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
http://ubiome.refr.cc/X4D28CW
[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 prausnitziiFor 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!
References:
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.
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Xu, Jia et al. "Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula." The ISME journal (2014).
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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.
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