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My n=1 Pre- and Post-Microbiome, Digestion, SCFA, Fat Malabsorption, Pancreatic Insufficiency, Leanness F:B Ratio, and How I Hea

Posted Sep 15 2013 10:26am

Functional Lab Testing: GI Effects Stool Test (GI Fx)

There are several tests I think everyone should get if they are suffering from any chronic conditions, cancer, or inflammatory condition. One is the Metametrix/GDX GI Fx Stool test.  This is one of the most advanced tests that accurately, reliably and thoroughly evaluates the entire intestinal tract and the gut microbiota.

Using PCR sequencing on the 16S ribosome of microbial species and parasites, it accurately assesses both our microbiome (genetics) and those of any parasites.  The old 200-year technology of O&P x3 (ova and parasite) from 3 samplings of stool should be over; to achieve a positive identification, one must rely on the luck and fortune of the microbiologist viewing the smear on the slide to observe a parasite glide by or tiny ova like needles in a haystack.  I believe stool cultures are equally primitive technology and unreliable. Over 80-90% of stool microbes are obligate anaerobes and/or symbionts which are difficult or impossible to grow in culture or without their neighboring microbes necessary to sustain life.

***Read the Metametrix/GDX Interpretative Guide for the GI Fx Stool Test: HERE .

Example of a Super Super-Organism: B. Pottenger

My m=1 Microbiome: Data for Epimicrobiomics Thinkering

Brent Pottenger is not only hawwt, lean, muscular, sexxxy and smart... so is his poo.

Characteristics of excellent health and excellent poo(a) Pancreatic Enzyme Digestion:  Elastase 1, marker for pancreatic enzymes (greater than 300 = decent; greater than 500 or immeasurable = PALEO AWESOMENESS).  No deficiency of pancreatic enzymes, fat malabsorption, undigested plant fibers, undigested fats
(b) No microbial overgrowths detected. Stunning gradient of Bacteroides/Prevotella. Exceptionally robust Prevotella populations detected
(c) No yeast overgrowths detected
(d) No parasites, worms, flukes, protozoa or pathogenic overgrowths detected
(e) No gut inflammation, anti-gliadin sIgA (current gluten reactions) detected
(f) No excessive or missing SCFA (products of microbial fermentation -- both good and bad flora)
(g) Excellent adiposity ratio of Firmicutes:Bacteroidetes (leanness) and correlates with Mr.Pottenger's BF (~~ 7-9% I estimate).

Digestion, Fermentation 101

Here's a primer on the gastrointestinal tract, digestion and fore/hindgut fermentation in humans.   I co-lectured with Tim Gerstmar ND at the inaugural Ancestral Health Symposium in 2011 at UCLA.
Ironically, I was ill at AHS and suffering from chronic fatigue (CFS).  Leanness was difficult to achieve, brain fog massive, and immune tolerances extreme (gluten, dairy, fiber, FODMAPS). It had all started immediately after a titanium dental implant, lasting from 2010 until summer of 2012 when I had it removed.  Nothing worked (yes, I tried everything). Finally, last summer, all the titanium, mercury amalgams, and gold crowns were extracted, and almost within 10 minutes I lost 5 lbs of peripheral edema and gained clear headedness.  Gradually signs and symptoms of metal toxicity, adrenal dysregulation and gut dysbiosis mostly disappeared.  A few months ago, I started dreaming again. Off/on I've been lucky to have leanness but it wouldn't last long.  Gluten actually was no big issue for me after Paleo, but dairy/nut intolerances became very problematic causing ankle swelling, mild joint achiness, and bloating.

Follow up is based on the latest labs below and Dx: bacterial/amoeba overgrowth. Starting to feel already even better and digestion improved.  Here are snapshots of AFTER v. BEFORE treatment.

(a) Pancreatic Enzymes (SIBO)
In 2011, my gut was not digesting. Enzymes were not produced at either the brush border (microvilli/small intestine) or apparently secreted in adequate amounts by the pancreas. Why? Gut stress, immune dysregulation from both microbial overgrowth and metal toxicity/suppression. With undigested carbs, fermentation occurs producing volative SCFA (small chain fatty acids) where it's not supposed: the small intestine. Undigested fats are delivered to the large intestine causing sometimes greasy, floating stools. I never had this, but the GI Fx test was positive. Undigested proteins (vegetable, meat) ferment into volatile SCFA, polyamines and stinky compounds (sulfur groups are stinky, like rotten eggs). Together, these further damage the small intestinal mucosal surface and induces SIBO (small intestine bowel overgrowth). Good protective flora are lost and both good and pathogenic flora overgrow, in the wrong place. Undigested fats and plant fibers make it intact to the feces. After treatment (surgery, Hg removal, diet, exercise, lifestyle, supps), this imbalance all reversed.  See AFTER, 2013. No red zones.

(b) Microbial Overgrowth (SIBO, Caecum/Appendix, Large Colon)

Overgrowth of 'good' flora occurred: Clostridias, Fusobacteria, E.coli.  A spike in SCFA propionate increased correspondingly.  I lost good species -- carb-eating Bacteroides, Prevotella, and huge populations of Lactobacillus and Bifidobacter. In his NYT article on the gut microbiota, Michael Pollan talks about how he lost his brawny Prevotella spike and developed a 'creepy E.coli bloom' after only one round of oral antibiotics, HERE .  He appears to eat a metric ton of fermented foods, so no doubt he has regained his Prevotella by now.  I'm so grateful that my gut did!  In fact the little tube became enriched by most of what seemed to be lost --Firmicutes, Bacteroides, Prevotella, Lactobacillus --- except some Bifido.  Prevotella is considered one of the best ecological microbiome metrics for neurotypical and healthy guts. In a recent study of autistic v. neurotypical children, it was found that the main 'core' genus missing was Prevotella by B Kang and James B Adams, PLoS, 2013 .  In the enterotypes of neuroatypical autistic children, Prevotella was entirely absent.  The researchers also noted that a gradient of both abundant Bacteroides and Prevotella appeared optimal. Prevotella is also one of the top 3 genera observed to line our GI tract from mouth to anus. Its primary role in the large intestines is digestion of human-indigestible plant polysaccharides from cellulose, xylan, glycan, resistant starch, pectin, plants, shoots/roots/tubers, fruits, legumes/lentils, seeds/nuts, and whole grains.    Children in Burkino Faso have the most stellar Prevotella spikes (53% of total B + F) on earth -- they eat little meat (or gluten grains) but obtain protein from both (1) consumption of termites and (2) I hypothesize...  microbiota-N2-fixation (amino acid byproducts from air (N2) + cellulose fermentation... ?incl carnitine, etc) from Prevotella, Bacteroidetes and N2-fixing symbionts from the termite gut microbiota.

For more info, read Dr. Leo Galland: Intestinal Permeability, aka Leaky Gut .  Once gut imbalance occurs, SIBO can take over and wreak havoc. Recall the gut epithelial layer tis one single cell layer thick. Undigested food and enteric bacteria, yeasts and parasites can quickly breach a damaged gut-barrier and proceed straight into blood circulation.  They can translocate to other organs and induce food allergies (soy, corn, nuts, eggs, citrus, dairy, wheat, oats, etc).  When the immune system tries to eradicate these perceived invaders with antibodies, then auto-immune diseases unfold. Muscles/joints, body fat and organs start to dysfunction when the immune-complexes (antigen+antibody) junk up joints, receptors, tissues and blood/lymph vessels.

(c) Yeast/Fungi Overgrowth (SIBO, Caecum/Appendix, Large Colon)
Normal is 'zero' yeast. Except for Mr. Pottenger's, I've never seen a report where yeast is less than 2. NEVER.  (I've never seen parasite-free/overgrowth-free result either.)  I run the GI Fx on nearly every client. Everyone shows fungal overgrowth and  it's indicative of dysbiosis.  Yeast is opportunistic and quite literally a bugger.  For over one year, I was on oral fluconazole 1-2x/month (I h**te pharmaceuticals especially liver-damaging ones). Nothing else controlled the yeast and in fact I had to dose escalate for only marginal control. When I returned to the U.S. my sister introduced me to Natren, and with immense gratitude, it worked in 24hrs (despite titanium/mercury).  Later, Natren, Prescript Assist, FloraMend and FloraBalance all helped to restore balance and minimize out-of-control fungi and allowed me to 100% discontinue Rx fluconazole.

(d) Parasites Are Not Paleo (generally speaking)

Overgrowth of pathogens, parasites and worms do not cause problems for everyone when the gut is anti-fragile, robust and resilient.  In fact, these stressors can even improve gut health and stability by stimulating the immune system.

However for the great majority of individuals sadly this isn't the case in my clinical experience. Perhaps, people's  toxome is too excessive. When parasites or pathogenic overgrowth are found in the context of dysbiosis symptoms, IMHO it is best to treat.  Test, not guess... Or treat empirically like you would treat a dog/cat/pet. There are many sources of parasites in the USA and third world countries (like China).  They are overlooked, underdiagnosed, and ultra prevalent. The CDC reports more than 60 million men, women and children carry the Toxoplasmo gondii parasite. Salads, fresh fruit and vegetables, pet dogs, pet cats, tap water, cash $$, electronics, work computers, open bodies of water, licking doorknobs, camping, etc. are all common sources of parasites.  Read Dr. Leo Galland: Parasites .

D*mn, can't get lean. Though I gradually appeared to regain health and hormones, I couldn't achieve leanness. Somewhere between 2010 and now, I picked up an amoeba growth (Endolimax nana, see above) and opportunistic bacteria Morganella morganii.  Both are relatively easy to treat with 2-3 rounds of combination botanicals which have anti-microbial/anti-parasitic/anti-candidal spectrums ( berberine , wormwood/artemisinin, oregano oil, curcumin, black walnut, herbs/garlic/ginger/biopiperine, etc). Sometimes these overgrowths can be benign. I have no symptoms except inability to achieve desired leanness and mild (but annoying) residual food intolerances.  Being compromised by metal toxicity, CFS and adrenal exhaustion may also have been factors for the inability to 'crowd' out overgrowth. In countries, like South America, anti-parasitics are sold over-the-counter. Several excellent botanical formulations are at iherb, my favorite international farmacy: Para-Shield , Thorne Berberine-500 , Curcumin +BiopiperineTricyline , Paradex , Scram , Vermi-Purge , Paracid Forte , etc. I've used Metagenics Parex before, but it appears no longer made in the US. Metagenics Candibactin-BR is also excellent but no longer at iherb.

(f) Gut Inflammation, Anti-Gliadin sIgA
Gut inflammation all normalized after treatment. I had been gluten-free for months prior to the initial GI Fx test but we had gone to France and Germany for Thanksgiving six months earlier and ate hordes-of-irresistible-gluten (e.g.buttery croissants). The positive anti-gliadin sIgA shows that the immune system was apparently still reacting. Depending on the person, antibodies may require 6-24 months or longer to clear.

(f) Volatile SCFA (products of microbial fermentation)
With gut dysbiosis, butyrate and SCFA were all disrupted and low.  Propionate spiked -- likely due to excessive fermentation in the small intestines by overgrowth of supposedly 'good' gut flora (Clostridias, Fuso and E coli).  After treatment, this trend flipped.  Butyrate and total SCFA were all up to upper-normal ranges. This indeed matches my overall health -- less food intolerances, better digestion, far less bloating/distention, improved sleep, resumption of REM/brain-dreaming, adrenal tolerance, good adrenal hormones, great gonadal hormones, regained ability to do endurance training.

(g) Adiposity Profile: Firmicutes to Bacteroidetes ratio
Too much of either Firmicutes or Bacteroidetes is not ideal. Both help in extracting energy from chemical bonds in food. SCFA are metabolites of Firmicutes and Bacteroidetes fermentation in the caecum/appendix and large intestine. Partly the way they work is that the SCFA end products bind to G-proteins ( GPR41 ) to control inflammation, brain-gut-gonad axis (cortisol/heart rate/etc), immunity and fatness. Just as omega-3 EPA + DHA increase lean muscle, reduce body fat and improve insulin sensitivity and inflammation , SCFA appear to do the same. Approx 55/45 to 60/40 may appear ideal.

Urine Organic Acids, Oxidative Stress, Toxin Evaluation:  2013

The urine organic acids ( ONE=optimal nutrition eval ) confirms that the gut dysbiosis was not severe.  No yeast dysbiosis was detected outside of normal range (very happy about the lack of brain fog/aldehydes/mycotoxins, too). In fact, vitamins, minerals, adrenal function, mitochondrial energy production and fat burning were all decent or exceptional.  It did point out that I'm a little low on detox nutrients -- vitamin A, all the B vitamins (being COMT (+/-) heterozygous), tocopherols, glycine, glutamine, magnesium and zinc.

The O.N.E. shows toxins -- alpha-ketophenylacetic acid (from my #*$&@ iPhone cover, styrene, synthetic rubber, resins, polyesters (sports bras, workout outfits), plastics, Saran wrap) and a-hydroxyisobutyric acid ( from MTBE, gasoline additive meant to help gas burn 'clean' now major contaminant in California drinking water despite banning in 2003 ). Apparently mod-high levels of both are being excreted in the urine (after having spent 2mon in Cali 'detoxing' LOL aha). These are endocrine disruptors and damage DNA.

My kids and I have the GSTT1 deletion (glutathione S-transferase T1), and do not detox many xenobiotics well. Studies are finding oxidative, DNA damaging, and hormonal effects with even low exposures of polyaromatic hydrocarbons, pollution, benzene , acrylonitrile (gloves, plastics)styrene , gasoline , mercury ( thimerisol sensitization -- eye drops, vaccines ), mercury ( low birthweight babies ), mercury ( compromised urine detox-elimination ), mercury in medical students ( increased mercury body burden ), and countless other chemicals/metals in GSTT1 null individuals.  This genotype is even linked to whacked  gender ratios of their offspring when chemically exposed ... Dr. Mark Hyman MD reports he has the GSTM1 deletion and its effects, here .

SIBO Treatment, Healing the Gut-Brain-HPAT-Gonad Axis, and Followup

How did this SIBO &!amp;#$@ mess get fixed? Functional medicine labs, diagnostics, and treatment provided all the tools that were needed to finally reclaim my prior health, leanness, and brain-gut-gonad axis.  I am thankful for the opportunities to interact with several practitioners, my brilliant sister 'M', functional medicine doctors, and WAPF leaders over the last few years -- some very briefly -- they gave me the insight that I needed.

The root cause and antecedent event was the titanium implant which appeared to trigger some immune compromised reaction. There are implant failures (not me -- purrrfect, excellent ossification) but not many test Ig-positive on traditional or functional testing ( MELISA , Clifford ) at this time. Clifford CCR testing showed reactions to all mercury amalgam and nickel, but nothing for gold or titanium. After it and all metal were removed, the typical integrative medicine strategies all worked -- probiotics, raw fermented vegetables, exercise (earlier too fatigued to do any workouts), naps, yoga, laughter/friends, spiritual support, digestive enzymes, omega-3, mag/zinc/minerals, adrenal adaptogens, adrenal protocols (carb+protein+fat, every 4 hrs, sea salt 1/4 tsp daily), pycnogenol, gut support (marshmallow, slippery elm), betonite clay, charcoal, ghee, organic lard, rainbow vegetables, pastured pork and egg yolks, frequent bone broths, etc.  For followup, I hope the next phase will yield further insights.


Share and show me your GI Fx tests or integrative medicine lab testing results... I'd love to see it!
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