Saturday, April 25, 2015

Updates: New Website Launch THE GUT INSTITUTE.COM and Slides From PaleoFX Preso

TheGutInstitute.Com has launched!

Please migrate over there for all the latest news on the gut microbiome, studies, diagnostics, and gut protocol strategies for health optimization.

We had an awesome turnout that was beyond capacity for the premiere ticket holders at PaleoFX this year: 'Shifting Your Gut Microbiota and Your 100 Trillion Friends for Leanness and Fat Loss'. Thank you for everyone that attended! The slides may be downloaded at (enter email). I am considering with Matt Pepin, my Gut Guardians co-host, to send out a monthly Gut RxTracts with a compilation of the latest gut news, research abstracts, book reviews, and all things poop and gut related. How does that sound? I'd love to know which topics you find most interesting.

A couple of things I mentioned at PaleoFx:

10% of uBiome analysis, thanks Eli and Paul~! (Eli's referral code) (Paul's referral code)

Sources of chitin/chitosan for gut health and fat loss prebiotic effects
Fiber in cricket flour is 7% and contains chitin/chitosan
Pubmed studies on fat loss and chitin/chitosan

Sources of yacon in sugar free virgin chocolate in Raaka handcrafted bars (YUMMMM!) and 4 grams of yacon-FOS per half bar, thanks Bill~!
10% off 'YACON10' code

Prescript Assist, the only probiotic containing 2 strains of Bacteroides that is missing in nearly every study in overweight and obesity microbial signatures, one of the root problems in the obesity epidemic. This probiotic and other soil probiotics helped my family and I overcome gluten, dairy and other food intolerances so we could consume again on rare occasions without severe gut, brain or digestive issues.
The company just the other day announced their evolution to ENVIRO MEDICA (no longer Magnetic Clay)! I love it! Congratulations!!

AO Biome, soil probiotic topical spray: Nitrosomonas, live Ammonia-Oxidizing Bacteria (AOB). It produces more NO, nitric oxide, a vital signalling molecule important for not just athletic workouts and sex ahah.
"This living product is a first, not only for our company, but for the industry as a whole. We created it to counteract the damage that modern lifestyles and products have on the biome, which often lead to irritation, sensitivity, and more. Our patented beneficial bacteria is similar to a probiotic, and it works to enrich your skin’s natural environment, gently restoring harmony to the skin. Specifically, it actively converts the byproducts of our skin (such as sweat) into beneficial ingredients, leading to skin that looks and feels great. "

Mark Sisson's new soil based upgraded ultra high potency 10B CFU per cap -- used by Eli Markstrom, Spartan warrior in uBiome self experiment.

The HENRY Bar~!! My kids designed an energy bar that they will actually eat that's not full of non-Paleo junk. Thank you to my master tasters who gave it unanimous thumbs up -- my sisters, best galpals, Matt Pepin, Dr Emily Dean, Robb Wolf and CSA MMA gym (Kieran). Nearly all organic and non-GMO, the Henry is full of goodness like our puppy which it's named after. Check out later for more updates or contact me directly to get a box (I have some complimentary ones to send out!)

Abundant in wonderful ingredients (some are not part of 7 steps -- dairy and nuts):
  • 17 grams isomalto-oligosaccharides (for fat loss, leanness and losing gut-leakiness) which is also found in fermented foods like natto, sake and fermented soybean sauce (bibimbab, jajiang noodles)
  • 16 grams pastured, grassfed whey protein
  • 10 grams carbs from 85% organic chocolate, cashew butter, almond butter, dates and quinoa crispies

Tuesday, March 31, 2015

Heal Yourself Radio EP 002 - FROM DRUGS TO BUGS

Heal Yourself Radio with chiropracter and hawt Crossfit athlete, Dr Jonathan Chung DC


On this week’s episode of Heal Yourself Radio we’re talking to Dr. Grace Liu, a functional medicine expert with a doctorate in pharmacy. Her area of expertise involves the clinical applications of one of the hottest topics in science and medicine, the gut micro biome. This interview is full of great information about the importance of your gut bacteria, what foods to use to support it, and what to do if you’ve been on antibiotics. We also had a lot of fun talking about poop, whose poop Dr. Grace wants inside of her, and what might make my feces so interesting. It was a really fun interview, and I think you are all in for a little treat.

Save 10% on any uBiome kit or product with Dr.Chung's referral code #microbiome

Monday, March 30, 2015

Gut Guardians Postcast: Episode 16 – (Part 2) Thyroid Help with Robin Treasure

Gut Guardians Postcast: Episode 16 – (Part 2) Thyroid Help with Robin Treasure

Robin Treasure in Part 2 offers her insights on how our guts might play a role in our thyroid health. She advises on the proper testings to diagnose a potential leaky gut causing poor adrenals. Yet another reason to keep your gut sealed up nice and tight.
Be sure to check out Robin Treasures new program ‘Restore!’ to help build and nurture a healthier lifestyle.

Don’t forget to leave any comments or suggestions!

Show Notes:
Klaire Probiotics

Friday, March 27, 2015

Gut Guardians Podcast: Episode 17- Gut-Brain Axis w Dr. Richard Matthews

Gut Guardians Podcast: Episode 17- Gut-Brain Axis w Dr. Richard Matthews

Functional Neurologist and author of The Symbiont Factor, Dr. Richard Matthews, joins in on the microbial fun. In this episode Dr. Matthews talks about the gut brain axis and multiple conditions that stem from the gut. Did we mention zombies? Matt and Grace had fun exchanging ideas on gut health and mental health.
(Note: I had technical challenges, very sorry for the poor quality on my end. You’re not missing anything -- please enjoy Dr. Matthews and Matt).
Thoughts on the Gut-Brain and parasitic gut zombies?

Show Notes:
Amazon: Book 'The Symbiont Factor'
Twitter: @symbionthealth

Excerpts from The Symbiont Factor

“The Bacterial Ethernet
“Bacteria living within a colony are able to form interconnections between cells in a network, using very small microtubules that have been termed nanotubes (Dubey, Yehuda). These nanotubes allow bacteria to share information, which can take several forms. In one example, demonstrated by Ben-Jacob, bacterial colonies will self-organize into elaborate shapes to optimize their survival and will form complex networks of nanotubes where they share plasmids (small pieces of DNA) as well as other molecules from their cell.”

“Providing a sustainable environment in the gut where good bacteria can flourish takes more work and lifestyle change than that and is one of the subjects of the rest of this book. Expecting the growth of beneficial bacteria without eating fruits, vegetables and fiber-containing grains is like scattering tomato seeds in a parking lot. Even though a few seeds might find some earth and germinate, you probably won’t get tomatoes unless you provide dirt, fertilizer, compost and water! Likewise, trying to get the good symbiont bacteria to grow without making improvements in your stress, diet and lifestyle is like trying to grow those seeds in the dark or on a parking lot.”

Friday, March 20, 2015

New Podcast With Nourish Balance Thrive, Christopher Kelley: Have you checked your gut for the keystone species?

Have you checked your gut for the keystone species? 

New podcast with elite pro mountain biker, Christopher Kelley of Nourish Balance Thrive and me (aka )

Tuesday, March 10, 2015

uBiome Analysis: Microbiome Hacking to Improve Gluten Intolerance and Acne

uBiome Blog

Our co-blog and Elijah's post on his recent gut uBiome results, here, at uBiome's blog today.

His extended version at his blog: Microbiome Initial Data -- I Need a Recount
"Observationally, I have noticed several changes so far. First and best, is that my sleep has been incredible. I fall asleep easily, sleep through the night and wake up with a pep in my step. Second, my appetite is lower. I feel full all the time. My energy levels are good. There is marginal fluctuation throughout the day. Third, my poop is more regular both in consistency and frequency."

His earlier post at uBiome: How to Poop Well.

Eli's uBiome 10% off referral code

[Side B: extended version, lol]

Microbiota Hacking

Thank you Elijah for the generous introduction! I appreciate your enthusiasm and reaching out to me to collaborate on maximizing gut health and your 100 trillion friends.

Looking at uBiome stool analyses helps me to map out the bacterial terrain and landscape in the intestines. It is a ground breaking tool that I’m so grateful for. I look for landmarks and clues that tie in with published pyrosequencing studies.

Elijah is an elite athlete with superior performance and 8-9% body fat. I almost doubted that we could further improve any biometrics (sleep, skin, mood, performance), but, naturally, when we look at the modern dysbiotic gut, everything can be improved. Modern guts are particularly vulnerable because they are being assaulted from all sides everyday. Therefore several simple and easy improvements can dramatically reset overall health by emphasizing our gut.

Our gut is the initial site of nearly all disease (besides pure poisons). Our hunger, hormones, happiness chemicals and energy regulators all are controlled or composed by this master regulator organ that gut researchers call the ‘second brain’. Scientists report 80% of immunity is housed in the intestines. In my estimates, the gut doesn’t control all health, 24/7 all the time, but when it is disrupted, then ALL health may be disrupted. Whether you are an elite athlete like Elijah or a high-level executive or a super tiger-mom, a healthy gut lays the foundation for overflowing health, youthful energy, leanness and longevity.

Our modern lifestyles lend characteristic changes in the microbiome – depletions of vital good flora and overgrowths of opportunistic pathogens. I call the good microflora ‘gut guardians’ because these protect our gut from birth until death. Their absence signals death, whether it’s a slow, gradual, perpetual and mildly painful death or a more chronic course riddled by the common American standbys: cancer, cardiovascular disease, autoimmunity, joint degeneration, or diabetes-obesity.

Elijah’s gut profile exhibits the losses which everyone frequently experiences as a result of processed, refined carbohydrates, high sugar diets and use of antibiotics which were given for chronic ear infections as a child. His birth was C-section and studies show a lack of transfer of mom’s good microflora such as Bifidobacteria longum to baby without a vaginal birth.

Landmarks that stand out on Elijah's gut microbiota uBiome analysis:
  • low biodiversity (low phyla and species counts)
  • depleted gut guardians which secure longevity and leanness by maintaining metabolism and a tight intestinal barrier
             o Bifidobacteria (part of Actinobacteria: 3-fold below normal)
             o Bifidobacteria longum (180-fold below optimal;
                but at least its there! yay!)
             o Bacteroides (3-fold below normal)
             o Christensenella
             o Akkermansia
  • increased potential opportunistic bacterial overgrowths
             o Corynebacteria pathogens (possibly skin related)
             o Proteobacteria pathogens (6-fold more than average) including
                Cronobacter, Salmonella, Shigella, E coli, Bilophila

Faecalibacterium prausnitzii. In the side diagram, you can see how Elijah’s gut scored: doing well for producing butyrate, a fuel of the colonocytes, the cells that line the colon. Faecalibacterium prausnitzii is exuberantly represented. Most healthy humans have 3-10% or more and Elijah’s gut is no exception. His gut also houses plenty of Lachnospiraceae (34.64412%) and Pseudobutyrivibrio (8.86619%) This consortia of robust butyrate-producers may partly explain Elijah’s resistance to gaining fat and other dysbiosis-related disorders. Author of the Epidemic of Absence, Moises Velasqueze-Manoff, recently wrote an essay reviewing the vital anti-inflammatory role F. prausnitzii plays in protecting human health, ‘Among Trillions of Microbes in the Gut, a Few Are Special’.

Reviewing Elijah’s uBiome Results: ABSENT ALLIES

Bifidobacteria longum (part of Actinobacteria). The loss of Bifidobacteria longum by antibiotic drugs and poor dietary choices (sugar, unfermented gluten) contributes to increased gut permeability and subsequent spilling of microbial toxins and cell wall parts through the ‘porous’ barrier into circulation. The consequences are low-grade inflammation, oxidative stress, mood changes, and disease (food allergies, bloating, digestive disorders, acne, etc). Fortunately, prebiotic fiber and probiotics can selectively boost and grow these tender populations. Health and well-being track well with improvements in bacterial parameters in my clinical experiences.

How To Boost
Bifidobacteria longum, Roseburia,
Akkermansia muciniphila,
and Faecalibacterium prausnitzii
For Gut Barrier Restoration and Pathogen Resistance

Geurts et al 2013

Proteobacteria and other pathogens. A few potential opportunistic pathogens were identified. With gut guardians and allies, these easily overgrow at the first opportunity. Many of these may be gently weeded out and replaced by the populations missing, which will be stimulated by probiotics and special fiber. Normal skin microbiota residents are Staphylococcus, Corynebacterium (previously part of Corynebacteria), Propionibacterium, Streptococcus, and Pseudomonas. In acne, microbiota sequencing and culture studies show higher Corynebacteria, Staphylococcus epidermis, Propionibacterium acnes, and fungal Malassezia in skin lesions.

Elijah’s gut apparently showed detectable levels of Corynebacterium amycolatum (0.00499%) which is sometimes associated with opportunistic hospital infections. The gut profile also shows possibly suboptimal concentrations of 4 Proteobacteria implicated in dysbiosis, colitis and food poisoning:
  • Cronobacter sakazakii (12.51294%)
  • Bilophila wadsworthia (0.08107%)
  • Salmonella enterica subsp. enterica serovar Agona (0.00499%)
  • Shigella flexneri (0.00249%)

Fecal Facts For The Skin-Gut

Our goal to improve the skin and work from the inside out, starting with shifting the gut microbiota, 100 trillion friends. This is also the progressive new thinking in dermatology:
“In the treatment of acne, one of the prevailing tenets has revolved around the eradication of a bacterium known as Propionibacterium acnes… Rather than non-specific chemical destruction of P. acnes, with its far reaching effects on the human microbiome, investigators are exploring the possibility of utilising non-pathogenic bacteria to improve the skin, with collateral benefits to the gastrointestinal tract and the psyche as well.”

Disease or Defense?

With the lack of protection in the gut, bacterial and parasitic overgrowths may partially degrade the single-cell layer barrier in the small intestines (upper gut) where we absorb the vast majority of digested food and nutrients. Havoc and competition further lower the bacterial sentinels which everyday seal and maintain the barrier layer against being leaky and open.

An environment harmful for health ensues. Food and intestinal yeasts and bacteria may breach and ‘leak’ into the blood and lymph circulation which alarm the immune system, producing large amounts of silent inflammation which adverse affects many organ systems: liver, fat, and muscles. Instead of efficiently burning fat, the body burns other things, sugar and muscles.

An endless cycle begins. For many, the joints and muscles are affected (discomfort, arthritis, swelling, sarcopenia). Invariable digestion and food intolerances are ‘ground zero’ type of symptoms (excess gas, loose bowels, constipation, stomach aches). Gluten, soy, corn and dairy may produce bloating and/or brain fog. For some the skin microbiome is affected (acne, psoriasis or eczema). Our central nervous systems never go untouched with modern gut dysbiosis; headaches, mood fluctuations, fear, hunger, and cravings are hallmarks of mangled microbiotas that I observe.

Skin-Gut Microbiota Manipulation

The goals stated by Elijah are two-fold:
(1) reverse intolerance to gluten which causes bloating and
(2) improve mild acne on back

What we will do is enhance what the gut already has and repair-renovate what is broken. We discussed considering additions to the great smoothie blend that have been shown in humans to heal the gut and immunity rapidly (add 1-2 of the below). The below ‘feed and breed’ diversity in the gut microbiota including the specific species that are missing (Bifidobacteria longum, Akkermansia and Eubacteria).

Choose a personal diverse combinational blend of prebiotic fiber:
Elijah did all the below except GOS.

1/4 tsp glucomannan (in 2 cups water; maximum dose ½ tsp; avoid if any trouble swallowing or drinking water, will swell 20-fold in volume)
1 tsp acacia
1 tsp arabinogalactan
1 tsp modified citrus pectin
1 tsp GOS (Bimuno or  Jarro Baby Dophilus 1 tsp = 2.4 g GOS)
1 tsp inulin-FOS
1 TBS psyllium
1 TBS cocoa

To seed-weed the proverbial gardens in our gut and crowd out modern potential pathogens, I often guide people to consider rebuilding the gut with health-promoting probiotics and gently weeding with short-term, combination botanicals. For skin I have a couple of tricks which speed healing in the gut. These would empirically target pathogens whilst specifically restructuring what is often missing. They all lower the quiet ‘fires’ of inflammation.

Consider for one month a skin-gut regimen:
--Berberine 500mg twice daily (Thorne)
--Neem 2 caps daily (Himalaya)
--Grape seed extract Trader Joe's 50mg, 4 daily (or 2 twice daily)
--Liver detoxifier (NOW foods) 2 daily

Elijah decided to go with all the above for the skin regimen and for probiotics decided on Bifidus Balance +FOS (Jarrow) and Primal Flora Ultra High Potency (Mark’s Daily Apple). The ability to breakdown casein (dairy) and gluten-gliadin (wheat) may come down to what is in our guts and what isn't. The above probiotics contain strains which can help in digesting and degrading these potentially allergenic food peptides that induce food allergies, similar to what Elijah experiences. Primal Flora UHP is a soil based organisms probiotic (SBO) containing 10 billion CFU. Our recent ancestors  had daily exposures to dust and dirt which contain these species. SBOs are one of the best ways to 'seed' the gut with bacteria aligned to our ancient past and better ability digest a range of plant fiber including small quantities of dairy and gluten.

Stay tuned!


Christensen, Gitte Julie Møller, and Holger Brüggemann. "Bacterial skin commensals and their role as host guardians." Beneficial microbes 5.2 (2014): 201-215.
Bowe, W, NB Patel, and AC Logan. "Acne vulgaris, probiotics and the gut-brain-skin axis: from anecdote to translational medicine." Beneficial microbes 5.2 (2014): 185-199.
Grice, Elizabeth A, and Julia A Segre. "The skin microbiome." Nature Reviews Microbiology 9.4 (2011): 244-253.
Kong, Heidi H, and Julia A Segre. "Skin microbiome: looking back to move forward." Journal of Investigative Dermatology 132 (2012): 933-939.
Tap, Julien et al. "Towards the human intestinal microbiota phylogenetic core." Environmental microbiology 11.10 (2009): 2574-2584.
Geurts, Lucie et al. "Gut microbiota controls adipose tissue expansion, gut barrier and glucose metabolism: novel insights into molecular targets and interventions using prebiotics." Beneficial microbes 5.1 (2014): 3-17.
Al‐Ghazzewi, Farage H, and Richard F Tester. "Effect of konjac glucomannan hydrolysates and probiotics on the growth of the skin bacterium Propionibacterium acnes in vitro." International journal of cosmetic science 32.2 (2010): 139-142.
Cani, Patrice D et al. "Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability." Gut 58.8 (2009): 1091-1103.
Lee, In-Ah, Yang-Jin Hyun, and Dong-Hyun Kim. "Berberine ameliorates TNBS-induced colitis by inhibiting lipid peroxidation, enterobacterial growth and NF-κB activation." European journal of pharmacology 648.1 (2010): 162-170.
Čerňáková, M, and D Košťálová. "Antimicrobial activity of berberine—a constituent of Mahonia aquifolium." Folia microbiologica 47.4 (2002): 375-378.
Han, Junling, Huiling Lin, and Weiping Huang. "Modulating gut microbiota as an anti-diabetic mechanism of berberine." Medical Science and Technology 17.7 (2011): RA164-RA167.
Zhang, Xu et al. "Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats." PLoS One 7.8 (2012): e42529.
Xu, Jia et al. "Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula." The ISME journal (2014).
Yin, Xiaochen et al. "Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula." Systematic and applied microbiology 36.3 (2013): 188-196.
Katiyar, Santosh K. "Proanthocyanidins from Grape Seeds Inhibit UV–Radiation‐Induced Immune Suppression in Mice: Detection and Analysis of Molecular and Cellular Targets." Photochemistry and photobiology (2014).
Nichols, Joi A, and Santosh K Katiyar. "Skin photoprotection by natural polyphenols: anti-inflammatory, antioxidant and DNA repair mechanisms." Archives of dermatological research 302.2 (2010): 71-83.
Afaq, Farrukh, and Santosh K Katiyar. "Polyphenols: skin photoprotection and inhibition of photocarcinogenesis." Mini reviews in medicinal chemistry 11.14 (2011): 1200.
Kar, P et al. "Flavonoid‐rich grapeseed extracts: a new approach in high cardiovascular risk patients?." International journal of clinical practice 60.11 (2006): 1484-1492.
Vinson, Joe A, John Proch, and Pratima Bose. "MegaNatural® gold grapeseed extract: in vitro antioxidant and in vivo human supplementation studies." Journal of medicinal food 4.1 (2001): 17-26.
Subapriya, R, and S Nagini. "Medicinal properties of neem leaves: a review." Current Medicinal Chemistry-Anti-Cancer Agents 5.2 (2005): 149-156.
Khan, M et al. "[Experimental study of the effect of raw materials of the neem tree and neem extracts on dermatophytes, yeasts and molds]." Zeitschrift fur Hautkrankheiten 63.6 (1988): 499-502.
Kumar, Venugopalan Santhosh, and Visweswaran Navaratnam. "Neem (Azadirachta indica): Prehistory to contemporary medicinal uses to humankind." Asian Pacific journal of tropical biomedicine 3.7 (2013): 505-514.
Lee, SH et al. "In vitro effects of plant and mushroom extracts on immunological function of chicken lymphocytes and macrophages." British poultry science 51.2 (2010): 213-221.

Friday, March 6, 2015

Peering into Four uBiome Stool Analyses (Part 1): Benefits of BIONIC FIBER; Emergence of Toxin-secreting Clostridium Botulinum and Loss of Over 1/3 of Gut Diversity and Species With 'Raw Bob's Red Mill Potato Starch'

Quantified Self Experimenter: R. Sprague

Recently Richard Sprague shared his data with me and asked me to review his uBiome analysis of his stool microbiome. He's a bona fide data collecter and fan of QS (quantified self). The other day he shared his oral microbiome results. Lot of wonderful things going on there in his mouth! For his gut on potato starch, not so much. We will compare this gut results to two other uBiome samples from individuals taking a Bionic Fiber combination (psyllium, acacia, inulin-FOS, etc) and a diet based around the 7 Steps for an optimal gut microbiota.

About Richard Sprague, 51 yr old QS-er, super healthy, lean (160 lbs, 6') and SUPER BRAINY:

"At the time of the three samples, I did not take any supplements or other medication of any kind. I drink one cafe latte per day, plus about 5 servings of alcohol (usually beer) over the course of a week. I am an omnivore, though I tend toward paleo-style eating (no processed food, plenty of fat+meat). I eat wheat- and other gluten-bearing food a couple times a week, along with dairy, and I don’t notice any difference at all whether I abstain or not."

Fiber intake (MyFitnessPal): 15-20 grams daily (below average; RDA for males 38 g/day, females 25 g/day if you subscribe to that)

Three uBiome gut results:
Sample taken on 5/16/2014 'Pre-RUMPS' (raw unmodified potato starch)
Sample taken on 6/6/2014   (on travel, camping, varied diet)
Sample taken on 10/17/2014  'Post-RUMPS' (raw unmodified potato starch 2-4 TBS)

Prior to the Oct 2014 uBiome he used 2-4 TBS 'raw potato starch' (RUMPS) sporadically for about 2 weeks to hack his sleep and stools. Both had some quantifiable changes: sleep increased from 6.27 hrs/night to 6.52 hrs/night and stools increased from 1x/day to 2-3x/day. Quality of stools may have worsened; he reports Bristol 4 or 5 (mostly 5) prior to RUMPS and 5 after RUMPS. Below I review May and Oct results. Our gut biome changes hour by hour depending on diet and lifestyles. There are many 'drivers' but what we stick in our mouths is the biggest driver. I decided to only compare these May and Oct results as 'best' gut representatives.

How Citizen Science Helps Us and Our Guts

I love ubiome -- it is not diagnostic but it is a valuable tool that tells us the terrain of the lower gut and a little bit about the upper gut (small intestines). It gives us the profile for all the bacterial colonies in the colon. With tools that Richard developed on his github, one can integrate the raw taxonomy and play with them in Excel. (AmGut data FYI is not so simple). uBiome also has fantastic turnaround times -- only 2-3 wks for results to come back. I just submitted mine this week, and looking forward to pouring over it soon. 

Fecal samples have limitations. They may or may not represent what is going on at the mucosa level. Sometimes vast changes are going on at the intestinal mucosal level but they don't spill over into the lumen and resultant fecal matter to truly tell us the representive microbial colonies going on there. Still I like poop. What we poop is what we are, just as what we eat is what we are. Diet is the biggest driver for shaping the gut microbiota. By just modifying diet and dietary supplements, we can perpetuate a better gut as well as better health.

Another limitation is that looking at bacteria alone doesn't give us the big picture for life in our guts; non-bacterial colonies such as yeasts/candida, parasites, helminths, and protozoa are also significant contributors to gut health and dysbiosis and they're not not analyzed. These are better seen with a urine OAT (organic acid test) for clostridial and yeast metabolites or a specific Genova or Biohealth 401B parasite analysis. 

The science is still in its infancy. uBiome and other institutions have not identified all the species. Depending on someone's gut composition, the unique # of species known and identified is about half to 70%. Therefore 'species norm count' will not add up to 100% (though 'phylum norm count' and 'order norm count' are typically close ~96-97%).

Sprague's Github Tools to Help You Analyze Your uBiome Stool Samples

Sprague has created a couple of tools to help you manipulate and play with your big data from uBiome after you get your results back. I find it helpful and excellent to see the phyla, order and species on the Excel sheets. Patterns emerge, changes can be tracked and a nice story happens.

He has a 'Getting Started' short list of instructions and very easy to follow steps to take the 'raw taxonomy' from uBiome's dashboard and transform into different data files (JSON, EXCEL, TXT, etc). Read his 'Beginner's Guide' for great info!

Citizen Science Reveals Dramatic Loss of Diversity and 36% Extinction of Known Species

Let's talk about Sprague reported no change in sleep on some days and slightly better REM on some days. He reports "I have 92 nights of data where I tracked my sleep and whether or not I took potato starch. Of the nights when I took potato starch, my average sleep was slightly higher (6.5 hrs vs 6.3 hrs)." When he used lower doses paradoxically sleep might have been even longer but he had only a few data points (n=8) and couldn't conclusively say at this time.

Several potentially adverse changes occurred on the gut profile I noticed as we have seen on previous studies involving use of Bob's Red Mill potato starch (Folz family AmGut -- higher blood sugars on RUMPSan episode of fat gain/higher blood sugars/gout/NASH with long use 1.5 yrs on RUMPS). 

One of the most debilitating factors for a gut is to lose diversity. Antibiotics cause fat gain or lead to modern diseases because they lower gut diversity. The same species that keep us lean and immunoprotected are the same ones rapidly killed off by broad spectrum antibiotics. To make a dysbiotic gut model in rodents, scientists can give 5 round of antibiotics and a single round of Clindamycin to give you an idea how simple and easy it is. Microbiota 16S rRNA studies tell us that low diversity in the gut is the hallmark for a poorly functioning gut, one that is vulnerable to infection and inflammation (Le Chatelier et al, Nature 2013). 

36% Loss of Species
40% Loss of Orders
Depletions and Extinctions
Associated with "Raw Potato Starch"

In the first May sample, Sprague reports that 49% of the species were known and identified by uBiome, then as many as 65% were for the Oct sample. With dramatically less diversity and species, more species were known and identified, including some known toxin-secreting strains. For the orders, it was worse. The diversity destruction included 40% loss of known and identified orders from initially 45 orders down to only 27 orders. That is a lot of ecological devastation it appears. With high dose of a singly sourced 'fiber' or food, this is what occurs. The SAD (Standard American Diet) does the same thing, providing little in terms of nourishment and spectrum of fiber to the gut flora. Many species perish and so do the functions that they serve us with. Our gut flora are the silent organ that provides 10-15% of our energy, make dozens of vitamins and anti-cancer chemicals and keep us lean and healthy.

What extinctions did Sprague's gut appear to go through? Some good and some bad. The appearance of significant toxin-bearing strains (including Clostridium botulinum) might be notable as this is the 2nd case I've seen now associated with raw starch utilization.

Source Tap et al EM 2009
Principal coordinate analysis of OTUs from the faecal microbiota of 17 healthy human individuals. A principal coordinate analysis was performed using the full distance matrix. Each OTU was pictured as a disk whose area was proportional to the number of sequences and the heat colours accounted for the prevalence among the 17 individuals. Operational taxonomic units represented by a unique sequence (singleton) were not plotted.

The Gut Landmarks on uBiome Stool Analysis That Signal Good Health 

The landmarks that I look for are based on research by Tap et al and gut researchers on 4 different continents who have characterized the gut species found in abundance in healthy controls. I call these the 'ancestral phylogenetic core microbiota' since these are also found in abundance in rural living and ancestrally living individuals such as the Amerindians, Burkina Faso, Hadza and Malawai inhabitants. The above is a PCA showing the most prevalent OTUs that are hallmarks of health I believe. When I look at the gut profile of a healthy person, these are the ones I always find.

Faecalibacterium prausnitzii is very special. It is a gut barrier and immune system warrior and known as a keystone 'Peacekeeper' (Nature 2015, fantastic photos).You can see above it is a red-orange and found in robustly in concentration of hundreds in 94% of tested healthy subjects. In clinical trials, it is low where diseases are present and high in disease-free people. It is a harbinger for bad health if it and several other 'ancestral core' species are depleted. Moises Velasquez-Manoff recently wrote an essay outlining all the unique and protective aspects about F. prausnitzii and why all guts need it: SciAm "Among Trillions of Microbes in the GUT, a Few Are Special". Check out Gut Guardians in April, Moises will be a guest on our podcast with my co-host Matt Pepin!

How does Sprague's QS experiment stack up? Unfortunately after amputating over 1/3 of his gut species, many of the phylogenetic core are depleted. The initial levels were awesome but after a high dose of single source of 'fiber', many on re-testing were gone and dramatically diminished numbers.

The Problem with Depletions... Where's the Faecalibacterium prausnitzii??

Notable known species depletions associated with 40% reduction in orders (read more about each species HERE and poss consequences of loss). This pattern is a hallmark for raw starches (which are not part of human native diets; only #gerbilfood). The same pattern I've reported earlier and why leaders in ourpaleo blogosphere considered avoiding it -- here.
  • 17-fold reduction Faecalibacterium prausnitzii (only on species found in Faecalibacteria); how to raise F praus here; F praus doesn't eat starch at all, preferring to selectively dine on oligosaccharides, pectin and other varied non-starchy fermentable fibers
  • 50% Roseburia, major human butyrate producer and keystone immunity protector
  • 7-fold reduction Christensenella, potent fat burning species
  • 4-fold reduction Akkermansia, keystone mucosa lining protector
  • 14-fold below optimal Bifidobacteria longum, majority fecal bifidobacteria species and keystone immunoprotective species for babies and adults (optimal: 45% of total fecal bifido)

The Dysbiotic/Disease Gut Microbial Fingerprint

In several studies now, the gut microbial fingerprint has been characterized. Invariable they all look similar in many respects:
--low diversity
--depletions of known and identified 'good flora'
--overgrowths of known and identified potential pathogens

Sprague's gut like many on the potato starch has now taken on this profile. The loss of important immunoprotective species such as Faecalibacterium prausnitzii (17-fold depletion) is probably not a good sign. Further depletions of other known and characterized species associated with longevity and good health has also been decimated. The destruction of diversity perhaps has led to the emergence of a couple of pathogens that Sprague's gut didn't have earlier. His diet sounds varied but his reported fiber intake is somewhat low and suboptimal (15-20 g/day).

For Sprague 4 clostridium species were shifted signficantly by the experiment, I noticed. Two potentially pathogenic strains shifted down in abundance and two worst strains grew robustly and appeared to take their places.

Clostridium asparagiforme -- became extinct or undetectable.

Clostridium clostridioforme -- lowered by 50% which I think is an improvement

Clostridium baratii 0.55877%-- 5-fold increased, may secrete toxins similar to botulinum. Note: the concentration and abundance of this strain is higher than the phylogenetic core Bifidobacteria longum (0.18584%; 3-fold less, mmmmhhh...The pathogen is outnumbering a potent gut guardian)

Clostridium botulinum Ba4 str. 657 (0.00253%) -- new appearance to detectable levels of the Toxin B secreting strain isolated from a botulism case. Let's say our stools represent 10-100 trillion bacteria in the GI tract, therefore 0.00253% may be a proxy for 0.25 to 2.5 billion Clostridium botulinum bacteria in the gut. I don't think that is a trivial amount, sadly, if the data is semi-reliable. Researchers report that toxins from Clostridium are several thousands-times more toxic than other endotoxin releasing opportunistic pathogens in the human gut and considered one of our planet's most neurotoxic chemicals. Botulinum B toxin interferes with neural transmission of release of acetylcholine, key neurotransmitter in our calm and restorative nervous system (PSNS) and can lead to muscle paralysis (Nigam et al 2010). Botox for use in wrinkles is A toxin and stronger than B toxin. In Asperger's/Autism Spectrum individuals, Clostridium and other gut pathogens (Enterobacter, Sutterella, Desulvovibrio) and low gut guardians (Eubacteria, Lachnospiracea [Coprococcus, Roseburia intestinalis, Roseburia faecis], Bifidobacteria) appear to form a unique microbial signature  (De Angelis et al 2013; Midtvedt 2012).  RUMPS-raw potato starch appears to create this hallmark Aspie/autism signature.


Emergence of Several New Pathogens With 'Raw Potato Starch' in Sprague's Sample

Let's detail the the species that appeared to emerge in Sprague's QS n=1. Sprague reports no digestive issues or health problems. His HgbA1c pre- and post-test is still acceptable 5.0% and sleep/mood/energy/skin/digestion all remain good.

Clostridium botulinum 
Known and identified Toxin B secretion strain Clostridium botulinum Ba4 str. 657
  • This strain was isolated from an infant botulism case in 1976. The strain is a bivalent Ba strain, that simultaneously produces two different toxin types 
  • C botulinum some strains also appear to be hefty starch and sugar eaters (Macfarlane et al 2000 AEM). Many of the clostridiums are. They are ancient primordial survivors. Some good for us but some not so.

Clostridium baratii
Another Clostridium is associated with inflammation and autoimmune dz like Kawasaki's. C baratii appears 5-fold higher compared to the initiation of the experiment.

Clostridium clostridioforme
High Clostridium clostridioforme which is associated with diabetes, low gut diversity, inflammatory conditions and human invasive and severe infections like bacteremia. Often it produces alcohol and other toxins, which are associated with inflammation, artery hardening, and histamine responses. Alcohol from microbial fermentation results in blockages of multiple enzyme pathways in the host including the degradation of histamine. When more histamine accumulates, subsequently, the host has more allergic reactions, congestion, rash, headaches or other manifestations of high histamine. These are all secondary to a dysbiotic and imbalanced gut.

Raw RS2 selectively appears to increase toxic, adhesive E coli and Clostridium in both small and large intestines

Person "A" and Amped-Bionic Fiber is Associated with Lower Toxic Clostridium Levels

In this series of posts, 4 uBiome analyses will be reviewed. The third column in the above comparison is of a gentleman who was also on potato starch 2-4 Tbs for 6months, then switched to an 'amped version' of Bionic Fiber for 4 months. Besides Sprague's example, Person 'A' is the second case of associated potato starch-enrichment of Clostridium botulinum.

On the other hand, Bionic Fiber is associated with reduction of Clostridium strains per studies (see below). I think now, Person 'A' is on a downtrend for Clostridium.

Person 'A' reports numerous improvements since starting Bionic Fiber: better sleep, better skin, better brain (decreased fog and fatigue).

BENEFITS OF AMPED BIONIC FIBER: Bionic fiber is a combination of diverse fibers that the gut flora absolutely thrive and love to eat. It works because they selectively stimulate nearly all the phylogenetic core that Julien Tap et al and gut researchers around the world have identified as the core consortia that protect human health for millenium as observed in both individuals that still live non-urbanized 'dirty' living and those that live in Europe, Korea, and USA. The basis of bionic fiber discussed here. For vital 'Peacekeepers' like Faecalibacterium prausnitzii and super immunoprotective gut flora, it potently stimulates these colonies along the length of our guts for human leanness and longevity.

Velasquez-Manoff, Nature 2015

Person 'A' took for four months prior to the uBiome sample an amped version of BIONIC FIBER inulin, acacia, glucomannan, psyllium, baobab fruit powder and larch arabinogalactan.

Inulin, GOS, FOS and other oligosaccharides purge pathogens like toxin-secreting Clostridium strains

Butyrate looks like it is quite good with really high Eubacteria, Ruminococcus, Lachnospiraceae and other Clostridiales being robust and abundant (we'll review in detail in future posts). These are higher than Sprague's initially and post-potato parade.

According to Person "A":
"So about 3 years ago started having somewhat generic symptoms - brain fog and fatigue, dry/flaky skin mostly on my face. Switching to a perfect health diet (or at least trying to follow PHD [PERFECT HEALTH DIET, PAUL JAMINENT) helped quite a bit. [Fiber]: 15-20 grams of fiber per day on average. We eat a good amount of rice and potatoes, some freshly cooked, some cooled and reheated. Probably average 1 serving of vegetables a day (mostly broccoli, brussel sprouts, green peas) and 2-4 servings of fruit per day (bananas and berries mostly). We've also been re-incorporating beans lately - probably 2-3 servings per week.

I started RPS about 1 year ago and quit almost immediately due to some joint pain and excessive gas. A few weeks later I tried again, but started with a much smaller amount and built up to the 2-4 tbsp/day recommendation at the time. I didn't notice much of a difference, other than really great bowel movements - very regular and consistently a bristol 3 or 4. The brain fog and fatigue continued to be occasional - no real change with just the RPS.
Then about 4 months ago I started mixing up your bionic fiber, dumped the RPS but still used some plantain flour. I'd say I get about 20-30 grams of supplemental fibers a day now, with inulin and acacia being the majority. Glucomannon, psyllium, baobab, larch are included as well in very small amounts. I've now dropped the raw plantain flour in the last couple weeks.
Since switching to the bionic mix, here the changes I've noticed. Bowel movements slightly worse actually. Still fairly regular, but get bristol 2 every now and then. Brain fog and fatigue still present, but noticeably improved. Skin appears to be healing as well, but not all the way there yet. Skin is improving - dryness, texture, moisture. I'm not really sure how to describe it and my doctor never thought it was anything to worry about - he just said to use lots of moisturizer... It wasn't painful or itchy, just unsightly to look at!"

To Be Continued...

We'll talk more about
--Bifidobacteria longum
--how Bionic Fiber bionically raises buytrate producers