Sunday, September 15, 2013

My n=1 Pre- and Post-Microbiome, Digestion, SCFA, Fat Malabsorption, Pancreatic Insufficiency, Leanness F:B Ratio, and How I Healed SIBO and the Gut-HPA-Gonad Axis

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!


Anonymous said...

Hi Dr. BG,
Glad to see you back! I'm glad you figured out your sweet spot! You're looking lean enough to me. No need to be a skinny b**tch.
Well anyway I'm COMT +/- and Mthfr --
bhmt +/- just basically screwed. Had huge hashimotos goiter, had to have my thyroid removed, now just basically f**cked as far as energy. Just thankful girls are in college. So tired... thanks you give me hope. Kathy

Dr. B G said...

Kathy --

Thanks for your kind words and thoughts! I AM BACK!! MOJO AND MICROBIOTA.

LOL At least I can fit into all my clothes... it was disturbing when I couldn't and quite frightful. SIGH. Too vain -- but kinda my barameter for the health/hormones/biota.

OKAY -- that's a genotype triumverate of f**ckeduppedness...!!!

You are toxic, no? EVERYONE IS. MY KIDS -- they have similar results as me for the GI fx stool test and ONE nutritional/toxin/dysbiosis eval. Guess what? My 12 and 14 yo have worse markers. We all have dysbiosis but different pathogenic organisms.

These genotype deletions and null alleles all compromise the pathways for elimination of post-industrial modern waste, heavy metals, and endogenously-produced carcinogenic and inflammatory estrogens. The outcome is compromised gut barriers, SIBO, inflammation, molecular mimicry (gluten/casein appears like thyroid tissues to the immune system), and subsequent autoimmune disease. I had Hashimoto's in college (40# wt gain in 3-4months). My sister had the goiter (Grave's). Both cause perpetual, endless fatigue (after thyroidectomy or I131 in Grave's).

I'm sorry for the current condition -- no fun for you.

What are you doing?
Fermented foods at every meal?
Identification of body burden and your individual toxome?
Have you had functional medicine lab testing? Curious? (I'd love to see your microbiota and urine organic acids!)
Are you on Nature-throid or Armour? Is that titrated to symptom control?
How are your adrenals?

The problem I have with SCD, GAPS or ketogenic diets for SIBO is that they all further compromise the adrenal/thyroid axis (either simple glucose/honey or low carb), inevitably. I meet VERY FEW INDIVIDUALS with decent adrenal function these days. Too many stressors. SIBO is a d*mn big stressor...

Xifaxan is all the big rage but I just don't find it sustainable. The price is outrageous as well; most insurances won't cover or require 20 hoops of overrides for MD/NDs to jump through. Data for relapses are not apparently entirely out. Many report failures. Pimental is paid off as a speaker/researcher. That makes me dubious with the anecdotal reports.

The spectrum of antibacterial activity is not bad but it fails (as far as I know) to cover pathogenic yeasts, parasites, viruses or worms. Preference for broadspectrum herbals with combination synergy of therapeutic value seems to me healthier, sustainable, safer and more effective. Most anti-microbial herbals also show anti-malarial, anti-protozoa, anti-parasitic, anti-viral and anti-candida/yeast activity in studies, especially in combination with other herbals, even at low dosages. The GI fx stool or Nutri-eval or ONE cannot measure all the possible pathogenic organisms or viruses in the gut (yet).

Good thing your girls are in college (and hopefully safeguarding their health from stressors, bad dorm food and enjoying their indpendent time) -- and you have time to nourish and nurture yourself. Hang in there!!


Ed said...

Grace - awesome post. Tons of information.

I'm dealing with a flaky, itchy scalp, and occasional digestive issues. I'm thinking of finding some sort of integrative / functional practitioner to help go through stool testing to come up with a treatment.

I guess my question is, how do I select a practitioner? Can you suggest questions to ask to filter bad ones and identify good ones?

Dr. B G said...


Yes -- bite off what you can and save some for later. LOL.

Personally for a provider, I am very picky.

I look for
--bedside manner
--open mindedness
--functional and integrative medicine approaches
--paleo or GF or simply nutritionally competent (e.g. not low fat)
--covered by insurance or reasonable cost or bitcoin or trade services

Sometimes DIY and biohacking are often the best for non-acute health issues. Everything is related and the gut is often central whether it is male pattern baldness or itchy flaky scalps.


zek said...

This is an interesting post. Mostly above my head, but interesting.

I'm 31/M. I've had amalgams since childhood. I had a root canal in Sept. 2005. Within 3 months, I had begun gaining visceral fat - unusual as I'd always been rail thin. Within 6 more months, I was spaced out, lethargic, brain-fogged, and that has persisted to the present day.

I don't know whether to suspect the root canal itself, or mercury from the huge gob of amalgam that was sitting in the root canaled tooth for 8 years, galvanically corroding on top of its gold post.

I've had my amalgams removed and am detoxing with Quicksilver IMD (intestinal metal binder), liposomal glutathione, R-ALA, and chlorella. Not much to show for it yet, but it's only been a month. If I don't start seeing gains in the coming months, I will have to look at the root canal.

Anyway. I did not know this about dental implants. Just wondering if you have any recommendations on a course of action in the case of a root canal. Extraction, I guess, but then what? Move to West Virginia?

Thanks for your great blog.

Dr. B G said...


I'm sorry -- I have some commitments the next 1-2 wks so I'd post more for you but check in later w/me, 'k?

Google 'wapf root canal' or look in their journal for root canal.

You need to seek the help of a biological dentist who knows how to deal with root canals and the subsequent anaerobic infections at the site where the nerve endings/circulatory connections tie off. Root cause (no pun intended) is that there is probably now low grade chronic infections associated with the prior tooth, mini absesses so to speak and putrification. Each tooth is innervated and provided nutrients via the circulation and nervous system.

That is the most common consequence.

Getting the gold crown off was actually probably marginally good to stop the galvanization.

When the dentist removed the amalgams was it done safely -- O2 canula, high suction vacuum at the tooth, air filtration unit, dental dam? That is another potential factor to any new onset metabolic changes. The 'vapors' from drilling are inhaled causing significant toxicity and these start coming out 3-6 months (depends on the person) after the antecedent event. This is a big problem unfortunately with any removal, even the safest ones. People are just sensitive and vulnerable. As our health/gut function declines, it just gets worse also. You probably look healthy on the outside, so good luck because normal people will not understand what you are going thru.

Personally I've had all 3 issues and metabolic derangement/edema/fat issues (not a root canal but a cracked tooth which was developed a baby absess).

There are no easy answers but I'd encourage you to seek more information to make the best, sound decision.


Anonymous said...

Dr. BG,

I've gone through a similar battery of testing in the past year, primary for suspected leaky gut (which was confirmed) -- a stubborn case I couldn't get rid of; brought on by antibiotics (and then taking a gut-healing supplement for months, without ridding of the dysbiosis).

Interestingly I have found that sulfate and electron deficiency are key to my issues. Not just leaky gut, but the vulnerabilities/deficiencies UNDERLYING leaky gut.

One of the major things that flagged me to this was a glycine deficiency (as in your case). Glycine is the major amino feedstock for sulfated molecules throughout the body.

The other thing that flagged me to a sulfate deficiency was a toxic backup of phenols (implying a shortage of phenol-sulfo transferase).

All of these have parallels to the autistic disorder template.

Anyways, since avoiding dietary-borne sulfites, taking glycine, and getting dermal sulfates (Epsom salt) daily, plus throwing in earthing for good measure, I have seen a massive upswing in my condition.

The fact that you seem to be experiencing an ever-changing cast of infections from all manner of microbes is reminiscent of my experience (I've gone through yeast, bacterial, and fungal dysbiosis in the past few years, and am now free of all), and suggests you might also benefit from some attention to sulfation, and electron supply generally.

Dr. B G said...


Thank you for your comments and insights. YES. I hear you. Our sulfates are not great. Being in China without a home water filtration system has limited baths and soaking in Ancient Minerals or Epsom. We've moved and hopefully can get into the habit of doing this someday.

Grounding -- (big smile) I haven't mentioned but for the last two years have done as much barefoot yoga that I can outdoors on soil or lawn. I believe it has made a large different (but hard to quantify). I sleep better on these days and overall feel better -- could be direct sunlight, fresh air and seeing greenery effects as well! But I do concur this is an overlooked magnetic resetting or deficiency.

Is that what you had meant by electron deficiency? Could you clarify?

I believe you are correct on the sulfo and glycine biochem pathways. We drank bone broth everyday almost so I was shocked quite frankly. It is the sulfation and we probably have some genotype that predisposes to problems. Thank you for your thoughts.

Congratulations on all your progressive changes and renewal of health -- spirit, gut and brain! I find great inspiration and comfort in stories like yours.


TonyC said...

Thanks for the reply, BG.

(Anon again; this time I'll use my dummy Google account so you can email me if you'd like)

What I mean by electron deficiency is a shortage of anti-oxidant (and hence anti-inflammatory) negative charge-carriers, AND/OR free electrons. (The latter is not really recognized in mainstream biology but your own experience with grounding testifies to it).

Besides being anti-oxidant, it does seem to be commonly accepted that these charge-carriers have a (cellular) immune function. So that would tie in to the opportunistic infections issue.

Check this paper out (by Dr. Seneff et al) for more "Is Endothelial Nitric Oxide Synthase a Moonlighting Protein Whose Day Job is Cholesterol Sulfate Synthesis? Implications for Cholesterol Transport, Diabetes and Cardiovascular Disease"

Among touching on the above points, it also proposes that sulfated molecules (specifically heperin sulfate proteoglycan, HSPG) have a critical role in glucose metabolism by BUFFERING GLUCOSE. In other words, there's more than just insulin involved.

Dr. Seneff's paper may be the "missing link" in this sense, and with regards to a number of other aspects of health that sulfate touches upon.

The only thing I would add is that grounding/earthing probably works with these molecular (-) charge carriers to disinfect, antioxidize and keep inflammation under control.

But the glucose buffering would explain what I and others have experienced as sometimes sub-optimal performance even on a ketogenic diet (for me, a noticeable "slow down" about 4 months into paleo). In specific, your central nervous system ALWAYS needs glucose, so any problems with glucose metabolism will have consequences (the CNS can be "fired up" with caffeine, as is commonly done, but then you are pushing into adrenal fatigue territory, if you make use of this too much). Of course, one should be making glucose via gluconeogenesis if there is a shortfall, but if there is a problem USING that glucose, you'll still get the "slow down" effect.

Further anecdotal proof, in my case, comes from eye dysfunction. I've experienced a slow gradual degredation in eyesight for 20 years, with an oddity of noticeable "slow days" where my focus and vision is worse than on other days. I now believe this to be a consequence of intermittent sulfate deficiency: low sulfates mean worse glucose buffering, which means glucose metabolism dysfunction in the eyes (cornea and lens). The reason this is paired with long-term degredation is that the "slow downs" (poor glucose utilization) also imply glycation damage, which would have a long-term cumulative effect.

I am probably the only one who has figured this out.

Your point about genetic vulnerability (which may tie into the low glycine) fits right in. In my case, I have traced the sulfation deficiency back to a methylation deficiency (we have the MTHFR A1298C mutation in my family; my sister even has the homozygous version, which I may have as well). In my lay research I've connected methylation deficiency to a downstream sulfation deficiency, so that pretty much explains where my vulnerability comes from.

I've found, though, that I can supplement around it (in specific, I am back to super-high energy, alertness, and low to no chronic symptoms, with a HFLC diet). So whatever your genetics, one might be able to "hack" around them, to optimize health and be less restricted in diet. But it looks very likely to me that you have something similar going on.

zek said...

Thanks, Dr. B. G. I will report back if I do decide to get the root canaled tooth pulled.

Just out of curiosity, what did you replace your titanium implant with? Bridge?

Dr. B G said...

hey zek

did you see this?

I have yet to replace the implant...bit of a little procrastinator so when I open my mouth, the back looks like a homeless person's!


Dr. B G said...


I think you're totally right on about the sulfation defects being downstream from methylation defects. Even if not, it is parallel or analagous somewhere. GST for glutathione requires adequate sulfation as well...

I can only imagine a nirvana or mecca of methyl donors and abundant sulfur and minimal oxiditive processes where our ancestors evolved, no??

Have you seen this evidence based of sulfation deficits?


Dr. B G said...


Thank you again for your insights and thoughts. Your eye improvements are quite astounding. I appreciate hearing all your research and experiences. The Seneff piece is eye opening but more so is your connection between sulfates and glucose buffering/CNS glucose-dependency. I agree -- glycolytic activity depends on gluconeogenesis. The glucose buffer for the sole benefit of the brain makes sense -- an evolutionary tradeoff --> smaller guts to divert energy to the all glucose-engorging brain.

The sulfate reservoir can take quite a pounding from VLC paleo, no? Yes -- I'd totally agree.

What are your thoughts on the gut's role and absorption of dietary sulfates? The article cites 5-25% of inorganic sulfur is absorbed via the GI. Humans lost the ability to efficiently absorb iron from plant sources (when we became carnivorous, IMHO). I wonder if sulfur from liver and hunted game provide easier to assimilate sulfur??

The microbiota assist on nearly every nutrient's absorption and assimiliation, so I would not be surprised there is impaired sulfate absorption (just like minerals and B12/intrinsic factor) when the gut is impaired... I have to admit all the latest hacks to my gut (anti-parasite regimen, SBO supps of Clostridium butyricum and Bacillus licheniformis, kraut, Asian paleo, etc) have made huge impacts on my energy too.

Whats in W Virginia? Are you Denver fan too? Glad to hear your energy and alertness are so perky now!


Lynh said...

Hi Dr BG

I have had the same test done (Metametrix- Gi effects and organix urinary test). I would love to share my results but don't know the best way how.... This is so interesting and I appreciate your time and effort. Let me know what you think is best as a platform to share results.... Dropbox? Not too experienced with it. Anyway I have fungal overgrowth, two parasites, and pancreatic insufficient enzymes, as well as achromobacter bacteria in high amounts! And trying to bring up beneficial bacteria as well. Think my trigger was three months of swallowing toothpaste due to lack of access to clean water... Then super low carb paleo. Bad bad combination. No excuse for how stupid I was I know. It's a long road to reshaping gut flora and treating everything or knowing what infection or parasite to treat first, but I think you have got it spot on. If my results help someone else get the test, I would be happy. I had no fungal overgrowth in GI test but did in urinary one. Looking up supplement your sister recommended!

LJ said...

Oh email me! If you want

LJ said...

Sorry my email address is the one for the previous two comments....Lynh

Dr. B G said...


Thanks for your comment. Would love to hear more and see the GI fx results. I don't see your email. Please forward on PDF if possible.

My email is (Left-side)


Unknown said...

What a fantastic share. Congratulations on a successful self-diagnosis. A few notes: you're misrepresenting Mr. Pottenger's poo, glancing over fat malabsorption evidenced by sky-high triglycerides. Is zero yeast really normal (might that be Mr. Pottenger's problem?). Taking into account studies showing decreased bacterial adhesion/sensitivity due to titanium exposure, it all makes sense. Sensitive gram-positive bacterial strains were lowered, allowing opportunistic yeast overgrowth. Anti-gliadin figures were stricken from the After lab report where the Before report states they represent only gluten sensitivity when gliadin is a product of fungi.
Effect of Titanium-Ion on the Growth of Various Bacterial Species:
Hydrogen breath tests, the gold standard in diagnosing SIBO, don't take into account fungal production of hydrogen gas. Meanwhile, fungi are decimating wildlife to near extinction events (bats, snakes, frogs, bees). Where are the bacteria which would normally control fungi? "We were truly stunned to see just how common fungi are,"
May as well wrap it up with this; invoice me for reading. Celiac disease is not about wheat. The sugary-sweet gluten-free diet feeds the problem.

Dr. B G said...


HELLO DUDE. Where are you? What do you do?

Yes -- you are correct there are just a few anomalies in Mr Pottenger's labs. The pancreases are fine so I suspect the high fat diet lends itself to the overflow of TGs.

I think for the GDX/MM GI fx stool test, 'zero' yeast/fungi just means 'normal'. One plus or more I believe are magnitudes higher than normal (7-8% subfractions of total flora). I could be wrong but that was how I interpreted.

Thanks for your analysis and contributing links. I concur with the yeast overgrowth factors. Yeast does a lot to hijack our biochemistry and immunity. I was not aware of the potential for gliadin production. You don't think that is collateral effects from intestinal permeability?

I didn't know about titanium adversely affecting normal oral/gut flora... that makes sense in hindsight of my symptoms.

Have you heard of IAP? intestinal alkaline phosphatase?

I am blood type A/non-secretor (FUT2 -/-). I have less IAP technically and apparently the A blood type antigens neutralize a lot of IAP. lol. I've been somewhat sickly my whole life until the SIBO reversed and fixed (or earlier when I had no massive immunity issues, off birth control). Apparently I think it is related to IAP and utilization of the biota on the fucose in our endogenous mucin and crosstalk. Would to hear your thoughts on the topic later.


Unknown said...

Hi grace, how do you rock so hard? Honored to speak with you. I'm in Palm Beach County, Florida, a professional recycler for 25 years trying to reinvent my career in health and sanitation. Presented this poster, AHS13:

I tend to doubt zero yeast is normal. Perhaps one of their many roles is metabolizing glycerol, the backbone of triglycerides along with free fatty acids, all of microbial origin. Is it any wonder probiotics lower cholesterol? Diet shifts flora while lipid levels appear dependent on flora. Did you know anorexia includes very high cholesterol as well as high methanogens? Counterintuitive stuff. Things like bacillus subtillis are also known to utilize glycerol (maybe that's the health secret of natto).

Don't know anything about IAP, but thanks for the inspiration to research in connection with fungal toxins inhibiting the enzyme from doing its job tightening gut junctions:

This area of research where fungi cause leaky gut (SIFO) and gliadin as part of the fungal cell wall appears to need more attention. Dietary gluten becomes a matter of molecular mimicry:

I believe I saw something in one of your blogs about toxic pollution in China as cause of the fierce diabetes epidemic and couldn't agree more. Yet nations still believe diabetes caused by poor diet and being sedentary. But what about pollution's effect on sensitive gram-positive bacteria (lactobacillus, bifidobactiera) allowing gram-negatives (e coli, clostridium) to flourish along with opportunistic yeast overgrowth? Children are born imbalanced from imbalanced mothers, a matter of microbial predisposition.

I've been inspired to learn from a dog with a seizure disorder of gut origin and practice a lot of prevention myself. Current favorite flora-shifting supplements are OptiMSM (organic sulfur) and niacinamide. I think they both apply to your situation; it's about pH balancing and raising innate immunity. From Palm Beach County With Love.

Dr. B G said...


I have more to write but I have to jet for a while. So you know all about biofilms? This is why I like the SBO probiotics like B licheniformis. They are super powered biofilm busters.

For candida and other pathogenic overgrowths which are protected and hidden from the immune system in biofilms, soil based organisms like B subtilis and B licheniformis are like the immuno-SWAT team. Take out the invaders and their slimy matrices and fortresses....

Blood A antigens bind up IAP and block. It's pretty GI fukcered... Type A's have ~half the IAP and AB only ~20%. IAP has something to do with cholesterol processing too. Seriously I don't get it yet... maybe you can help ;)

Biochem Biophys Res Commun. 2006 Mar 3;341(1):33-8.

Involvement of intestinal alkaline phosphatase in serum apolipoprotein B-48 level and its association with ABO and secretor blood group types.
Nakano T, et al

Serum levels of intestinal alkaline phosphatase (IAP), a protein implicated in transcellular transport of chylomicrons, vary among ABO blood groups. In rat enterocytes, IAP is associated with chylomicron secretion, but the rat expresses only blood group A. It is not known whether chylomicron secretion may be affected in humans who express multiple blood group types. Serum samples from 40 healthy subjects were obtained after overnight fast and 3h after a high-fat meal, and assayed for IAP and apolipoprotein B-48 (apoB-48), both proteins exclusive to intestine, although only apoB-48 is found in chylomicrons. The two proteins were greater in subjects without blood antigen A (B and O) than in those with this antigen (A and AB); 2.4- and 4.7-fold for IAP and 1.5- and 2.0-fold for apoB-48 before and after the meal, respectively. Moreover, IAP and apoB-48 levels were strongly correlated in the subjects with the secretor phenotype (r > 0.81). These results indicate that IAP is strongly involved in chylomicron formation and fatty acid metabolism might change among ABO blood type. In addition, ABO blood type classification in apoB-48 measurement would improve the diagnostic value in the evaluation of metabolic syndrome.
PMID: 16412386 [PubMed - indexed for MEDLINE]

gotta run will be back

Unknown said...

I'm not alone in fearing SBO probiotics, especially spore-formers setting-up shop. Natren's founder speaks out against them.

Other biofilm-busting products are nattokinase which I think is good, serrapeptase which I've tested and seemed too powerful and lumbrokinase from earthworms which is supposed to be super-powerful. This product, InterFase Plus, however, gets great reviews from experts:

I'll try to learn more about IAP and report back, but please know you're dealing with a total laymen. The last time I thought about my own IAPs, it just turned into a big party. I don't think I'll be much help regarding blood type effect on IAP (don't even recall my own blood type), but . . .

It's fat and cholesterol which modulate IAP activity:

As previously stated, cholesterol/lipds are dependent on flora. I've read most GI symptoms associated with Celiac disease, for example, are caused by fat malabsorption. A high fat meal leads microbial endotoxins (LPS) and inflammation:

So maybe the key is to reduce gram-negative bacteria, source of LPS, which you've done. But fungi and their toxins may still be high at +3. That's where I believe OptiMSM and niacinamide help.

Recap: fat modulates IAP and microbes modulate fat.

Dr. B G said...


Don't go away... I'm not done. 'Recap: fat modulates IAP and microbes modulate fat.' WOW. That is epic. I need to digest that!

I love your poster. That is truly spectacular work!!!

Regarding potential problems with all probiotics, I concur. In immunosuppressed individuals, there is a danger for bacteremia and sepsis. This is seen with any probiotic including Lactobacillus and Licheniformis.

Before I started on extended courses of Prescript Assist, I spoke with the owners of PA. Jarrod (co-CEO) and I used to do Crossfit at the same Walnut Creek gym. There are no reported adverse effects that we are aware of. There is one study of one year's length with no reported adverse effects that I read.

Clin Ther. 2007 Jun;29(6):1153-60.
Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial.
Bittner AC, Croffut RM, Stranahan MC, Yokelson TN.

The aim of this study was to extend a previous 2-week assessment of a probiotic-prebiotic complex in patients with irritable bowel syndrome (IBS).
In this open-label, partially controlled, 1-year (14 [2] months) extension study, data were collected from patients with IBS who continued treatment following a 2-week study of the efficacy of the probiotic-prebiotic complex. Data were collected at 2 and approximately 60 weeks after the end of the original study.
A total of 25 patients entered the 2-week extension and 22 completed the approximately 60-week follow-up study (20 women, 2 men; age range, 20-70 years; all white). Results in the control group 2 weeks after crossover to treatment were similar to those from the original study, with reductions in IBS subsyndromes, as follows: general ill feelings/nausea (P < 0.001), indigestion/flatulence (P < 0.001), and marginally colitis (P < 0.03 [1-tailed]). Treatment was associated with a continued reduction in general ill feelings/nausea at 4 weeks (P < 0.007). At >or=52-week follow-up, the rate of remissions was 81.5% to 100% (P < 0.003).
Based on the results from the present 1-year extension study, treatment with this probiotic-prebiotic complex may be an option for short-term (2-4 weeks) and long-term ( approximately 60-week) reductions in IBS symptoms.

Dr. B G said...

The two most telling studies that make this SIBO protocol work is that RS + NSP + SBO work synergistically... and are quite frankly failures if used individually or separately. This is seen in clinical studies as well and in real life anecdotes (and in my personal health failures ~two years worth! lol).

Firstly you need both non-starch polysaccharide fiber (like psyllium or hemicellulose) and resistant starch (RS) for optimal transport of the substrate to the distal colon.

Secondly, fiber alone doesn't do anything. NILCHO if the gut is extinct of specific specifies that consume RS, like soil based strains and commensals.

J Nutr. 1999 Nov;129(11):2081-7.
Psyllium shifts the fermentation site of high-amylose cornstarch toward the distal colon and increases fecal butyrate concentration in rats.

Morita T, Kasaoka S, Hase K, Kiriyama S.

We examined the combination effects of psyllium (PS) and resistant starch on large bowel short-chain fatty acids (SCFA). Rats were fed one of the following four diets: low amylose (LAS) or high amylose cornstarch diets (HAS, 50 g/kg diet) with or without 15 g PS/kg diet (LAS/PS and HAS/PS diets). HAS and/or PS were substituted for the same amounts of LAS in diets. Cecal butyrate concentrations were significantly higher in rats fed the HAS and HAS/PS diets than in those fed the LAS and LAS/PS diets. However, butyrate and total SCFA concentrations in rats fed the HAS diet decreased along the length of the colon and fecal butyrate concentration was reduced to one-third of that in the cecum. In contrast, the HAS/PS diet maintained higher butyrate concentrations throughout the large bowel. Fecal butyrate concentration in the HAS/PS diet-fed group significantly exceeded the sum of the concentrations in rats fed the LAS/PS and HAS diets. PS supplementation to the HAS diet significantly increased fecal starch excretion by 10 fold compared with that of rats fed the HAS diet. There was a positive correlation between fecal butyrate concentration and fecal starch excretion (r = 0.709, P < 0.0001). In a further experiment, ileorectostomized rats were fed the HAS and HAS/PS diets. From the difference in fecal starch excretion between normal and ileorectostomized rats, starch degradation by large bowel microflora in rats fed the HAS and HAS/PS diets was deduced to be 96% and 63%, respectively. These findings support the hypothesis that PS may delay the fermentation rate of HAS in the cecum and shift the fermentation site of HAS toward the distal colon, leading to the higher butyrate concentration in the distal colon and feces.

More recently, another plausible mechanism has surfaced in the
synbiotic combination of resistant starch, Lactobacillus acidophilus and Bifidobacterium
lactis [34]. These investigations identified enhanced apoptosis of carcinogen-damaged cells in
rat colon by the combination treatment [34]. In contrast, the probiotics provided no protection
when a low resistant starch diet was fed and the resistant starch had no protective response in
the absence of the probiotic [35].

Dr. B G said...

So Keith, yes if one is immunosuppressed and not consuming RS, then I believe the potential for probiotic induced bacteremia is real and significant. However, RS helps to move these nice critters to the rectum where they deeply DESIRE to return to the soil for their ancient life cycle, no? I should show you the coolest studies using radio labelled isotope-RS and the bacteria that 'ride' on the RS granules to the further destination of the large intestines...

Unknown said...

Well, people do eat dirt and clay. Most pregnant women in Africa eat clay, though I'm not sure if it's for microbes, but for magnetic properties in clay (drag out the offenders detox). But lots of animals eat dirt and feces as probiotic. Proactive elephants eat shit from one another before it hits the ground. Pica is interesting, often misinterpreted stuff. Self-medication. Even dolphins eat mud, once misinterpreted as mass dolphin suicide when the pod was probably very ill. Dolphin diabetes is barely on the map, swimming in sick seas of terrestrial pathogens. And check this article out about heavy metals in dirt of China which should be associated with China's diabetes epidemic due to compromised metal-sensitive gut microbes:

Thanks for restoring my faith in SBOs, not that I plan to try them. I do, however, enjoy bee propolis first thing every morning. Ever research propolis?

WIth bees under attack by pesticides, their own gut flora is damaged, an overlooked cause of colony collapse disorder. Who knew bees also have gut flora? In China, the problem is so severe they are forced to pollinate by hand, see here:

Vitamin D3 is the next thing I place in my mouth to raise innate immunity. Are you on it? It's about intracellular calcium absorption where calcium signals/stimulates macrophage activity. All the major gut diseases include vitamin D deficiency because that's where D is absorbed or malabsorbed. It's not about sunshine and diet. Recommended dose is 5,000 iu/day. I know there's controversy. But the world is D deficient as well as zinc deficient, important because D absorption requires a zinc molecule at the base of the vitamin D receptor. Zinc does a lot more; I've read zinc picolinate is best for systemic bioavailability. I'm also into boron and occasional hyaluronic acid (HA) because microbes degrade HA using their hyaluronidase enzyme, especially fungi. My selenium of choice is SE-Methyl L-selenocysteine. I like transdermal magnesium because oral mag may feed fungi more directly. And I do use a probiotic, Kyo-Dophilus which is only lactobacillus and bifidobacteria. All these things are about raising innate immunity so I can consume a diet of 100% french fries and ice cream lol. Just joshin'. BUt if you want to send in something to kick ass like SBOs (because sometimes one has to club a few seals to save a few whales), look into the herbs, chanca piedra and coptis (berberine). I repeat, OptiMSM and niacinamide top my list these days. It's not easy trying to love forever™. I never would have come to use all these things were it not part of a nearly 4 year trial trying to heal my seizure cluster-prone dog, testing the things I was giving her myself. I plan to complete a paper about gut-brain-eye axis and gut origin of seizure. G'morning!

Unknown said...

I mention gut-eye axis because my dog's gut problem progressed to photosensitive seizure. Yet in South-East Asia, the "massive" problem is blamed on too much studying and not enough sunshine:

Myopia is about insulin resistance where toxins of gut origin cause cell wall rigidity and leptin resistance which dysregulates histamine receptors leading to hypothalamic inflammation and optic neuritis. That's where sulfur (MSM) helps to allow insulin in and acidic waste out. Happy days.

Unknown said...

Invoice me for reading either of my last two posts.

That's fascinating information regarding synergy of resistant starch and probiotics. Here's reference [35]:

And I love the imagery of SBOs' "desire" to return to soil, riding starch granules through intestines while busting biofilm.

Have you heard about retrogradation where temperature affects quality of resistant starch (RS)? Maybe this is origin of the expression "cool beans." Basically, cool yer beans and potatoes for optimal RS. See here:

Dr. B G said...

Keith Bell,

I am so honored to get to know you! Thank you for not going away~!! I luv u and want to invoice you ad infinitum for sharing all of your thoughts. Please don't ever stop ;)

Ok said you shared a litany treasures and gems.

" Did you know anorexia includes very high cholesterol as well as high methanogens? Counterintuitive stuff. Things like bacillus subtillis are also known to utilize glycerol (maybe that's the health secret of natto)."

No!! I didn't know this as I'm still becoming quickly familiar with enterotypes and the niches of each player in the gut ecosystem -- predators, cross feeders, scavengers, prey, etc. Lol. This makes marvelous sense. Did you know that the source of probiotics in mothers' breast milk is from the myenteric lymph circulation?? The same circulation where postprandial triglycerides are transported to peripheral processing. B subtilis and other commensals would certainly enjoying dining with routine regularity at the source, no? B licheniformis too I suspect. Don't worry if you or your dog would abstain from SBO probiotics as the source of b licheniformis includes also raw dairy and ground dwelling birds -- ducks and chickens. Does your dog hunt?

Your canine is fortunate to have such a learned and big hearted caretaker. What has worked to control the seizure activity? Have you looked into taurine? The role of toxins like pesticides or mercury?

I don't know much about MSM or niacinamide. I suspect that after I fixed the gut, sulfation should be improved but as you suspect it's probably not. I used to take slo-niacin and felt nicely calm on it. It's not the same but I wonder if the cholinergic activation of both niacinamide and niacin achieve untold benefits?

From your fungal IAP link (much appreciated) "the intestinal and placental isoforms are inhibited competitively" shows how fungal toxins are so poisonous to the fetus whilst in utero. The AP during pregnancy has vital roles for uterus health and maintenance. Poor baby, no? This is what SIBO and SIFO are rendering our populace? Children appear to have such leaky guts nowadays and how much is attributed to mom as you mentioned? Thank YOU MOM. This was certainly what McBride-Campbell also writes in GAPS. If baby has autism or psych disorders, look no further than mom with candida (or dad from exchanged flora).

Hugs to Palm Beach,

Dr. B G said...


I profoundly appreciate all the China links. I wasn't aware of the hand pollination. Terrible. It's close to the end of sustainable food and crops, no?

Metals are a enormous problem both in food processing and contaminated cropland. Electronic waste and batteries leach cadmium arsenic and mercury into rice and grain crops. Aluminum is heavily used in baked goods and processed noodles. Titanium in cellulose pill capsules. Everyday there are discovered scandals.

"Myopia is about insulin resistance where toxins of gut origin cause cell wall rigidity and leptin resistance which dysregulates histamine receptors leading to hypothalamic inflammation and optic neuritis. That's where sulfur (MSM) helps to allow insulin in and acidic waste out."

Does your dog have hyper insulinemia and insulin resistance? Toxins cause this. Did you know high dose insulin blocks the MMC migrating myenteric complex which is like the pacemaker or heartbeats of the antrum and intestines which sweep small intestine and other contents down the pipe hole? Disruption of this directly leads to SIBO. Likely SIFO too.

Asians consuming a lot if white rice which is pretty high glycemic index thus raising spikes of postprandial insulin. Now the modern Chinese diet includes sodas, juices, refined snack food and other sweets which all raise insulin, destroying the muscular synchronicity and contractions of the gut. They have pretty much no NSP or RS in the diet.

Adore your cool beans thoughts which made me guffaw~!!


Dr. B G said...


I truly want to hug you for all of your fungal highlights! Another reason I find that when our gut lacks commensals, SFB and naturally occurring SBO strains, we are deeply damaged. Our immunity suffers. The studies on the blog from Ivanov et al and Chernovsky et al which show that T1DM models reverse or mitigate autoimmunity when commensals like soil originating SFB are present at the ileum are quite landmark. They echo the human experience, no?

SBO produce anti fungal compounds. These aren't necessary super potent but since they tend to produce a myriad of related biochem antifungals there is the pharmacological synergy of multiple compounds. More efficacy that way too! And the endogenous 'good fungi' won't be as likely to be killed off. SBO work symbiotically I suspect with all the normal commensal fungi and bacteria...

Soil has mold in it so this evolution isn't shocking. Many plants to ward off mold at the tubers, roots, and shoots produce antifungals -- terpenoids, quinones, tannins.


Anonymous said...

Could you address the timing of the weed, seed & feed?

Everything all at once? Start with the weed first for a few weeks and then move on to the seed/feed stage?

I'm just trying to figure out when I should start using all these:

kefir, potato starch, SBO probiotics, bentonite clay, physillium husk, GI Microb-X


Unknown said...

Thanks so much, G, for the SFB lead, so much to learn there . . . I couldn't agree more with "when our gut lacks commensals, SFB and naturally occurring SBO strains, we are deeply damaged."

The problem may be children are born imbalanced. But there are also environmental factors at birth such as vaccination. There a NO comprehensive studies about collateral damage to flora by vaccination, yet we have the nerve to vaccinate within 12 hours of birth without allowing the immune system reliant on flora to develop. Current, cruel protocol should be reduced and begun perhaps as late as after two years of age. My dog passed by accident in September 2012 before I had a chance to heal her and she was actually doing so well. Thanks so much for your thoughts. And, yes, I strongly suspect sugar imbalances of gut origin as cause of her seizures and I communicate regularly about this issue with humans suffering epilepsy while their disorder is treated by doctors from the neck up. One of the mechanisms among many is alcohols/aldehydes produced by microbes, especially fungi, dysregulating insulin production, creating reactive hypoglycemia, a problem associated with schizophrenia, as well (so many must be misdiagnosed as insane when the problem is metabolic). I also strongly suspect vaccine injury in the case of my dog. In her case it seems a combination of fungi and perhaps more importantly, clostridium overgrowth, perhaps due to consuming feral cat poop. The joys of life! When vets wanted to do spinal taps and MRIs, I ordered endoscopy to confirm her ulcerative condition as she had so many GI symptoms. Gut origin of seizure is still barely on the map.

To lighten things up, you've been so life-enriching. And that photo doesn't hurt. Pardon me while I faint.

"Did you know that the source of probiotics in mothers' breast milk is from the myenteric lymph circulation??" Nope, that's fascinating, considering there's 3-5x more lymphatic fluid in the body than blood.

Anonymous said...

Hi there Dr BG,
I am trying to follow your protocol for healing the gut with the guidance of a friend who is also following it and is also a nutritional balancing consultant.
I JUST started and have been trying to read your blog, much of it is over my head but still so inspiring.
At the start of this post you said that there are several tests you recommend for anyone with chronic issues. Can you list the rest of those for me?
I am also wondering what you know about chronic high histamine/low methylation and DNA mutations that prevent healthy detox pathways. And how that may fit in here?
I am curious because I am so tempted to try and feel I will need to try the fermented foods as I travel this route but I am weary of making my current condition worse by adding to the histamine issue. I know there is some debate about the chicken and the egg with this issue. Some think the symptoms are a result of the gut and metal issues and others think it can contribute or cause the gut and nervous system issues.
Do you have any insight or ideas?
Thank you! SBC

Dr. B G said...


Thanks so much for your comments. The funny thing about histamine and undermethylation is that mercury can make anyone appear histamine sensitive and undermethylation. The root causes certainly need to addressed and assessed first. As you're aware hair testing is one way to see metals (imperfect but still decent).

Until we removed our metals and fixed our guts, my kids and had many of the undermethylation signs. Many improved after addressing these. I hope that helps!

A healthy gut is practically mandatory I discovered to detox and achieve proper methylation patterns. I suspect histamine in our large surface area guts is the component that you are talking about.


Anonymous said...

@ Keith Bell, I'm interested in your comments about niacinamide. Do you have a preferred dose?

@Grace/Dr B-G, re: mercury, if removal of amalgam fillings is not possible, do you see another way forward to detox the body? I've been following many of your protocols and have been including betonite clay for the past 2 weeks. Suggestions?

Thanks so much for all your work!

Kor said...

Dr. B G,

Thank you for being so open about sharing your own stories and struggles with us. I've been struggling with some very similar issues for 10 years, and it's only been within the last few years, thanks to blogs like yours and others across the primal/paleo/functional med community, that I've found other like-minded folks seeking their own answers in a sensible way.

Have been following a primal blueprint for about 4-5 years now, and like you, found that even a wonderful whole foods diet isn't always enough. I decided to seek help from a professional functional med doc., and had some of the Metametrix labs done. Also had a positive SIBO breath test earlier this year. Rifaximin didn't help at all. Have been on long-term Diflucan several times with some success while on the drug, but that is obviously not a long-term solution.

I came across this post through the recent RS frenzy, and after reading through it, decided I'd share my lab results and see if you might have any recommendations. Don't mind sharing further med/treatment history, other lab results if appropriate.

GI Effects.


Thank you for all your contributions to this community.

Dr. B G said...


I wish I could say there's an alternative but seriously USA doesn't allow a speck of lead-dust from lead paint in residential and commercial homes, no? Why do we have mercury amalgams where daily we chew, expose to acid and hot contents, and breathe the mercury vapors and lick the amalgams??

OK with that said I think a health gut can overcome much. Clay is definitely a start. strengthening the foundation of the gut architecture from the groundup includes the 7 steps!


Thank you for taking the time to write and compile the uploads for me. How are you? Tired? Mentally frazzled, fucked and fatigued? BEEN THERE! Living on antifungals is NO LIFE ;)

You didn't mention any anti-parasite regimens. Has this been addressed? How many rounds? Has the adrenal function (low VMA, homo, 5-OHI)? Does your sleep suck in quality and length? Were you supplementing glutamine right before the tests? What is the date on the Triad same as July 2013?

How many amalgam fillings do you have? How many mercury vaccines? Have you had acute mold exposures? Does your home have undiscovered mold, fungi or water leaks/damage??


Kor said...

Dr. B G,
Thank you for your response! Your predictions are dead on :)

I have done a little anti-parasite work on my own, last being a couple months prior to these labs. The only thing I have tried is an herbal syrup produced by the Master Herbalist at Barefoot Herbalist. Can't seem to find his actual store atm... The doc who ordered these tests for me didn't seem interested in addressing parasites.

Also haven't directly addressed adrenals. Would extreme sensitivity to caffeine be related to this? One cup of coffee in the daytime makes me super jittery, then in the evening I can't breathe. Takes days to recover from exercise. Almost always wake up around 2-3 AM and probably every hour or so again after that until time to get up. Extremely light sleeper. What would be a good way to begin addressing this? Have been diagnosed hypothyroid. Couldn't tolerate thyroid hormone - made me irritable. Have been taking Thyadine, which I think has helped a bit but still always low body temp and cold.

Yes I was supplementing L-Glutamine - have made gut health my mission the past couple years. Thought it might help healing leaky gut.

I live in a very old house, and I suspect there's a bit of mold around. I have lived in other locations over the past few years though with continued problems. No Acute exposure. I do have a couple amalgam fillings I should probably have replaced. What is the best substitute filling?

Suddenly developed an allergy to eggs a couple years ago :( gives me a stomachache. Sucks!

I'm thinking of giving Prescript Assist + RS a try. So far I've experienced increased bloating from RS; gas has subsided a bit. A little scared I'm just feeding SIBO.

Thank you Grace!

Dr. B G said...

HEY YOU ~! :)

The parasite(s) haven't been cleared yet so you may want to consider the long term merit of further therapeutics. The MM/GDX info sheet is listed on this blog and their list of recommended botanicals. I don't know what the Barefoot Herbalist uses but typically they're all pretty similar to the ones listed on this blog that my family, clients and I have used -- wormwood, berberine derivatives, herbs. It takes several rounds sometimes to get the little buggers ;) Don't give up and stay patient. Many parasites have cyst/dormant forms and will persist in the system.

This botanical formulation from a paleo supplement company DFH (LUV LUV LUV THEM) which teaches functional medicine is very good. For formulas, I wait 2 wks then repeat the course. I take also 2 capsules of digestive enzymes (NOW platinum or Dr.Venessa's) to assist the killing. The below has anti-fungal properties. Soil based probiotics have anti-fungal scope and spectrum, as well as gut healing benefits.

Adrenal health is tough -- until the gut recovers it is super hard sometimes. Have you read the standard books or Dr. Lam MDs adrenal website? No thyroid dosing will help until the adrenals get a bit more perky. YOURS APPEAR SUPER POOPY!!! I'm so sorry.

--no caffeine
--no chocolate due to stimulatns
--no stimulants
--no stimulating people, activities, exercise, Xfit, metcons, TV shows, ANYTHING
--try to nap, rest, gentle yoga, yin yoga!

What adrenal botanicals have you tried? Gaia is awesome. This is the one my children and I are currently loving up! They both sail thru midterms and finals on it and now getting straight As or A(-)'s!! I'm so grateful for this magnificient combo you have no idea ;). I also take royal maca. In the states, I put my children in Ancient Mineral magnesium baths. Super soothing and calming. Ck it out.

You are so allergic to me it appears -- 8 food groups. You may be like me also allergic to MERCURY on the Clifford testing. The immunity can be so f***KCrd and reacts strongly to everything. You may want to strongly consider with your biologic dentist safe, integrative removal to switch to non-BPA composites. Personally I couldn't recover neither my gut not adrenals until the mercury came out. I dunno why. Wish I could tell u. Everything was fuckered UNTIL they came out. Hope your immune system bounces better than mine!

We've had identical paths my friend. I was on Thyadine too -- it's great for iodine which has tiny antifungal effects. A better gut, adrenals, SBO probiotics/kraut, and mercury removal however has nearly fixed the thyroid. All health needs strong adrenals, including thyroid function. Focus on adrenals must always come first my buddy.


Kor said...

"You are so allergic to me..."

Nooo I'm already allergic to enough wonderful stuff. Don't say I'm allergic to you too! J/K :)

I found a couple biological dentists who said they replace with BPA-free composite fillings. I have contemplated having this done several times in the past, but I think you've compelled me to pursue it.

I'm also going to give SBO and a few rounds of parasite + fungal botanicals a try. Think this one is worth a try? iHerb is fantastic, isn't it?!

I've only tried rhodiola and ashwagandha as adrenal support before. Going to try out the Ethical Nutrients Stress Rescue you mentioned. Will also focus on chilling out and improving sleep.

Do you think regular Epsom Salt baths are helpful for the magnesium?

Would you say any particular flavor of paleo was important during your healing? Lower-carb? Pro-starch, etc? Or just more important to focus on the other things and avoid the foods I tested positive for?

Grace, you truly rock all the day! Your generosity is well appreciated.

Dr. B G said...


UR VERY WELCOME! Glad you're not allergic to me!


Absolutely baths are hydrotherapy and very soothing for some reason. You should look up the studies with hydrotherapy and CFS.

If your dentist is good, they'll advise you to do the Clifford test which will help make sure that you're not allergic to the products that plan to use. It's an imperfect test but better than nothing. This was the test showed that I developed Ig reactions to all mercury amalgam alloys that were tested (yes all 100%). I'd be curious what you're results are.

The NOW product is not bad however it has grain alcohol. If you don't need a liquid form, consider that the grain may not be optimal since it's an alcohol and second it may contain mycotoxins from the fermentation.

I think any diet that complements adrenal protocols are great. Free the Animal/resistant starch, PHD, Primal blueprint are all fantastic because the advise complex carbs at each meal along with fats and proteins. As the gut colonies move around and the populations shift, hopefully the symptoms will mirror improvement. Hopefully displacement occurs from the small intestines back to normal.

Have you considered clays and charcoal? These helped me considerably to sop up those weird aldehydes, alcohols and toxins. These alone are super curative sometimes. have you read the genius Keith Bell's thoughts on fungi? He posted some goodies here:

Curious factoid --did you know that the fungal species Geotrichum candidum found on the GDX is also found on the top layer of a Finnish viili yogurt?

Thank you for curiousity and sharing your journey.

Dr. B G said...


Don't know if you were reading the convo with the other person 'Mike' about parasites like giardia.

Pathophysiology and Management

The fun thing about parasites is that they can be asymptomatic or cycle between (evading the immune system) bad/good times. Read the article -- it also explains how conventional testing are BIG FAILS. The integrative medicine testing you did with PCR DNA amplification is the progressive, advanced (and only) way to go for accurate and reliable ID of protozoa, helminths, worms and other parasites.

I love this article because basically it explains the pathophysiology between ALL SIBO and SIFO -- how the microcritters that turn aggressive (aka pathobiont) invade and deliberately suck the life out of us.


Once excystation occurs, Giardia trophozoites
use their flagella to “swim” to the microvillus-
covered surface of the duodenum and jejunum,
where they attach to enterocytes using a special
disk located on their ventral surface.13 In addition,
lectins on the surface of Giardia bind to sugars on
the surface of enterocytes.14 The attachment process
damages microvilli, which interferes with
nutrient absorption. Rapid multiplication of trophozoites
eventually creates a physical barrier
between the enterocytes and the intestinal lumen,
further interfering with nutrient absorption.13 This
process leads to enterocyte damage, villus atrophy,
crypt hyperplasia,15 intestinal
hyperpermeability,16,17 and brush border damage
that causes a reduction in disaccharidase enzyme
secretion.18 Recent research also demonstrates the
presence of cytopathic substances, such as glycoproteins,
19 proteinases,20 and lectins12 that may
cause direct damage to the intestinal mucosa. Trophozoites
do not usually penetrate the epithelium,
invade surrounding tissues, or enter the bloodstream.
Thus, infection is generally contained
within the intestinal lumen.13

Giardia trophozoites scavenge nutrients in
the intestinal lumen for sustenance and growth.
Glucose appears to be the primary energy source,
with other sugars appearing not to be utilized. The
amino acids alanine, arginine, and aspartate are
readily used by Giardia trophozoites for energy
production. It appears Giardia lacks the ability to
synthesize most amino acids and is thus dependent
on scavenging them from the intestinal milieu.
Animal models suggest Giardia is unable
to survive in the small bowel in the absence of
bile acids. Uptake of bile acids by Giardia may
explain the fat malabsorption often seen in giardiasis
patients.6 Chronic giardiasis also results in
malabsorption of lactose, vitamin B12, and fatsoluble
vitamins, which can result in weight loss,
nutritional deficiencies, and failure to thrive in
children.12 Exposure to bile is the primary stimulus
for encystation, where trophozoites transform
into cysts that pass out with the feces.7

Kor said...

Dr. BG,

Just wanted to say thanks so much for thinking about me and posting this. I've been super busy with work recently and haven't had much time to read the recent posts and comments. I will definitely look through all this carefully.

Quick updates though- my iHerb shipment got lost in transit! So they're reshipping it today... so haven't been able to start the adrenal support or parasite herbs :( First appointment for amalgam removal next week! I had to poke around a bit to find someone who used the rubber dam during removal and BPA-free composites.

I had a question (probably a pretty dumb one!) I wanted to get your thoughts on related to this. I've heard of people claiming they re-mineralized their dental cavities by supplementing K2. Is it completely ridiculous to think someone could just get amalgams removed and not refill with the composite? Just begging for infection?


Dr. B G said...


BUMMER Xmas postal traffic, eh??

My daughter has a cavity that we are just watching. It hasn't worsened but then it didn't reverse in the last one year (since our USA appts). Now we are hardcore doing fermented cod liver oil + butter oil most days. I think whether they re-mineralize or not highly depends on dysbiosis and whether the minerals and nutrients (like K2) are available and plentiful enough. I have hope!

Now if you are talking about a tooth that has been artifically drilled on, then I am told that they don't just remineralize. Who knows? The surface is quite damaged and is a magnet for adhesions (where as enamel is not, right?)... so if it were me, I would not take any chances of decay. Did you ask your biologic dentist? I wonder what they would answer?

Ellen said...

Sorry- I'm chiming in here late- and this is my first post. Am reading so much valuable information here and I keep clicking on links that take me further and further deeper and deeper. Anyway- Dr. BG for adrenal support-- have you heard of stresscare? and if so- do you think it's any good?

Dr. B G said...

Hi Ellen,

Actually I've used Himalaya and love them. Please let me know how it works. Different botanicals sometimes work differently for each unique person. Also it depends where on the adrenal healing curve you are -- some have high cortisol only at night, others during the day or completely flat-lined. The botanicals help normalize all the curves in addition to yoga, exercise, laughter, etc. Good luck!

Ellen said...

Thanks for your response Dr. BG. I have been using this particular product for a few months-- the Stresscare and I LOVE IT. My cortisol tends to be higher at night so that's when I take 2 of them and it makes me sleepy so I can nod off and it knocks me out-- all night. And during the day, if I start feeling a little "stressy" I'll pop one and it's very calming. Honestly- I've never felt a product work like this before. That's why I thought I'd ask because it feels a little too good to be true? KWIM? I was concerned that one of these herbs might be hard on the liver.

Scott C said...

Hi Dr. B G

Thanks for all the work you've done. I've been taking RS and SBO (AOR Probiotic-3) and my digestive issues have been improving (though up and down). I'm hoping to add in the psyllium and ORAC green superfood soon.

You mentioned in a comment that gut health may be related to male pattern baldness. My hair started thinning in the summer, and looking back on it this was around the same time I started having digestive issues, heart burn, as well as anxiety. Now that I've started with the probiotics, I've noticed my hair looks thicker (though this could be entirely in my mind). Has there been any research done on this?

Also, is there any benefit to taking non-SBO probiotics along with the SBO?


Ross said...

Hi Dr. BG,

This is my first time posting on your blog - I found myself here via Free the Animal and Cooling Inflammation.

I've been blown away by the quality of the content in this realm of the blogosphere, and I feel very lucky to have stumbled across it. From reading your comments beneath the articles, it's very evident that you're an extremely bright, switched-on, and humorous person who is also giving of her time seen as this blog appears to be completely non-profit. The world needs more people like you, Grace, so thank you for showing up!

Now that I've buttered you up (kissed your arse?!), I have a few questions to ask! Haha!

If gut issues are evident (either through felt-experience or confirmed via testing), is it prudent to firstly start weeding before moving on to resistant starch, plantain flour/psyllium and SBOs? I ask because I have tried potato starch (2tsp) and FOS (1tsp) with SBOs (Prescript Assist), and I feel pretty awful after a week or so of doing it. My "insides" feel bloated and out of whack, and my stools have pretty much turned to mush - not the effect I was looking for.

Now I had a MetaMatrix stool analysis done around a year and a half ago, and I also had an Organix Acid Test late last year, too. The stool test showed no yeast or bacterial growth, and the Organix Acid test showed no markers for SIBO or SIFO. Despite this, however, I still believe that I have a level of gut dysbiosis, evidenced by my lived experience. I feel horribly boated and lethargic if I eat anything with a lot of sugar in it, and I can also "feel" a die-off reaction if I take anything anti-microbial/bacterial/fungal. For example, I tried a 9g course of lufenuron for candida last year, and I had the biggest die-off reaction ever. This to me is evidence enough that dysbiosis is present, even if it is not evident on the tests.

I'm therefore hesitant to push on with the RS, FOS and SBOs in case I am inadvertently bolstering the enemy I'm trying to eradicate (or rather bring into balance). Some of Tim's posts seem to have this push-through-it mentality attached to them, yet I've noticed you are much more observant to the weeding aspect of gut issues. My personal experience aligns with your cautionary notes, and I'd be much more inclined at this stage to focus firstly on dealing with the dysbiosis, before then moving onto the pre-biotics and SBOs.

On this point, Grace, have you ever used either of these:

The latter appears to be the go-to product for dealing with dysbiosis for a lot of Functional Medicine Practitioners.

Once I get my gut into a better balance, I'll feel more confident about going ahead with the pre-biotics and SBOs. My aim is to get my tregs up to ensure that my body has a controlled suppression of inappropriate antibodies. And according to Dr. Art, the best way to do this is to take a probiotic containing Clostridium!

There's light at the end of the tunnel!

Thank you once again for all your much-needed writings in this area.

Dr. B G said...

Hi Ross,

Thank you for your kind and wonderful comments. For me, taking potato starch is the litmus for gut problems.

A ton of people don't notice any health improvements despite taking for weeks and months. Results should happen in 3-5 days. Their microbiota are likely deficient. This is a form of SIBO/SIFO. Lacking commensal organisms sets up the small intestines. They are usually invaded but asymptomatic, generally speaking. In depth talking will obviously reveal however a myriad of health issues that are ALL gut-related.

Others (like you may) experience exacerbations of their health. They have severe SIBO/SIFO.

Silver and biocidin are all great and may or may not weed sufficiently. For me, removing mercury triggered improvements in immunity (Tregs), gut and brain. The change was immediate within minutes and hours. Candida is difficult to get rid of if mercury is at the core, I'm sorry.

Finally, probiotics can be gradually added to improve candida yet hopefully not flare it or cause excessively uncomfortable die-off or other reactions. I've heard of lufenuron but no experience with it.

I'm surprised the initial GI FX stool test didn't show candida? That is odd. If the commensals were 'high' green then those species could be also causing problems by overgrowing in the small intestines.

Ross said...

Hi Grace,

Thank you most sincerely for your reply - please take me at my word when I say how much I appreciate it.

If taking potato starch is the litmus test, then I have most certainly confirmed a gut issue that failed to register on either the GI FX stool test or the Organix Acids test. As I stated previously, taking PS with FOS and SBOs had a negative effect on my gut health, evidenced by
bloating, brain fog, lose stools and exacerbation of auto-immune like symptoms. This has been demoralising, as I feel like I've been dealing with an underlying gut issue for an eternity now, and the postive RS stance on Free the Animal had given me some renewed hope. The advocation to "feed the
good guys in order to overcome the bad guys" was appealing to me and made sense on many levels, yet in reality I think I've simply been feeding the viper-filled cages that you alluded to in previous posts.

As such, I feel that I now need to focus heavily on weeding my gut and also on discovering whether or not mercury is a problem for me. For example, I had several mercury fillings in my mouth between the ages of 21 and 26, before having them removed by a mercury-free dentist in 2008. Although the dentist used a rubber-damn etc,I was simply sent away with a one-month course of chlorella to take in order to "mop-up" any mercury that had entered my body - I now know that this was highly inadequate. Can I ask, Grace, how
you would approach a mercury issue? Are you aware of Dr. Chris Shade and his mercury detox protocol?

As for taking probotics whilst also weeding the gut, I think that a candida-focused product called Syntol might be worth a shot.
As well as having enzymes which are purported to breakdown the candida cell wall, it also contains b.subtilis at a level of
1 billion CFUs per capsules (I checked this with the Andrew Arthur Medical, the company who makes it). I may also consider taking the AOR Probiotic-3 product alongside this for the clostridium bacteria that seems to be so important to immunity.

Finally, related to this last point, can I ask if you think it is beneficial to take substances that are said to stimulate innate immunity such as
yeast or mushroom derived beta-glucans?

Thank you once again for your time.


Spencer said...

Is there anyway I could email you my GI effects results? I know you're probably being hit up and down by people. I posted on FTA a couple weeks ago about floating stools. I just have a few questions.

Justin said...

Dr BG -
Love your blog and the work you are doing with RN. I shared my GI test and would appreciate your thoughts. I started PS after taking this particular test and it has really helped my GI symptoms.

The post previous to the test results has a brief RS testimonial after 30 days of testing.


ballabolla said...

I am inspired by your n=1!!
The stool test is not available here so I am faced with a dillema. Shall I first do a larger test of my stool or a general DNA test via 23&me?
I have MS, SIBO and a dysbiosis. I am currently working on my gut with prescript assist, P3, bionic RS and a ketotic diet: I am approaching keto-adaptation and feel good. With the ketogenic diet I combine the AIP and Wahls paleo plus protocol.
So, what do you think I can do best?
Thanks in advance!

Dr. B G said...

Hey anon,

Thx for your testing. I'm behind so it's prolly good u posted here.

Briefly my thoughts
--how do you feel now?
--better tolerance of 'food'??
--are you avoiding RS2, fodmaps, starch and other things you don't tolerate??
--do you have IBS symptoms like diarrhea and/or constipation?? heartburn/GERD??
--what skin v muscle symptoms and signs do u have?

That's wonderful that you are considering reducing the fungal component of the gut

The overgrowths of bacteria are likely in the small intestines which affect nutrient absorption and sadly immunity. Are you tired? Energetic? pooped by 2pm??!

What parts of bionic fiber, my 7 steps and probiotics are you finding work for you or make you feel more f*ked?


Anonymous said...

Grace, thanks for your reply.

--how do you feel now?
*My main issues are arthritis, skin dermatitis, diarrhea/constipation and waking early.

--are you avoiding RS2, fodmaps, starch and other things you don't tolerate??

*I am just now starting to experiment with the SCD diet. I avoid gluten, dairy & nuts. Also, Eggs, coffee & Natren's Holy Trinity make my upper left abdomen feel like it is full of gas.

--do you have IBS symptoms like diarrhea and/or constipation?? heartburn/GERD??

*I typically have diarrhea or constipation. I also burp quite a bit.

--Are you tired? Energetic? pooped by 2pm??!

*I tend to do well on energy. I do have anxiety that drains my energy some days.

--What parts of bionic fiber, my 7 steps and probiotics are you finding work for you or make you feel more f*ked?

*Probiotics have helped my stools some. After first learning of resistant starch, I tried potato starch & SBOs for 2 weeks and had worsening of symptoms. Assuming that I had SIBO, I tried oregano, allicin and berberine for a month but I didn't notice any difference in symptoms. I have a breath test scheduled for this next week & currently taking Candibactin-BR. I also started walking 10,000 steps a day.

I would love to see what your thoughts are! Thanks Grace!

Dr. B G said...


Jump to 13:00 of Dr Marshall's talk about IBS and the gut profile. It's u

So it's high on everything except
--good bacteroides
--good everything else! like E coli

Of course it misses all the fungi and the gut profile you showed had not a small quantity 2+ saccharomyces. Read this many will help

IBS is 100% fungi and sibo/sifo (both bacterial and fungal overgrowths in the small intestines)

No high dose RS, starch, fodmaps for 2-4wks is often the best and helps seal and heal the gut. Try to increase mucus with the link below

During the 'weeding', bionic fiber version B with inulin is the best for antifungal strategies because it selects the species that are better at pathogen evictions.

Please let me know how it goes

Anonymous said...


I took your advice and I am avoiding starch, RS and fodmaps. However, this only leaves me with fruit for carbs. Is there anything wrong with eating a ton of grapes for calories???


Jose said...


I have a question about the titanium implants that you removed. Where were the titanium implants made? I noticed that you said they were amalgams...I think this may imply that they were not pure titanium? Any details would be greatly appreciated.

Also, how did you replace the titanium implants? That is, did you use zirconian? Or something else? How are the replacements working out?

Thank you,


Dr. B G said...


Are you dealing w implants? There are ceramic ones that are purported to be less antigenic. No mine were pure 100% ducked titanium and many testing won't show the allergenicity. When I did the Clifford, nothing for titanium products showed up.

For me I had to remove all mercury amalgams and do chelation to correct the immuno reactivity. Took 12-18 months. Good luck.

ben said...

Hello Grace. I was wondering if you could help me analyze my stool results. At 32 years of age, I have had chronic fatigue going on 4 years now. I also tend to have some GI issues, such as constipation and bloating after eating fruit. My adrenals and thyroid are off a bit and have been working to fix.

I had a question I was hoping you could help me answer.

Prior to this test, I spent 6 months eating tons of resistant starch in the form of heated and cooled potatoes, rice, and beans. I also ate fermented foods every day with every meal (did give slight bloating sometimes) as well as Potato Starch 2-4 TBS each day along with the other bionic fibers. I also used 6 or 7 probiotics, including the ones you recommend like Natren, Prescript Assist, VSL3, etc.

On my stool test, my Lactobacillus, Bifidobacter, and E. Coli all came back really low and in the first quadrant. If I was eating all that resistant starch and fermented foods and taking all those probiotics, why are all of my Facultative Anaerobes so low and basically nonexistent? Does this point to SIBO?

If you could briefly explain I would appreciate it so much! Thank you Grace you rock!

Dr. B G said...


Thx for your sweet and intense comment!


Sorry for the frustration. There sounds like digestive issues (because that can be at the heart of the viper damage in the small intestines).

ben said...

thanks grace!

my stool test showed no yeast (actually had a 0-I know this can be a bad sign), parasites, or anything at all detected.

So how do I figure out what is causing this? Is there another type of test to try? I'm not sure what other test might be good to try to get to the bottom of this.

Any recommendations as far as diet go? Right now I'm just doing a low FODMAP but I know that's just a plug and not a realistic long-term fix.

Thanks again!

kwi said...

I removed two root canals, the problems persisted. Just one cleared (earing lost). Still have 3 screws inside me (titanium i guess from 2 surgeries) and some plastic material(from another surgery). Some issues come prior to the surgerys, (birth?)
I have ropeworms, ascaris/tapes probably, giardia, hpylori, candida, white tomgue imfections and immune system ....ocd

Anonymous said...

Hi Grace, I've been trying to contact you since you moved back to USA. We skyped for a consult in when you were in China. I'm the one who wrote the very long health history. Please email me when you get the chance to do another appointment. My email (edited) went as follows:
Hi Grace,
I'm so very sorry for the very very late response. You had emailed me asking how my progress has been since doing your protocol after our skype session.
I introduced all the extra things you recommended (inulin, arabinogalactan, stress guard etc). I have the following to report:

You have changed my life! By following your recommendations, you have achieved what NO OTHER PRACTITIONER HAS ACHIEVED IN 21 YEARS with me.

As you may remember I have had an incredibly long poor health history and seen many of the "best" practitioners and spend 25+ thousand dollars over the years in the process. It took about 6-8 weeks of the 3-4 tablespoons of potato starch, banana flour, inulin, and arabinogalactan in my water kefir drink for the results to really take off.

As you may remember I had been doing almost all of your protocol (as recommended on your blog) and had seen amazing improvement in my digestion and regularity, and the reversal of Hashimoto's antibodies.

The extra things I have noticed:
I can tolerate nuts - they don't block me up and I don't get cysts from them
I can eat lentils and dahl - they don't block me up
I can eat meat - it doesn't block me up
I can eat rice- it doesn't block me up.
I have had no new cysts or acne in months. My skin looks awesome and people say I look 30 (I'm 40).
I am averaging 2 BM per day
Even if I forget to have my probiotics and shake or digestive enzymes - I STILL go the next day. Any one of the affore mentioned foods would have had me blocked up for 4 days or so. (I never used to forget or skip anything cos I was paranoid about it causing more cysts or constipation)
Even if I have a heavy meal or meat, I STILL go the next day (maybe only once, but then the next day back to 2-3 times). I've had to eat out on the odd occasion - so I've had a gluten free Thai curry with coconut rice.

I haven't had my day 19-21 hormone tests done yet. My life has been cra-zeee the past few months. Even with all the stress though, my gut has remained on track.

I'm back at the gym now and my body seems to be handling it very well.

Hope your book is coming along well. Did the boys (Richard and Tim) finish their book and did they finally decide on a name for it?

Many thanks,

P.S. Would like to book another online appointment in the next month or so too.
I haven't yet, but would soon like to try a bit of dairy. Some occasional yogurt or milk kefir would be awesome.

Dr. B G said...


I just sent you an email. I'm so glad to hear you are doing so well! Congratulations on all of your progress and look forward to hearing more soon.

Anonymous said...

I just had a thought. I wonder what gut health looks like for those populations that regularly consume human milk into later childhood, and even adulthood, like in some parts of Mongolia.

Not sure if there is any data around but it would be interesting huh? Anyway, I was just curious, and thought you might be too

Dr. B G said...


In Mongolia they breastfeed until 9 yo? That is crazy lol! My 2nd did until 3.5yr. How about you?

For HG, I've read the lactation lifestyle also decreases fertility and spaces out birthing longer. Might be an advantage if mom needs to replenish vitamin and nutrient stores.

The mares' milk that they drink and make fermented wine and yogurt is supposed to be quite healthful. I find it fascinating all the cultures that were so ingenius to ferment diary from their local livestock: yaks, horses, camels, etc.


Anonymous said...


My little guy is nearly 3 and we are nearing weaning.

This stuff is incredible.

The boob juice story is only beginning. I believe (just like cognitive function in the first 3 years) this is the tip of the iceberg for BM and it's biological appropriateness.

:) Jess

Dana said...

Hi Dr. BG,

Just stumbled upon your website.

I noticed at the end of your article you stated to send our GI test results to you.

I would like to know if you can go over my test results. I received the test results but my doctor will not go over them with me (I can't go in to his office because my health insurance is not great)I would love to know what the results mean as Ive been suffering with stomach issues all my life.

Can you please let me know where I can send you my results?

Thank you so much!

Dr. B G said...


clikc on my name to contact.

Unknown said...

Hi, I've been listening to your podcast, and I'm really learning a lot. I recently had the GI Effects profile done as well as the NutrEval profile. I tested positive for Klebsiella pneumoniae and Proteus mirabilis, and showed low levels of bacterial diversity. I had been eating Paleo and doing well, and then I had to take antibiotics for bronchitis last March (last resort), and the GI problems started right after that. My functional medicine practitioner has me on berberine and uva ursi for the overgrowths, but hasn't been much help with diet and re-seeding the good bacteria, other than telling me to take Klaire Ther-biotic. I've not been tested for SIBO, so I don't know if these overgrowths are in the small or large intestine. I've lost a lot of weight battling this, which is a worry. I'm not sure what to eat or what supplements to take. I would love to send my results to you to get your take on what I should do.

Dr. B G said...


Feel free to contact me. It is certainly tough in many circumstances if the whole ecosystem is not addressed and able to shift. I like newer tools we have to catch toxin burdens, look at potential pathogens (yeasts, clostridia) and organic acids.

Good luck!

Unknown said...

Hi! I came across your blog and podcast today. What great information. I'm finishing up a treatment of abx for SIBO. I'd like to get your recommendations for repopulation with probiotics. I have BIOKULT and SaccB. Wondering if you could recommend others? Thanks so much!

Dr. B G said...

Elizabeth May

Thx for your wonderful comment. Please see step #3 -- it lists all the probiotics I love you can easily order. What your on is great but consider broadening the spectrum of flora. Also don't underestimate visiting organic gardens and farms for their flora! 'FARMacy'!