Saturday, October 5, 2013

Gut I.Q. and the Distal Gut Microbiome as a Driver of Health and Disease


Human Distal Gut Microbiome

I've been reading this cool article by Marchesi titled 'The Human Distal Gut Microbiome' that summarizes the effects of our distal gut (butt-end) microbiome on longevity, metabolism, disease and mental health.  Naturally having had SIBO, I can't decide if the proximal gut (front-end) or the distal gut is more important. Perhaps it depends on which is more ravaged and broken?  If I had diarrhea or chronic constipation, I guess I'd say distal. But since I've had neither, for me, it's the proximal gut.  When I had SIBO, I couldn't function or digest at my optimal. I was bloated after celery. Looking at water made me fat. This clearly sucks.  

A Few Updates: Post-Parasite Eradication

My family and I just returned from a sunny holiday in Macau and Hong Kong. We've all just finished our anti-parasite courses and the first I noticed is that we can eat dairy and gluten without almost no damage...full restitution of digestive function.  It's been 3 years.  Prior, I couldn't even eat peanuts or drink beer without waking up with ankle edema and abdominal bloating to 7-8 months preggers status for several days. I gained no weight on this trip of daily buffets, pervasively excellent feasting, and endless oral delights... I lost maybe half a pound. We ate some foods that were restricted forever -- Portuguese egg tartlets, ice cream, gelato, cheesecake, and cappucinos.  (TMI -- no fartage, no fatigue, no fat bloated belly).  

Gastrointestinal IQ: What's Your Gut I.Q.??

I'm into testing, not guessing.  Biohackers like fixed numbers and objective metrics.  These give data to track, follow and fix, rather than fuzzy logic or haphazard subjectives like 'I feel better' or 'I have more energy'.  

Body temperatures are alright... OTOH some urine cortisol 4 times a day plus full thyroid panel (rT3, FT4, FT3, antibodies) and full steroid panel (DHEA-S, anabolic progesterone, testosterone, and excess fat-inducing estrogens, E2) are more comprehensive and provide a fuller metabolic profile. 

Fasting or post-prandial glucoses are meh... But give me a darn HgbA1c (or fructosamine), fasting insulin and post-prandial insulin, then we can begin talking.  

What I'd really love to see are the mechanics of the mitochondria, fatty acid intermediaries and the gut dysbiotic end-products and organic acids. (Genova ONE= optimal nutri eval by urine; GI fx stool test; my samples here). What is living in the gut? Do you have the good spikes in Prevotella? Balanced Firmi/Bacteroidetes?? Viruses, CMV, adenoviruses? Mycobacteria? Pathogenic fungi and candida? Worms? Parasites? Protozoa? Pathogenic, opportunistic bacteria that were selected and fostered after those ten rounds of Z-paks from the primary medicine clinic or prophyactic Amoxicillin from the ol' dentist, which extinguished all manners of the soldier microcritters?

 (I'm sorry -- parasites are not paleo...Have you watched Planet Earth??! Even elephants and wild chimps hunt and seek out clay and other zoopharmacognosy to rid themselves of pathogenic parasites...) 

What is the microbiome in the proximal or distal gut? Guessing doesn't get you anywhere... You can speculate for a hundred million years and yet one won't know. I certainly didn't. I had pathogenic overgrowths and an allergy to heavy metals (mercury, titanium) which explains why despite perfect paleo and attempts at GAPS or SCD diets or FODMAP avoidance, nothing worked completely or brought a full, sustained return to normalcy.  Have you been there? Done that too?? 

I remembered what normal was (endless energy, flat tummy) but I think a lot people do not know because either they've never known normal or simply forgot because it was too way way way long ago... Some just have never had normal hormones, normal digestion, or normal mental function.  Yes these are all related to the gut because the gut microbiome is the major driver of all health and disease.  Perhaps this was not quite the case 10,000 - 25,000 years ago.  Certainly now with so many gut-disrupting factors that play into our epigenetics and core health, the gut cannot be ignored.  Fortunately the literature and technology are all catching up to clarify and highlight...

Why We Are Sick and Fat: Calories In (SUPERORGANISM) = Calories Out (MICROBIOTA) + Calories Out (HUMAN) + HEAT*Fluxxx

Source: Marchesi 2011.

Centenarians and the Microbiota

I'll go over this one below soon -- BIG THANK YOU TO TATER/TIM AND M.O. FOR THE PDF!!! What is it about healthy, long-lived centenarians? I dunno... Their immunity? Their guts? let's delve deepper and find out more...

Cultivable and pyrosequenced fecal microflora in centenarians and young subjects.

The above diagram is from the Marchesi piece (adapted from Biagi et al).

Biagi et al studied the microbiota of centarians (C), elderly (E) and young (Y).  Distinct differences were noted.  The microbiota of centenarians were distinctly unique and different from both the young and the elderly groups. Less Clostridium cluster XIVa, higher Bacilli and rearrangement of the Clostridium cluster IV composition were noted in the centenarians. Some things were expected in centenarians -- lower diversity, less of the good butyrate producers, less Bifido, and more pathogenic strains.

Quite unexpectedly, special characteristics of the gut ecosystems of the long-lived were discovered in this Biagi et al 2010 study which may define what an elite microbiota with a high G.I.Q. looks like.

(a) Enrichment of special butyrate producers Anaerotruncus colihominis et rel. (Clostridium cluster IV), and Eubacterium limosum et rel. (Clostridium cluster XV). Biagi et al concluded in a 2012 followup 'The increase of E. limosum is high (approximately 15- fold), and could point to a group of bacteria characteristic of the long life.'  E. limonus is a soil strain which lives in ruminants like sheep and cow. Its very good at converting METHANOL. In one in vitro colitis model experiment, E. limonus had positive outcomes.

(b) Increase in facultative anaerobes, such as bacteria belonging to the groups Bacillus. Does this include my favorite soil based organism Bacillus licheniformis or Bacillus subtilis?  Does B licheniformis and B subtilis produce supercharged bionic Gut I.Q....?!  What are foods that contain these?  ANSWER here.

Biagi et al also found the connection between "The decrease of both Clostridium cluster XIVa and F. prausnitzii group members was also correlated to frailty condition, hospitalisation, antibiotic treatment and non-steroidal anti-inflammatory therapy."  Clostridium cluster XIVa is also referred to as the Clostridium coccoides/Eubacterium rectale group which are potent cross feeders of resistant starch and raw potato starch in clinical experiments.  E rectale are poor RS fermenters but they live symbiotically with keystone gut species that eat and ferment RS to secondary food (substrates) which E rectale consumes like a hog on fire. Hattip: Tater/Tim.

Smart, Young and Resilient Gut I.Q.
Intestinal IS (Immune System) = HOMEO- and ALLOSTASIS

Smart Gut I.Q.

There are a couple of elements that I believe are fundamental in a stable, homeostatic gut ecosystem that will take one to advanced longevity:
--genetics (respect your ancestry... don't mess genetic expression with synthetic hormones, vitamins, endocrine-disrupting pollution, pesticides, GMO food/products, lifestyles, thoughts or people)
--super tight junctions and intestinal IMPERMEABILITY
--balanced flora
--special 'keystone leaders' like E. limosum, B subtilis, B licheniformis, and many others
--seed (return to the earth and intake healthy earth -- soil based organisms in fermented organic vegetables, fresh salads, and supplements if necessary (list here I like))
--weed (avoid mercury, toxins, food allergens/gluten and detox/chelate safely)
--feed with fiber (resistant starches, heirloom and native tubers, organic whole non-gluten grains, lentils, chana dal, legumes)
--exercise daily to move the gut (peristalsis), e.g. 10,000 steps or one hour mild to mod intensity. SIBO causes impaired gastric and intestinal peristalsis (and vice versa, sitting/atrophy can affect SIBO)
--misc (avoid unnecessary hospitalizations, CDAD (iatrogenic or antibiotic-induced C. difficile-associated diarrhoea), antibiotics, and other gut irritants like non-steroidal anti-inflammatories (NSAIDs) -- ibuprofen, motrin, aleve, excedrine, etc)

Resistant Starch Study Results and Positive Outcomes
Source: Conway 2001


Anonymous said...

Everyone that reads this giggles (ha ha Hi-Maize up your butt) but I think you will get it.

Great post. One of the themes I latched onto early in my RS journey, was that less civilized people have less problems in transverse and descending colon. Years of pushing fiber hasn't corrected this. Years of pushing RS may.


Dr. B G said...



Would you like to see a S.A.D. study in Green African monkeys ( Cercopithecus aethiops ssp vervets)?

Wheat/gluten for 3.5 years in both cellulose and psyllium arms caused horrofic intestinal permeability, SIBO, denuded villi, short mucosal height, gut hypertrophy, cellular edema and universal microvillar disarray...

J Nutr. 1987 Feb;117(2):253-66.
Intestinal structural changes in African green monkeys after long term [WHEAT/GLUTEN +] psyllium or cellulose feeding.

Don't f*ck ur ancestry...primate or otherwise...

Senneth said...

Do you have a post about how you fixed yourself? I am having no luck with the SIBO. Thanks!

Dr. B G said...


The posts before and after also provide info and sources.

What have you tried? What didn't work? What is working?

Do you have dental amalgams? Vaccines? Pets? Travelled or camped?


Anonymous said...

What are your thoughts on this?

B Sub not safe?

It's hard to know what to think.