it, and induced intractable GERD for several days.

So... I'd have to disagree with you. A lot of people are probably the norm bell curve like me for gut dysbiosis from modern living and abx. I think RPS is a terrible way to start to try to heal the gut -- 'cheap and easy' way to gain a gerbil gut that lacks the gut species that make us uniquely human, smart and huge fat-burning machines.

I have warned Mr Nikoley as well - the high dosage RPS for over the last 1-2 years probably prevented the healing of his autoimmune Hashimoto's. Thoughts? Would love to entertain unscientific pseudoscience speculation. I recommended he get a gut test and fix what is missing and lower the pathogens.

Sid Dishes said...

I think gerbil gut is a bit of a premature conclusion since we're all still on a steep learning curve about this stuff and the science is in its infancy. I know people who have done well on the RPS. Personally, I saw benefits for the first few months, though long-term it wasn't so good so I've moved on to other fibres since.

Can it worsen autoimmunity? I think so, transiently at least, but so can everything else that's immunostimulatory if it's not at the same time expanding the core anaerobic commensals that are going to help resolve the underlying immune dysregulation.

Christie said...

I can walk 20,000 steps each day easily after switching over to inulin.

While taking RUMPS I could not do this. The stress would knock me out. I was forever holding back.

+ my thyroid is thriving now.

I don't understand why Dr. Grace even recommends adding it after health is recovered. Why even bother?

JOHN PROCKISH said...

thanks
no potato starch
what about green banana powder or plantain powder

thanks

Anonymous said...

Green banana flour has at least other prebiotic stuff for it (inulin, FOS, etc). It's the whole banana transformed into flour.

Overall, I'd have to agree with being careful about RS ... a year ago, it gave me some haemorrhoids (I never had any, it happens while taking raw PS as suggested by R. Nikolei and Tim Steele). I can tell you, I ditched the powder pretty fast ... And why did I do this ? I was already lean and feeling good on a natural whole food diet. Pfff, what a waste of time! Thankfully, it was cheap!

Anonymous said...

First of all thank you for another amazing post !

Just one question please:

Due to potential benefits I have decided to start taking some B. longum probiotic on the daily basis alongside my various fiber intake.

I am just wondering if large "mainstream" brands like NOW Foods, Swanson, Healthy Origins etc are an acceptable source of probiotics?

They rarely get mentioned and unfortunately brands recommended here are difficult to find and expensive to import to my country so I am wondering if there is something inherently wrong with big brand probiotics?

Thank you very much

Anonymous said...

Hi Grace! Thank you for all the information you provide. You have helped me tremendously! I have Celiac's disease- diagnosed two years ago. It was causing seizures, fatigue, brain fog, anxiety. I tried low carb paleo for 6 weeks, felt only slightly better, but lost no weight (about 30 lbs over weight)! I stumpled upon this potato starch stuff, but as a Christian, I found the Free the Animal site offensive, but have really appreciated your approach.... I experimented with your advice. I now have the most energy and mental clarity I've ever had my entire life!!!! Going strong a few months now!! Better than amphemtamines like adderall :). Im so anazed at such simple approach. I didnt notice results with potato starch so i didnt take long. Havent noticed much with inulin either. But AOR dramatically helped and then added in beta glucan and that has been miracle for me! It seems to cut down inflamation? So I now take aor, beta glucan, threelac(also reallly wonderful!) and garden of life. i also eat refried beans i prepare traditional style (soaking and using beef tallow). I feel the best ever and i just cant thank you enough! Im a cpa and will be going back to work this tax season!! I feel amazing and so much energy!!!! PS. Im thinking to try yacon syrup (essential living foods offers one that is source verified) :)

Anonymous said...

"RPS - 'cheap and easy' way to gain a gerbil gut that lacks the gut species that make us uniquely human, smart and huge fat-burning machines."

What exactly is a gerbil gut?
Are you really suggesting that those who take RPS are going to turn into gerbils?

Dr. B G said...

Anon

WOW THAT IS STUPENDOUS~! Do you see the gut fingerprint for 'celiac' on this post? This fingerprint is missing bifido, lacto and cluster IV F prausnitzii, but is overrun with a tremendous # of gut vipers from the lower gut. Actually even overgrowths of the good XIVa Roseburia is sometimes seen. I think it is not wonder that celiac gut is one of the most difficult but now I have met more than one person who has healed and restored the celiac gut to the point they can consume gluten with no problems (hattip: Eddie B).

I'm so glad your brain fog, seizures, anxiety, fatigue and fat block are all improved! Isn't it wonderful! The AOR is certainly a game-changer for many including myself. I found also the Prescript assist and Bacilli family all helpful for gluten and dairy digestion and allergies.

Threelac (soil probiotics) was used by my sister in her recovery of her daughter with autism spectrum and has signs of celiac. I am very glad to hear of all the changes you notice.

Please let me know how the yacon syrup works out! It may help further eliminate vipers commonly associated in the celiac fingerprint. Don't forget bifido/lacto. Matt and I talk about Renew life (again, Eddie B has had wonderful results and he attributes to Renew -- thx Eddie!) and how it reversed Matt's dairy/gluten dual intolerances.

Where do you get beta glucan? GF steel cut oats or oat bran?

I had a boy I helped -- he had seizures only 1/year but obtained improved focus and less ADHD with the soil probiotics (and excellent high fiber diet, kombucha, etc). We have to see if the seizures actually are eliminated. How are the frequency, duration and severity of your seizures now? Ketones are as you are aware helped, but we can replicate by having improved SCFA and butyrate production from a balanced, harmonious and collaborative gut ecosystem. How is your fermented foods?

Dr. B G said...

Anon,

I was joking. Crociani et al 1994 had broken down the bifido strains by animals and sewage. In rats they found (different from the Tachon et al study):
B animalis
B globosum
B pseudolongum

So to me when these are enriched in a human gut, they make a pattern that might be considered more non-human or rodent like. It could be 'cow gut' too because these above were enriched in bovine rumen as well.

Human ones in the Crociani study were
B adolescentis
B angulatum
B pseudocatenulatum
B gallicum
B bifidum
B longum spp infantis
B breve
B catenulatum
B longum
(not pseudolongum or animalis -- for some reason)

Personally I feel many modern guts are amputed in bifido strains -- we should have diversity yet there are only 1-2 strains if at all. It is scary when I see none or none detectable. Studies show even 70% of young individuals have guts that lack B longum, yet in the epic studies by Tap and Dore et al for nailing down the phylogenetic core in healthy subjects B longum was found in nearly all tested and it is considered #5 out 66 in abundance in unique OTUs. I've polled several of my gut researcher friends, 'which Bifido is most important' and unanimously all said B longum (one was actually a bifido gut researcher).

Honestly I don't know much about bifido except that it is very important, in addition to our soil based and environmental probiotics. Getting some will never hurt. Maintaining a robust population in your gut garden is likely to reap many benefits and protection from the diseases that the B longum probiotics appear to improve and ameliorate:
--anxiety
--high cholesterol
--high TG
--low HDLs
--obesity
--diabetes
--NASH/fatty liver
--allergy, atopy
--asthma
--celiac
--gluten/gliadin enteropathy
--NEC
--diarrhea
--constipation
--chemo/rad induced dysbiosis
--IBS, IBD
--etc

In short: try to confirm B longum and consider RPS avoidance to minimize its suppressive competitive effects in the gut ecosystem as RPS heavily and naturally selects populations of bifido that eat starches (breve, animalis, lactis adolescentis, pseudolongum, globusom, etc).

Dr. B G said...

I believe those brands are very acceptable. If you are on the 7 steps for healing and not recovered yet and avoiding allergens make sure the product is soy, dairy and corn free

Dr. B G said...

Christie

That is so interesting. And I have no explanation except there must have been a worsening of a metabolically deranged gut fingerprint. Glad to hear things are sommuch better! Thx!!

I kept it but may reserve the right to remove later if gut testing show suppression across the board despite 7 steps and 2-3 TBS of other fiber (so kinda diluted to 10% of total amended fiber). It's just a fiber like pectin or beta glucan. I think other than Hadza few ancestral societies consume raw starches on a daily basis.

Dr. B G said...

John

As these are whole foods I believe they have great vvaud and merit for healing guts if people do not have intolerances to them or FODMAPS since they contain oligos and inulin. They contain healing botanicals for the mucosal membranes which have been shown in human and animal studies to expel pathogens and quickly aid sealing of the gut

Dr. B G said...

Sid

Our commensals maintain mucosa homeostasis and vipers do the opposite. In autoimmune disorders the vipers eat starches and RS2 so deterioration can occur. Also b LONGUM is the ultimate protector of the barrier function. In one study the reduction of the abundance of b longum compared with other bifido was associated colorectal cancer and IBD. (however in diverticulitis, there was overgrowths and invasion by B longum).

What fibers are working now? Is the antibodies and symptoms all eliminated and resolved now? What is ur stool test results?

Anonymous said...

Hi Grace! You are so kind and wonderful- thank you for the response! Im the girl with Celiac and epilepsy ! I was having up to 5 seizures a day, but for most part they went away once I went gluten free 2 years ago. But even after going gluten free I still had severe brain fog and fatigue... Which is TOTALLY gone now since taking AOR and beta glucan. Everything I ate gave me brain fog! Now I can eat anything and I feel GREAT! Except still cant do gluten! I know because i had accidental exposure lask wk and i vomited ( i vomit everytime I'm exposed to gluten!) i dont mind that i cant eat gluten, because I feel so great, healthy and happy!! I take beta glucan from Jarrow. I think its derived from yeast? Not sure if thats not great but it is definitely part of the puzzle for me! I am Irish ancestry and i know our diet before the potato was oats! And i have been eating a sprouted gluten free verified oatmeal :). I also ordered Floramend because i saw you mention that! Im in love w these probiotics and love trying them all!!! Oh, i drink a lot of kombucha too, but not other fermented foods.... I also drink a lot of raw milk (im lactose tolerant). And i still consume lots of gluten free bakery goodies :) im just sure to eat beans first for fiber! :) Thank you so much. Cant emphasize enough how much your blog has helped me!! So great of you to offer this info :). Gut health is so fascinating! -Carrie

Anonymous said...

PS I definitely dont eat RPS. i sometimes take inulin, but i do consume onions everyday :) I have the most mental clarity and energy ive ever had my entire life.... Its the aor, threelac, betaglucan thats has helped so noticeably! You are awesome and i am so grateful you do this blog! carrie

dr j said...

Grace,
you must be getting closer to an ah hah moment re CAPP2 . I still feel that if aspirin works so well, then we need to factor in the green leaf and its included salicylates and other factors .

You are building up a top 100 fecal transfer donor hit parade. :-)
johnnie

Sid Dishes said...

Psyllium and GOS are working well. I'm currently experimenting with a few other prebiotics but it's too early to say. Symptoms are improving but nowhere near resolved. I haven't retested the antibodies yet, I think it's too early. IMO, as it stands right now, stool testing is a waste of money, sorry.

Dr. B G said...

johnnie

Hey Gorgeous ~ yes I am collecting them ;) UR NEXT!

You know I just got this "Effect of traditional leafy vegetables on the growth of lactobacilli and bifidobacteria" (hat tip Keith). So our greens have salicylates and other inulin for the gut guardians and soil probiotics!

http://informahealthcare.com/doi/abs/10.3109/09637486.2014.945155

Dr. B G said...

Carrie~!

Yes I love gut health too! I love hearing your story and hope even someday that accidental gluten exposure won't induce vomiting (fingers crossed for you!) Give me an email and I'll provide some add'l things you may want to give a whirl! (click on my name).

Isn't it most fascinating how gluten and gut damage breaks the gut-brain axis and causes seizures, ataxia and other consequences? What a connection. Before I had CFS (chronic fatigue). Hundreds of yeast and microbial proteins were found in the brain of CFSers in one study compared with nonCFS controls. So sealing, healing and maintaining the gut barriers and motility are the priorities in gut health. It is so wonderful you are finding delight with kombucha and sprouted oatmeal. When they sprout, they are coated with lacto and other bacteria, and studies show even dead, cooked lacto is 50% or as good as live lacto for our health.

Anonymous said...

So very thankful for this information and the ongoing discussion. This is one blog where I absolutely must read the comments . . . they add so much!

Also, I would be exceedingly glad if there were a continually updated acronym dictionary for this website. I'm sure spare time is at a premium for everyone, but it would make a big difference to all us rookies. :-)

Dr. B G said...

Anon,

Yes green banana flour is awesome, I find, and needs insoluble fiber or high insoluble fiber diet (7 Steps) to bulk up the stools otherwise like RPS it may slow transit of the gut.

Sorry to hear about the hemorrhoids!

oberon said...

How do you find Akkermansia on the ubiome report? I have even searched the raw feed and it isn't there. It seems like the entire Phylum (Verrucomicrobia) isn't there.

Dr. B G said...

Sid

There is a circus of cherry picking unless one reads the whole body of microbiota and RS/fiber research. In modern life, most of us have compromised guts with low diversity and lot gut guardians. My problem is a fiber that further lowers these guardians -- for some the problem is immediate (me, until I boosted the gut guardians). Like for you, perhaps, it might have taken longer if you started off with more or started with better diversity.

I am not surprised you eventually had problems with PS because so far in disease state human trials, it is not impressive. Lagakos on his caloriesproper blog once noted that RS2 raised insulin in several studies. A new one is the Bodinham 2014 study with 40g HAM-RS2 in T2 diabetics. Oddly high dosage RS2 raised: triglyercides, liver fats, LDL cholesterol and was associated with lower butyrate and propionate.
http://www.endocrineconnections.com/content/3/2/75/T1.expansion.html

It was a good study 12wks -- the researchers were likely feeding the vipers or creating a scenario where there was a tipping point where the insulin sensitizing flora (Akk, Christensenella and B longum) were mowed down.

In IBD, ulcerative colitis, RS didn't change symptoms. Again -- it didn't improve the losses of Akkermansia which is a factor in the entire, whole root problem (low diversity, amputation of gut guardians).
http://www.ncbi.nlm.nih.gov/pubmed/25037189

"However, faeces from the UC cohort had lower proportions of Akkermansia muciniphila and increased diversity within Clostridium cluster XIVa compared to controls.

CONCLUSIONS:
Gut fermentation of NSP and starch is diminished in patients with UC. This cannot be explained by abnormal gut transit and was not corrected by increasing RS/WB intake, and may be due to abnormal functioning of the gut microbiota."

Even if you are tolerating psyllium and GOS well, you don't know if you are overgrowing vipers with them. Dysbiosis means even the commensals are vipers sometimes.

Several wks ago I ran by Tim and got his approval to discuss my concerns, my health, his health turn (all improved now) and potentially detrimental changes with RPS.

What I think occurs when people take high dosage PS whether they have a healthy gut or mildly dysbiotic gut is, based all past and today's N=1s:
--sometimes improved digestion, SCFA because suddenly get gets fiber (for first time lol!)
--gradual loss of gut guardians, then later progress loss of gut guardians (even with other fiber; see Child 1 and Tim's report (c))
--loss of diversity
--overselection of narrow bandwidth of bottom feeders including animal, starching eating bifido (adolescentis, animalis/lactis, breve)
--overgrowth of commensals
--the kicker perhaps depending on inter-intervidual gut fingerprints: loss of a keystone gut guardian
--trigger (stress, diet/sugar/gluten/etc, etc -- more loss of gut guardians or growth of vipers)
--commensals become vipers (eg me/reflux/Prevotella; Tim/fatty liver/Roseburia)
http://www.ncbi.nlm.nih.gov/pubmed/?term=%22roseburia%22+and+%22+fatty+liver%22

--dysbiosis to the point of manifestation of disease



Testing helps to figure out 2 things

(1) --how many gut guardians are there (Genova is great -- it tests B longum down to species because it is important; lactobacilli process sugars and fructose for us; both of these are low in NASH/fatty liver. In reflux/GERD, all these are low are well)
http://www.ncbi.nlm.nih.gov/pubmed/?term=fatty+liver%2C+longum
http://www.ncbi.nlm.nih.gov/pubmed/24966608 (recovery of NASH/fatty liver parameters with Akkermansia)
http://www.ncbi.nlm.nih.gov/pubmed/?term=%22lactobacilli%22+and+%22+fatty+liver%22 (B longum is superior, but lacto probiotics effective as well)

(2)--what the vipers and ID any overgrowing and invading commensals

Sid Dishes said...

There is a circus of lies, cherry picking unless one reads the whole body of microbiota and RS/fiber research.

Agreed very much. I've read a fair amount of the primary literature and mostly disregard blog blatherings. I've not read nearly as much as you but certainly enough to be aware of the massive clusterfuck of contradictions and gaping black holes of uncertainty. For this reason I think it's best we don't play gin with Pubmed abstracts since for every study you can cite that reached a certain conclusion we can find another study that came to the opposite conclusion.

Case in point: you recently blogged about Prevotella and how you used to think it was good because Burkina Faso kids are full of it but then again so are HIV and other disease ridden Western guts so now you think it's not so good. A study just came out a few days ago showing they're low in Parkinson's disease. So which is it, evil viper or gut guardian? These terms are meaningless; whether they are associated with disease or not clearly depends on a whole host of conditions in the gut.

You're a big fan of stool testing. Ok, suppose we get this information and we find out there is dysbiosis. How does this information change the management? It's not like we can micromanage the situation even if we find that something specific is overgrown. Surely the most logical approach is to attempt to expand the commensal populations by feeding them what they like and hope that they displace the pathogens. Of course RPS is not a great choice if there is significant dysbiosis since it feeds all kinds of stuff but it's not like we can just surgically remove the bad stuff. I think the success of FMT for C. diff teaches us that the best way to "weed" the gut of nasties is to let the good bacteria do the work for us. How to achieve that, well, I would argue no one has the answers yet. If inulin cured disease we'd have heard about it by now since it's been on the market for a long time.

Dr. B G said...

Sid,

Yes I couldn't agree more -- for every symbiont, you can find that it's also a Janus-faced opportunistic pathogen in another study! Just like Prevotella, which is very common because we get gut damage from grains, its favorite fermentable fiber.

"It's not like we can micromanage the situation even if we find that something specific is overgrown. Surely the most logical approach is to attempt to expand the commensal populations by feeding them what they like and hope that they displace the pathogens. Of course RPS is not a great choice if there is significant dysbiosis since it feeds all kinds of stuff but it's not like we can just surgically remove the bad stuff. "

It is worth trying. Because of genetics and a burden of cumulative toxins that disrupt gut health (mercury, aluminum, arsenic, PCBs, plastizers, flame retardants), it is definitely far harder now than let's say even 1-2 decades ago!

Yes shifting things by multiple strategies. For Tim, he uses and still uses a botanical tea that is antifungal, antiparasitic and antimicrobial. It's not just the RPS ;)

Seeding and weeding have to a part of every gut protocol if there is any level of moderate to severe (or refractory) dysbiosis.

Earlier I had both a parasite E nana, and overgrowths of yeast and bacteria. As soon the gut was seeded with soil probiotics, FloraMend/etc and weeded, my gut resumed gluten and dairy tolerance that I haven't experienced for 7-8 yrs. Every case is different of course.

Refractory cases (like mine was) was related to tenacious subclinical infections.

Dr. B G said...

oberon~ Should be on a line item. Are you missing others: Bifidobacteria longum, B adolescentis, B bifidum, etc? Christensenella?

Dr. B G said...

I think FMTs are less effective for upper gut disorders (like autoimmunity, chronic fatigue, celiac, etc). For the colon -- yeah -- absolutely effective. In C difficile, the viper is known. For other conditions, it is not so clearcut and there can be multiple subclinical infections or overgrowths.

Have you seen this test? I like both 401H Biohealth and GDX 2200 Stool.
http://biohealthlab.com/test-menu/parasites-and-pathogens/gi-pathogen-screens-401-401h/

dr j said...

Grace,
the cow thistle plant referred to in your link via Keith is one tough mamma ( http://informahealthcare.com/doi/abs/10.3109/09637486.2014.945155 )

here is one plant from the study- its herbicide resistant which might offer a clue-
https://www.daff.qld.gov.au/__data/assets/pdf_file/0004/75640/Management-of-common-sowthistle.pdf

its everywhere in including Australia (!)
john

Sid Dishes said...

Oh I agree. I don't think FMT will prove enormously useful for chronic conditions. C diff is a straightforward overwhelming infection. Chronic illness is more like smouldering low grade infections and dysbiosis, but more importantly, lack of butyrate producers and immune dysregulation.

I haven't seen that test.

Dr. B G said...

Sid,

EXACTLY. Everything is broken "lack of butyrate producers and immune dysregulation". And as you have probably noted, in many instances high butyrate producers are present, but they are all in the uppergut.

Your theory to have targeted expanse of "the commensal populations by feeding them what they like and hope that they displace the pathogens" is the optimal goal. Just getting there is what I find most challenging.

I love raw potato starch -- I wish everyone should/could/would take but because it appears to lower commensals, I find that adding at the end of gut recovery is probably best. It doesn't have advantages early in gut healing. Other fibers also produce big butyrate and lower pathogens.

By no means is inulin a superfood. I like it but its not without its issues as well (but very little lol). It has its place mainly because it feeds the symbionts in BOTH the upper and lower gut. It feeds the soil probiotics that I love. IBS folks are unlikely to tolerate it because its a FODMAP. After some 'clearing' and weeding (like using yacon), many typically have no problems later to tolerate if it was initially a problem.

oberon said...

Dr BG, some are there, some are not. Akkermansia is not there. Christensella is. Here is my raw feed.

https://dl.dropboxusercontent.com/u/22368269/gut.txt

Dr. B G said...

oberon

What are your thoughts? Your bifido is 2/3 animalis and total only 0.0062%. A really interesting strain Bifidobacterium thermacidophilum! Aquificae Do you do hot springs or have a well?

Your XIVa and Roseburia are excellent. F praus quite good. Rumino/IV good.

Low -- Akk (undetectable), Christensenella, bifido
Super low -- pathogens

What is your phenotype in regards to hard gainer, obesity, and insulin resistance? Any challenges? Or good!?

What diet, work outs, supps, prebiotics/probiotics are you doing? Any high dosage HAMS or RPS and how long now?

oberon said...

Thanks for looking at my data, Dr BG. This report is actually quite old, end of April. It was after 3 weeks or so of potato starch supplementation. But I stopped the supplementation quite a while ago, it wasn't helping my main problems (rosacea & frequent loose stool). It turns out I have SIBO (hydrogen breath test), so I took a course of rifaximin. Helped for 3 weeks or so, then things went back to my normal state. My naturopath wants me to test again, which I will do next week, and perhaps pursue a more herbal route if I test positive again.

I generally have been overweight most of my life, but not the last year or so; paleo + crossfit have made me quite lean and strong, finally. I definitely can gain weight fast if I am not careful about the carbs, but aim for around 100g of carbs a day.

Right now I am taking Ultimate Flora Colon Care (80 billion bacteria, lots of bifido) and Prescript Assist once a day, plus vitamin D and fish oil. The Colon Care seems to help more than anything else to keep me regular. I suspect a ubiome test today would be very different than what I had in April.

After I get re-tested, I'm thinking of supplementing with GOS to jack my bifido numbers and see if that helps.

oberon said...

Oh, and no hot springs or well. No idea where the odd strain comes from :)

Dr. B G said...

Oberon

Thx. So the Roseburia being kinda high actually might have been related to an overgrowth. It also wasn't the ancestral phylogenetic strain R intestinalis but one thats not well identified. R intestinalis was not on your raw taxa. Hopefully it will return with the Akkermansia, bifido and B longum. Congrats with seeing the gains with Xfit and Paleo! Maybe you can lick the barbells and get some akkermansia JK!

With targeted prebiotics like GOS-inulin it's possible to up the gut lining's occupation of these vital symbionts by 10 to 100 fold in just one to two months, though the stools may not expressly show the magnification. Symptoms however will improve i think you should notice. I think plenty of inulin and GOS/OS based food are great too -- onions, greens, SUNCHOKES, beans, small amounts of steel cut oats and roasted tubers. Kombucha?

Have you looked into yeasts and candida? Actually I looked further that Bifido strain isnt typically in humans but bovine and pig. Any raw milk or dairy products? Have you had antibiotics growing up or c section or formula? Skin disorders are also related to lack of acid and other digestive support -- bile, enzymes and sometimes motility. Dairy is a common allergen for skin (casein looks like yeast proteins). Sounds like there is some persistence of permeability in the upper gut

Michelle Rick said...

Dr. BG

Great stuff. Crazy to think so many unknowingly make a change in their diet thinking their gut will improve, but end up experiencing the opposite on LC paleo, VLC etc. (LIKE ME)

On microbial fingerprints for different symptoms and conditions:

What strains do you think might be absent in nut intolerances? Or could it just be disrupted brush border and microvilli that impair digestion as a whole and manifest with nuts because they're tougher to process?

I have regained tolerance to every FODMAP I have tried over the past 4 months. Just 6 months ago FODMAPS were a no go. Great to have that back, some of my fav foods. However, raw nuts still give me trouble, some more than others. I understand that soaking can improve digestability but feel like from an evolutionary perspective some were probably eaten in their raw, unprocessed form often if possible (ie. not acorns cuz of toxins etc.) Interestingly, pistachios are easier digested for me though they are higher FODMAP and polyphenol (and delicious) .... almonds and cashews are much worse. Thoughts?

Night shades and citrus? --- I've read both can be irritating from a permeability stand point, what do you think? Oranges are problematic for me but not lime or lemons. Tomatoes, peppers, and eggplant too, but no trouble with potatoes.

I also tolerate full fat, high quality fermented dairy products with little digestive issue, but milk (cow's) I still experience symptoms even with small quantities in a soup or something.

I'm avoiding the above mentioned foods right now... Overall I've seen fantastic improvements in symptoms, and hope once I get the metals out of my system my gut will be able to continue to heal to the point where these are no longer an issue.

Final question: How does stomach acid cause retrogradation during digestion? To think a healthy gut makes it own RS3 makes tons of sense to me and I'd love to read more. Damn, the body is intelligent--- sometimes I feel so oblivious to the half of it.

Stay awesome

oberon said...

Thanks, Dr BG. I haven't looked into yeasts or candida; any good tests out there? I suspect my naturopath will want me on low FODMAP/SCD for 1-2 months after weeding, but after that I plan to target some prebiotics like crazy.

I haven't tried any enzymes, I think I will; which one should I try first? I think I generally have higher than average motility. I am indeed sensitive to dairy; I tested high on a food sensitivity panel, and I notice nasal congestion whenever I have it, so now I avoid it.

But I used to have a lot of dairy. A few years ago I had a week of raw dairy just to try it, but that's it. I did have lots of antibiotics as a kid, though I am 38 now.

Dr. B G said...

oberon,

Losing body fat as you have with xfit and paleo should help boost Akkermansia, which has been shown in studies in animals and humans. It would be wonderful to see a ubiome currently then after 4 wks of targeted microbiota 'rehab'. I am sorry if the raw potato starch made low levels of Akk, B longum and Christensenella potentially early extinct.

Can you do me a favor?

To remediate the biggest problems with modern dysbiotic guts (like yours and those after raw potato starch-induced 'damage'), please consider trying Version B of bionic fiber to restore the guardians of the upper gut. Did you see improvement in loose stools with psyllium? Psyllium feeds B longum and indirectly Akkermansia FYI.

This is intended raise ALL the gut guardians to reverse SIBO and quickly repair upper guts. What it turns out to be is a fat burning formula. Please let me know if you achieve easy fat loss and maximization of leanness (which I've notice -- I have to stop it sometimes). I notice I gain some lean mass without working out.

VERSION B [the 'FAT BURNING' BIONIC VERSION]: Inulin 1-2 TBS + Acacia Gum 1 TBS + high ORAC green powder (optional) in 2 cups water

To amp up Akk -- you may add 1-2 TBS of organic yacon syrup (with carby meals). Do you like parsnips, onions and rutabagas? These are similar to yacon.
http://drbganimalpharm.blogspot.com/2013/11/how-to-cure-sibo-small-intestinal-bowel.html
http://www.iherb.com/Navitas-Naturals-Organic-Dried-Yacon-Slices-2-oz-57-g/59553
http://www.iherb.com/search?kw=yacon+syrup#p=1

Please don't hesitate to email me questions

Dr. B G said...

Michelle Gorgeous GODDESS~!

UR awesome and so is all your deep thoughts and curiosity! YES ME TOO.

"Or could it just be disrupted brush border and microvilli that impair digestion as a whole and manifest with nuts because they're tougher to process? " I believe yes that is probably the inherent immune defect. I think you're seeing a spectrum of improved immunity and re-establishment of tolerance (eg this is GUUUUD). For optimal health, I think the immunity has to repair and no longer be hypersensitive, eg tolerant again. I think the proteins in nuts are the problem during permeability. Seal permeability and repair the immunity. Lisao gave some great ideas about berberine as a gut adaptogen which means it modulates and improves gut immunity.

I like the inulin and oligosaccharide GOS FOS studies from whole foods -- they appear to improve immunity, diabetes and inflammatory conditions. Try the above version B and let me know how it goes! It has allowed me to eat nuts again with only minimal bloating (had 8month pregger reactions 4 mos ago!) So glad to hear of your rapid progress!! Hope dairy and gluten get resolved soon too.

Yes the body's intelligence can override and transcend so much, no? I hope you continue your deep learning! So ancestral isn't it??! I bet our healthy elders have this gastric acid peaking like bombers! lol

Anonymous said...

Hi Grace,

Im wondering why you are still recommending green bananas and plantains since they are also high in RS2? Is it best to choose green, neutral or ripe ones when shopping? If I was living in Africa million years ago I would have chosen ripe candy tasting ones over shit tasting greens. :)

Dr. B G said...

I would too unless I was dumb or starving ;)

And in gastroenteritis traditional recipes what would confound me that they would COOK the green banana or green plantain before administering! Go RS3!

Raw green banana or plantain are whole foods with healing phenols, plant steroids, stigmasterol, inulin-FOS, hemicellulose, pectin, and other fibers. Mt Uncle GBF is 3.5 g RS2 for one TBS compared with 10 g for potato starch. Since the GBF studies show significant weight loss in diabetics, I suspect it does not impair the gut microbiota and skew the way that gerbil food without a fiber spectrum does

Anonymous said...

Dr Grace, how do you suggest we take Version B? As a meal replacement, or in between meals?

Chris said...

Dr. B G: I think FMTs are less effective for upper gut disorders (like autoimmunity, chronic fatigue, celiac, etc). For the colon -- yeah -- absolutely effective. In C difficile, the viper is known. For other conditions, it is not so clearcut and there can be multiple subclinical infections or overgrowths.


Well, I strongly disagree with this. Just as I've strongly disagreed with the RS stuff. I've suggested as much to Tim.

From personal experience the FMT works fine with the small intestinal stuff. It's great for CFS and IBS and autoimmune issues.

But with a few caveats: You have to do it top-down ie capsules (along with bottom-up if you want). You also have to make an effort to heal any intestinal permeability and you have to not be a dick when it comes to maintaining a decent post-FMT diet.

That means, give yourself time to heal the epithelial layer by eating a insoluble fibre and zero starch or animal proteins. This will also reduce the chance of post-FMT SIBO symptoms.

By the way, for what it's worth, I think Paleo is the dumbest pre- and post-FMT ... or leaky gut ... or SIBO ... or anti-inflammatory diet. But, hey, each to their own.

Point is; eat well to heal the gut. Increase motility to lose the SIBO (it doesn't need to be as complicated as the 7 step stuff). Do an FMT (with a particular type of donor). Eat lots of plant fibre. Go live life.




oberon said...

Hi Dr BG, sure, I'll give it a try.

Dr. B G said...

Chris

I'd love to hear more. Luv ur story. What issues cleared for you after FMT? How long out after FMT has remission been maintained? How did you find your donor, are they related eg similar genetics?

I say what I did based on some failures and the literature. OTOH I've heard amazing recovery stories as well but these are not as fantastic successes as the C diff cure rate of 90%

Which insoluble fiber works best have you observed? Psyllium can 'scratch' some epithelial surfaces if extremely patchy and inflamed. Yes. We concur on RS.

FMT will be the wave of the future both top down and bottoms up! Absolutely. Hopefully they will have the viable microbes that we lose from lack of vertical transfer from mothers and secondary to poor diets and antibiotics.

Paleo is missing things in its current iteration.... I have a post called legumes and tubers are Paleo (so are small seed grains too lol).

Dr. B G said...

Thx! And don't forget to ask your naturopath about yeasts. They may overgrow after xifaxan because it removes both gram + and gram - symbionts

Dr. B G said...

It has no energy or calories for you, only the gut flora. It can be with meals or between up to u! Please let me know how it works for you

Michelle Rick said...

Dr. BG,

I've been using Version B minus GBF for about a month now, tolerate it great, and have noticed improvements. However, I began exploring the metal connection further because it seemed something was impeding healing and sealing the gut wall (at least that's my deduction), not to mention my reminiscent symptoms (skin issues, mild indigestion, insomnia, neuro issues) all disappeared almost entirely after four weeks using a metal detox formula. Literally the best I've felt in a year after that, but within a week of running out my symptoms (which 7 steps and PHD made MUCH better, but still there) crept back. I'm a total believer in the metal connection now, and honestly their being disregarded in the medical community at large in the US seems insane.

Question: Do see kefir and yogurt (unsweetened, unhomogenized, grassfed) needing to be avoided for a time because of caseins allergenic potential? I didn't exclude it originally because its talked so highly of as a probiotic, but I have no idea whether that was a good idea or not.

Anonymous said...

Michelle Rick,

Which metal detox formula did you use? At what dosage?

Thanks!

Michelle Rick said...

I used MetalFree, a polypeptide cage binder deigned by Dr David Minkoff. Heard about it from Ben Greenfield. Its pricey but it really made a difference for me

http://bodyhealth.com/retail-shop/all_products/metal-free/

Michelle Rick said...

Dr. BG,

Also wondering if you have an opinion of or have used zinc carnosine? Mark Hyman has a few articles that recommend it and I've come across several studies citing its ability to potentially protect and improve the mucosa.

happy sunday, michelle

Dr. B G said...

oberon~
Low FODMAP wouldn't hurt for 2wks. The high Roseburia is also characteristic of IBS-constipation (similar microbial fingerprint in that way to fatty liver/NASH). Bifidobacteria longum, lactobacilli and soil probiotics can help to squeeze overgrowths of Roseburia and yeasts out of the uppergut.
http://www.researchgate.net/publication/259955798_The_gut_microbiota_and_the_metabolic_health_of_the_host

Unfortunately SCD and low fodmap diets will further lower the (non-existent) Akk and B longum. No probiotic exists yet for Akk but for B longum we have several
--Life extension GI bifido balanc
--RENEW Bifido MAX

I like NOW foods Platinum enzymes and Dr Venessa's Digestion Balance

The antibiotics really did a # but many things can be recovered. Ck out some organic or heritage farms -- try to volunteer or milk some cows ;) FARMACY beats drugs!

Dr. B G said...

Michelle,

It is quite sad how when I worked in research labs, mercury is a biohazard, yet dentists and drug manufacturing have used mercury for decades after their endocrine and neurotoxic effects were well documented. Things are changing -- the tide rises.

I'm not surprised you saw such improvements. And it is hard because for good detox, we need the gut yet when the mercury comes out, it will create dysbiosis. I do believe the probiotics and avoidance of food triggers helps because DPPIV is the digestive enzyme (and it is located throughout the body as well) which breaks down gluten and casein is inactivated by mercury. Vojdani is the brilliant researcher how did this research. So taking a break from all dairy will help -- it is not permanent but until you can restore healthy, long, not denuded microvilli!
www.townsendletter.com/Jan2013/enhancetest0113.html
www.glutensensitivity.net/VojdaniDiagrams.htm
http://www.glutenreactivity.org/InfToxDietPep[1]%20Vojdani.pdf

Dr. B G said...

Love Carnosine -- its part of many pathways. Zinc carnosine binds open ulcers and microulcerations. I also like gelatin, bone broths and gooey vegetable fibers
--okra
--aloe
--taro
--psyllium
--refried beans (LOL if people can tolerate FODMAPS)
--etc

Poha said...

Aloha Grace, love your blog! Sharing this link on satiety here:
http://www.forbes.com/sites/peterubel/2014/12/17/how-healthy-food-could-make-you-fat/
" ... people eating ... “healthy” ... experienced an elevation of a hormone called ghrelin, which slows metabolism and stimulates appetite ... Think about what this means for dieters. They eat healthy meals in hopes of losing weight and their damn bodies fight back, hoarding on to the calories they’ve consumed while, simultaneously, telling them they need to consume even more calories. ..." great pic in article too ...

P1 said...

Michelle Rick, are you familiar with the chelation protocols of Dr Andrew Cutler? I think you want to be extremely careful about that cage binder product to understand what is in it and how much is absorbed systemically. The worst possible thing to do when you are heavy metal toxic is to take a weak binder (one thiol instead of two) that is absorbed systemically. You just move the heavy metals around, and when they resettle they cause symptoms. I seriously messed up my life by doing this with high doses of alpha lipoic acid, taken irregularly.

Are you symptoms only gut issues, or do you have other issues? For me, the heavy metal symptoms were truly catastrophic: pituitary, hypothalamus, aerobic metabolism collapsed. Really it was like my entire life imploding. I have been struggling back from that and have made major strides, and in the process I have learned an enormous amount about the subject.

If you seriously think you have a heavy metal toxicity, I can guide you to which lab has the best testing, and give you some overview of proper chelation (which must be done very conservatively and with great caution because it can be extremely dangerous), as well as good intestinal binders.

P1 said...

Given the special role of B Longum, and given the fact that the body seems to do well with a high percentage of bacteria in this family being the Longum type, can you think of a way for us to ferment foods using Longum as the starter bacteria for the culture?

For example, could I add some berries to water and juice that, then drop in a B Longum probiotic (open the capsule and mix it into the solution), seal it in a jar, and then let sit at room temperature for two days before adding coconut milk or something else to help flavor it?

If there is a better way to ferment it let us know and that would be interesting to try.

Doggster said...

DBG,
Thank you for all of your insights and public contributions here. Looking at the uBiome options, what is your perception of the benefits of doing a multi-site test, like the 5- or 3-?

Doggster said...

P1,
Which lab and protocol did you find most helpful for yourself? Thx :)

Doggster said...

DBG,
So sorry, I meant 2- or 5-site, but you get it. :)