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Two Case Studies -- Diarrhea-IBS and Constipation-IBS and GI Fx Stool Test: Overgrowth of Pathobiont Klebsiella, Fungi Rhodotoru

Posted Jan 23 2014 1:40am
Here is a functional medicine case -- 5 year old austic boy with constipation-IBS  (credit: GDX Diagnostics)

Klebsiella oxytoca + Fungal Rhodotorula
Small Intestine Overgrowth
Credit: GDX Diagnostics

Buttloads of Butyrate flooding the whole body
Due to SIBO/SIFO


Per GDX/Metametrix
  • Here we find an even more severe overgrowth of K. oxytoca. Note that the assay is able to keep on  counting target genomes over many orders of magnitude. Here the oxytoca is present at 1.48 x 109 /gm, and  this child also shows concurrent extremely high levels of Rhodotorula sp. Incidence of Rhodotorula in our results is higher that from culture techniques, probably because it is identified microscopically, but grows poorly in usual culture media. 
  • Plenty of metabolic activity is shown by the abundant SCFA and balanced percentages. Note the normal level of Lactoferrin, showing lack of inflammatory involvement currently in this patient with very active IBS due to profound microbial overgrowth. The immune barrier is weakened as shown by low sIgA. 
  • Antibacterials and antifungals according to sensitivities. Immune support with glutamine (consider colostrums) and glutathione. Investigate food intolerances to lower the loading of GALT 



My assessment from the data on the GI FX stool test
  1. Overgrowth of pathobiont Klebsiella oxytoca (likely including small intestinal location)
  2. Fungal overgrowth of Rhodotorula
  3. Low commensal Clostridia (should be MUCH MUCH higher)
  4. Low fecal sIgA (immunocompromised)
  5. SUPER HIGH BUTYRATE and other SCFAs (because a SUPER BOWL FERMENTATION PARTY is going on in the small intestines and possibly colon due to inappropriate bacterial overgrowths)
  6. Poor mood, poor sleep, possible anxiety secondary to dysbiosis-related failure of tryptophan to be synthesized to serotonin and serotonin to melatonin. 80-95% of serotonin are produced in the gut.  Dysbiosis affects gut conversion of tyrosine to dopamine.


C-IBS needs tons of weeding weeding weeding......................................

And replenishment and repopulation of SBO commensals/fermented foods, basically the 7-Steps to cure intestinal permeability and SIBO/SIFO , small intestine bacterial and fungal overgrowth.

How does this occur? After a round of gastroenteritis or antibiotics, the commensal organisms and fungi that safeguard our gut domain are reduced in number. The pathogenic strains emerge without these.  Soon yeasts, fungi and aggressive bacterial take root in places that are normally kept clear. The small intestines are a frail target -- only one cell layer thick.  Full of moisture, oxygen, intermittently constant food, and a rich blood supply.  Once fungi or bacterial take hold, food can no longer be digested well.  The GI barrier becomes broken down.

For the host, bloating or brain fog are frequent symptoms.


Here are my thoughts on the spectrum of hyper-permeability/leaky gut/SIBO/SIFO symptoms
(a) Mildly Intolerant (gas, bloating, constipation, diarrhea, heartburn, ulcers, mental fog, cavities, enamel defects, nutritional deficiencies, anemia, vitamin B12 deficiency, hair loss, low thyroid, food cravings)

(b) Moderate (depression, anxious, allergies, ADHD, autism/spectrum, cardiovascular disease, Type 2 diabetes, osteoporosis, bone fractures, PCOS, fibroids, miscarriages, nerve pain, seizures, joint arthritis)

(c) Severe (failure to thrive, weight loss, weight gain, rashes, mood swings, infertility, migraines, bloody stools, bipolar, psychiatric disorders, alcoholism, cancer, autoimmune diseases, T1DM, celiac, rheumatoid arthritis).



In autism and other spectrum conditions, the gut-brain axis is broken.  In many cases, autism is reversed once the gut is fixed and no longer spilling out undigested food particles (gluten, casein) which resemble body proteins and other proteins of microbial origins.  In this case, like many spectrum cases, both bacterial and fungal overgrowths are present and the absent of commensals such as Clostridia. The problem in this C-IBS (constipation dominant IBS) case is not insufficient butyrate, but actually food fermenting excessively in the small intestines by 'regular/good' bacteria in the inappropriate place. Once a commensal grows aggressively, it can switch to a pathobiont status, exploring and invading an ecological niche.

One of the benefits of the 7-Steps to cure SIBO/SIFO that it is aligned to our ancestral heritage and tight association with the soil and abundant earth.  The earth not only feeds us with crops and herds but is the 'horticulture' that also provide wonderful organisms that serve to maintain the 'lawn of our gut' by weeding, weeding and weeding [hat tip: Brent Pottenger and here is his stellar gut GDX GI FX testing ].


The benefits of SBOs (soil based organisms) are--they are the key apex predators that control the growth of smaller critters and predators in the gut ecosystem
--weed out and decrease populations of pathogens
--secrete antifungals
--secrete antimicrobials
--tighten up loose intestinal junctions in hyper-permeability
--eat fiber (soluble, insolube fiber and resistant starches)
--provide food and gases for bottom feeders
--ferment fiber into butyrate which is an antimicrobial
--make butyrate which is a potent agonist for GPR41 receptors which immunomodulate and control inflammation
--improve immunity which improve food intolerances, asthma/allergies and (for me) gluten and dairy allergies
--associated with reversed autoimmune diseases ( prior animal pharm )




Case Study (Credit: FTA ):

Alex W.  // 
I’d like to add a success story here. Last August, just a week after starting graduate school, I came down with an intense bout of IBS-D (to keep it clean). Not unusual, as I’ve had the flu before. But this ‘flu’ did not stop, and stranger things began to happen. I developed tinnitus, neuropathy, dizziness, fatigue, muscle twitches and my sleep was terrible. 6 weeks later, I had lost 25 pounds (that I didn’t need to lose) and I was barely able to get out of bed. A colonoscopy, endoscopy, stool examination, countless blood tests and specialists later and still no answers. I took a medical leave from my program, and had to return to my home in California because I was no longer able to take care of myself.
It was around this time that I began experimenting with SCD and GAPS style diets. They did prove to help with some symptoms, but not all, and not with much speed. In fact, I would say that I got worse on these diets, as my sleep became a struggle, and that set everything back. Supplements like Vitamin C, Colostrum and DGL helped but were definitely not the answer, either. It was late December, and I had to make the call whether or not I was going back to school. I decided to go back out of desperation for wanting to be better, without really having made any progress. Not a wise decision, but I got lucky.
It was just two weeks ago, just at the start of the semester, that I began to follow the advice of Dr. BG over at Animal Pharm blog on correcting SIBO, as well as the advice here about resistant starch. I am so, so glad to say that I am 90% back to normal. My tinnitus is almost gone, my muscle twitching is nearly gone, my sleep is incredibly better. I can finally go back to teaching and researching without fears of passing out in the middle of class. The two biggest factors in my success was the inclusion of properly prepared starches (in Perfect Health Diet amounts) and supplementing with potato starch and psyllium husk twice a day.
I can’t speak for all the other successes and failures when it comes to variable carb intakes, potato starch supplementation and general paleo-style eating, but it worked for me. So thank you Tim, Rich, Grace and everyone else who’s been posting about this stuff. I’m not shitting you (har har) when I say that you saved my young life.



Have you had success with the 7-Steps?
What are the challenges?
Are you seeing improvements and optimization of gut/brain/muscle/genitalia?

I can't wait to hear your stories...

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