Monday, August 4, 2014

R. Intestinalis is a Big Phat Butyrate Factory and Eats Resistant Starch (RS3), Inulin, Chitin, Beta-glucan and Much More

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Body's microfauna and ecosystem (hat tip keith)

Intestinal colonization: How key microbial players become
established in this dynamic process
Source: El Aidy et al 2013
Germ-free rodents were inoculated then tracked as successions of microbial populations colonized the gut toward a final mutualistic community of primary plant polysaccharide degraders and their secondary degraders. I thought it was super neat to see the urinary metabolites, amino acids and fermentation products were all tracked real time. Butyrate notably increases as Clostridium clusters IV and XIVa take over. Bacteroidetes and Lactobacillus were the early settlers and gradually declined over the transition to stable components. These authors also included the integration of host saccharides that feed the microbiota: fucose and other glycan biosynthesis that is controlled by a genetic variant known as FUT2. This is the same SNP that directs how much glycosylated blood antigens are secreted on RBCs as well (blood types: ABO). Non-secretors release much less glycans to the flora on RBCs, intestinal epithelium, all mucous membranes and bodily fluids.

Clostridium cluster XIVa include Eubacterium rectale and Roseburia intestinalis, the productive butyrate factories that keep our gut mucous linings pink, pretty and pathogen-free. These guys eat everything.

They've certainly invaded their dual nices as both primary and secondary degraders of all things plant fiber and starch (in fact, both cooked and resistant). 10% of our digestible food escapes small intestine digestion and enter the colon for microbial fermentation. For a 150-200 g carb diet, this means about 15-20 grams digestible and cooked starch makes it into the mega composter (colon) and fill the big bellies of the flora like cluster XIVa.  That's a lot of starchy food considering tens of millions of microbes may live in one gram of poop or soil.

Roseburia favors and loves starches that escape small intestinal degradation and RS3, cooked-cooled starches.

R. intestinalis works synergistically often with Bifidobacteria. Whatever starch fragments that Bifidobacteria throw away, R. intestinalis can munch over.  If Bifido is not around (like after antibiotics), R. intestinalis might starve a little. On VLC diets, Roseburia drops along with starch intakes. What is most bothersome is that butyrate dips 4-fold as well.

Chitin (insects, Aspergillus) and beta-glucan (mushrooms, oats) feed Roseburia well (as does low dose RS2, green banana flour or RPS) in this study (Neyrink 2012).

High dose RS2 however will decrease Roseburia (Tachon 2013).

Roseburia's Favorite Foods Are: Starches, Inulin, RS3 Cooked-Cooled Resistant Starch

What raises Roseburia the MOST is starches and inulin (Van den Abeele et al 2011, others).

These fibers raise cluster XIVa nicely, at the same time protecting rodents from increased obesity, high insulin, high BGs, high TGs, and metabolic syndrome with an inflammation-inducing HF diet. All disease protection appears to correlate directly with Roseburia caecal population increases.

Feed Roseburia well for sustained longevity and health -- consider steps #1-4 to provide bifido and bionic fuel:


aerobic1 said...

When it sit back and observe the information (or perhaps misinformation) provided on health benefits of VLC diets, I have to wonder what the adverse long-term effects are that 25 to 50 grams per day of carbs may have the human intestinal microbiome. Strictly a hunch on my part, but I believe there is a soon to be reported strong correlation between VLC diets and poor gut flora.

Those VLC experts are the typically the same people actively promoting probiotics and prebiotics. Could that be another correlation?

Good carbs indeed got a bad rap along with bad carbs not because they were carbs but rather due to the massive daily consumption of carbs many tend to ingest resulting in obesity and diabetes. In theory, we make all the carbs we are likely to need from gluconeogenesis but at what expense does that do to our gut flora. There must be a middle ground somewhere.

Dr. B G said...

Well I think the VLC experts are doing their best. The gut microbiota knowledge is all new and subject to varied interpretation. Obviously we all fell into VLC for some reason -- for me I was hoping to prevent autoimmunity -- but then developed adrenal exhaustion and chronic fatigue. Long term for an apoE2/E3 and FUT2 non-secretor was not good! lol Live and learn. I was a tool. My body did make all the carbs I needed however my adrenals/HPAT axis paid the price.

We are flooded quite literally with info that now we can utilize that might help guide some of our food/fiber decisions. I hope we can open more conservations about these advances.

So there's a middle ground developing I believe. You're so right. 'Good carbs' were narrowed down too much in the frenzy for better health and avoiding refined gluten grains. One can still obtain 50 g net carbs with 50 grams RS+fiber. Those 50 grams will go much further. The food is nutrient dense, but dense for the microbes, not calories for the human host!

The slow-digesting carbs, resistant starch and other plant polysaccharides were pushed aside at the same time to avoid the 'bad carbs' by all the VLC except the WAPFers. If we do not feed the gut flora, the evidence is pretty clear, we lose them rapidly. Add a few rounds of antibiotics or alcohol, what's left and not entirely extinct? It would be truly awesome to test and research all of this to determine if it's true for everyone and what is optimal...

Anonymous said...

Dear Dr Grace,
I also suffered from adrenal burnout and chronic fatigue on VLC. But I had super clean teeth. In the last 6 months, I have uppped my "safe starches" and some RS, probiotics, fermented veg and more fiber from foods and supplements. I feel great but had a rpaid build-up of tartar on my teeth. 6 months ago, teeth and gums were rockstars. Yesterday, hygienist gave me a poor grade: inflamed gums and lots of tartar to pick off. (I'm ApoE4 FWIW) What am doing wrong? Thank you! Regina

Dr. B G said...

Hey Regina,

Our teeth and mouths are the doorway to health, eg the gut! How is your thyroid and adrenals now? These can affect inflammation if suboptimal despite great gut health.

For me I've had tartar if I overdo the D without K2, mag and A.

Probiotics are great to swish around in the mouth I think because it might mimic ancestral exposures prior to modern and movements away from local farming.

Oil pulling is an ancient technique to lower pathogens in the oral cavity and improve flora. Have you heard of it? good studies! I just did it this AM with sesame oil

Please let me know how it goes

aerobic1 said...

Yes, Grace, we do live and learn from our own experiences. My mistakes were the TYP “Auschwitz” diet and the Phinney and Volek's Keto diet. I lost a bunch of weight, had a great looking HbA1c and developed a rotten gut flora, suppressed thyroid function and lagging energy level to boot. I never achieved the lipid control or reversal of atherosclerosis that I was after on either diet. Those plans are perhaps better suited for those with poor glucose control. Thanks to the suggestions of the late Dr. Robert K. Su I am now out of that rut.

Anonymous said...

Thank you very much for your reply Dr Grace. I recently started taking a K2. Maybe I was over-doing the D. I also have that gene which is poor at converting beta-caratene to retinol but I just can't eat liver. My 23nMe said I am a real savage cavegirl: warrior gene, hemochromatosis, Apoe4. But I'm thinking it might just be the drinking water. I put a whole-house filter at the main in our basement. It's a tall narrow Chicago 1890 rowhouse. It's a long way from that filter downstairs to all the faucets and that filtered water is sitting in there. My dog is a hint. He rather drink filthy puddles than my lovely filtered water in his bowl.
I was also opening up an L.Plantrum in my mouth before bed and loved how nice my tongue looked in the mornings. Had no idea my teeth and gums were not happy. Thank you. Regina

Anonymous said...

I forgot to answer your kind question. I think my thyroid/adrenals aren't so bad. (guessing).
My eyebrows are full and I continue to bang out periods (sorry gents for the tmi) every 28 days like a machine. I'm 52.
I don't believe I have ever missed one in 40 yrs. I'm irish (probably inbred) and probably could've had 12-13 kids.
My dad had 9 brothers and 2 sisters. All of them died of heart attacks.
My energy improved the moment I stopped the SAD homer simpson diet.
GeneticGenie said I have fcktarded methylation.

I'm not sure how to proceed going forward but I will try oil-pulling. Thx!! Regina

Chris said...

Nice post, Grace. Just wondering how to reintroduce the Bifido long term? I'm under the assumption that probiotics need to be repeatedly used to maintain bifido because it won't colonise properly.

I was thinking a source would be fermented foods with added bifido. But given that this bacteria is anaerobic that seems pointless.

Any suggestions?

I have zero bifido and my FMT donor had none either.

Matt said...

Hello Dr. BG,

This is a question that doesn't have anything to do with this post: Have you ever seen a cavity healing? I've read in a blog comment of yours a while ago (at Whole Health Source) that you had managed to heal a cavity yourself. I have gone through times of terrible stress and I've recently discovered a handful of cavities on my molars; I follow a good diet and a couple of weeks ago I started adding RS, prebiotics and probiotics.
S. mutans and other buggers might be lurking around causing me all this damage so I guess it boils down to a bacterial/fungal issue (I have trouble breathing through my nose at night).

Do you have any advice? Thank you VERY VERY much for your time and for this great blog.

P.S: I started oil pulling yesterday night, so far it feels good.

Anonymous said...

Here's an N=dog story.
Friday before last dog throws up his dinner. Then spends the rest of the night throwing up foam which turns to pink bloody foam. Then starts having explosive bloody diarhea (like up the bedroom wall explosive). Vet says her protocol would be pepcid and metronidizole. Instead, despite serious guilt and shame, I bought 2 tinctures by Amber Technologies.
"VibactraPlus" with pau d'arco, cloves,grapefruit seed extract, olive leaf, etc. And "Parvaid" with goldenseal, echinacea, berberis, plantain and etc. Dosed him 4x per day of each. Plus bought a can of CO2 coconut water to plastic syringe into him. By Tuesday he was healed. I had to watch my fingers feeding him, he was so famished. Stools now perfect. Played a great frisbee game today. I'm creditting Dr Grace with her powerful insights into weed, seed, feed. Those were a very scary 4 days but we got through it without acid blockers or antibiotics. Phew. And thank you. Regina

Anonymous said...

The use of folate-producing strains can be regarded as a new perspective on the specific uses of probiotics. Within the genus Lactobacillus, the strains belonging to the species L. plantarum are expected to produce folate in the presence of preformed pABA, .....


Alex Webb said...

Dr. BG,

I'm the guy from a few posts back who was asking your opinion on how cannabis use might be affecting gut health. My own journey with leaky gut and autoimmune disease has been so problematic, despite undertaking all of your protocols. It would have made sense that cannabis use should have been stopped much earlier in my journey, but some combination of dependence and genuine enjoyment of the plant kept me using it during my time being sick. I just did a 'skin test' with some dried cannabis leaves, and sure enough, I broke out in a rash twenty minutes later. I wish that was just some kind of made up voodoo test, but the results are very clear. Lastly, a french group just published a study this year showing how cannabis can be cross reactive with other compounds that affect people with plant allergies. So I know this isn't a hot topic for you (or for much of anyone), but I did want to let you know my story and share the study with you in case the question comes up in the future. Thanks again for all your work, link to the study below:

G. Willikers said...

"The use of folate-producing strains can be regarded as a new perspective on the specific uses of probiotics. Within the genus Lactobacillus, the strains belonging to the species L. plantarum are expected to produce folate in the presence of preformed pABA, ....."
What are the implications of this for those with MTHFR (and FUT2) polymorphisms?

Unknown said...

Hemp oil rocks for oil pulling (seemingly better than virgin coconut oil). Never used sesame.

So, clostridia like to eat chitin? That's the fungal cell wall. And it's available as supplement. Will they also consume chitosan? Chitosan is a common supplement used for mercury detox, but maybe should be since it binds mercury strongly and irreversibly (?!). Such is the microbe-metal connection. Which chitinolytic clostridia make the most chitinase?

Shellfish having chitin shells can cause pretty terrible inflammatory reaction, of course. Maybe that's one reason they're not kosher.

People suffering shellfish allergy might rejoice in knowing they're having a very hard time building their own shells in the wild due to ocean acidification where bicarbonate ions are depleted due to the change in pH called "the other global warming." Oysters are dying by the billion on the Pacific coast.

Regina, maybe mechanism for starch leading to tartar build-up (interesting!!) is connected to overgrowth causing nutrient malabsorption such as magnesium deficiency. Mag is supposed to be important for enamel and bone mineralization, but I don't know anything about tartar (calcium malabsorption? too much free calcium and not enough intracellular?).

Dr. BG, great luck on your AHS talk today, "Re-Savaging the Gut, Solutions to the Identity Crisis of the Ancestral Gut". Here's hoping the video crew gets it right this year so we can view it. Identity crisis? Actually, someone was talking today about using NAC to heal narcissism as if it's an inflammatory disease due to glutathione deficiency. Sulfur for multiple personality disorder? Sounds right to me.

Unknown said...

Cool article:
"Preserved in plaque of ancient teeth, a fossilized microbial world"

Just now learning tartar is mainly fossilized bacteria and it can reveal dietary information.

Anonymous said...

Thank you for chiming in Keith.
I definitely need you guys big brains. I'm feeling over-whelmed.

Thanks for the link. "fossilized bacteria". Okay. Need to wrap my head around that.


Anonymous said...

I was wondering if you knew any good doctors in the Los Angeles area for gut dysbiosis and who can order stool tests like the GI Effects 2200.

Thanks, Sean

Anonymous said...

what about honey or other bee products like propolis, bee pollen etc as a source of beneficial bacteria? I think these are touted as good for the immune system and the expensiive Mannuka honey is recommended for IBS sufferers.

Anonymous said...

it would be great if we had a wiki or something to contribute like the best sellers for the various RS sources, for example does the Barry Farm plantain flour work? (only $3.50/lb or so on their website but doesnt say its "green") and then people could contribute what types of RS and soluble fibers worked/didnt work for them - for example Arabinogalactan seems to work well for me.

Dr. B G said...


Please email me. Click on my name. I'm sorry I missed this story earlier. I appreciate you taking the time to share this and for applying the weed, seed, feed philosophy.


Yes I think until the gut heals and immunity calms, I think whatever the gut is exposed to may cross-react. Thanks for your story. I hope the your plant tolerance improves later.


That's a super idea for the wiki! Green plantain flour from Barry's works from what I hear. It has many of the similar phytonutrients and botanicals that heal the gut like GBF (green banana flour) whilst also promoting high butyrate production by feeding a wide variety of gut microbiota because it supplies a broad spectrum of fiber -- RS plus vital oligos and glycans and fructans.

Unknown said...

Dr B G,
I am still confused what foods contain RS3-ONLY Cooked and Cooled starch foods, or do whole food sources like raw green bananas, plantains-i.e. green banana smoothie-and cooked- but Not Cooled-purple potatoes contain any RS3, b/c you occasionally refer to RS3 as whole food resistant starch, the bill of which both the aforementioned fit.