Crowd-Sourced Science n=4

Allan Folz's Gut Microbiome Study, n=4

Indiegogo

I *heart* science and I love places like indiegogo which encourage all kinds of experimentation and projects whether it's techno or food-related.  It's truly a brilliant evolution.

Allan Folz and his family of 4 are doing a gut microbiota study: Resistant Starch & Gut Biome Family Science Project for six weeks, testing pre- and post-microbiome.  Allan cultures his own viili heirloom yogurt, a type of Swedish or Finnish yogurt. As we know yogurt that has live probiotics has many health benefits for us. One study in rodents showed that yogurt with live cultures improved 'rodent swagger', leaner body mass, and testicular size in males and improved fertility (brood size) and nesting instincts (successful weaning) in female rodents. "Mice That Eat Yogurt Have Larger Testicles", Scientific American, 2012.


Besides contributing to the first RS n=4 study with pre- and post-microbiome 16S rRNA pyrrosequencing outcomes,  first-tier funding ($250) for this crowd-sourced experimentation includes a personal tour of Oregon Wine Country in Yamhill County and a hand written thank you.


Allan's goal:
(1) The goal of this project is to measure and compare the effects of resistant starch dose-responses on gut biome in as reasonably controlled a manner as possible by selecting an otherwise typical and healthy family that lives and eats together.
(2) A secondary goal of this project is to provide a proof-of-concept and, perhaps, a template for future crowd-sourced, small-scale diet and health experiments.




Study Design:

Purchased two "Microbes for Four" swab kits from the American Biome Project.

Provided a stool swab -- 2 children, 2 adults

Over the course of a 6 week study period food journal will be maintained for each participant and provide a daily diet supplement of resistant starch in the form of Bob's Red Mill Unmodified Potato Starch. Each participant will follow a unique supplementation regimen:

a) adult 1 - 2 TBSP PS mixed in water, consumed on an empty stomach

b) adult 2 - 4 TBSP PS mixed in water, consumed on an empty stomach

c) child 1 - 1 TBSP PS  plus 1 TSP whole psyllium husk mixed into yogurt

d) child 2 - 1 TBSP PS mixed into yogurt

At the conclusion of the study period the four test subjects will provide a second stool swab for comparison purposes. The lab results from both swabs will be shared publicly on the internet.

Allan: Our current diet is almost entirely home-cooked meals somewhere between primal/paleo-ish and WAPF. None of us has supplemented with potato starch previously. We do eat, a few times a week up to almost daily, an heirloom strain of viili yogurt that I culture myself. More details, including a fairly typical week of meals for us are recorded at the project blog.



Microbiome 16S rRNA pyrrosequencing Testing: PRE v. POST

Additional testing depends on several factors: funding, information garnered and availability.  AmGut is wonderful and provides the bacterial and Archae enteroprofiling. On the other hand, functional medicine laboratory testing provides valuable information about the other gut ecosystem including profiling for fungi, parasites, worms and pathogenic overgrowths, as well digestive enzyme capacities and pH.

Disclaimer: I am working for Allan!



Sample food diary  (follow up HERE)

Food Journal: Thurs, Dec 12
Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - ditto
Adult 1 - coffee & half-n-half
Adult 2 - coffee & half-n-half

Lunch:
Child 1 - don't know
Child 2 - don't know
Adult 1 - yogurt w/ granola; 2 egg omelet w/ deli ham; 1 corn tortilla
Adult 2 - ditto

Dinner:
All - roasted pork loin; brown rice, cabbage, onion, etc; sliced up fresh pineapple on the side

Evening snack:
1 c Milk & 6 squares (~0.7oz) 85% dk chocolate

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #7 Heal hormones and immunity -- take adrenal support, liver support, antioxidants etc

Source: Miller, 1999

HOW TO CURE SIBO/SIFO, Small Intestinal Bacterial/Fungal Overgrowth (protocol):

Step #7 Heal hormones and immunity

Take adrenal support, liver support, antioxidants etc 

(I use biocurcumin and berberine to combine with anti-microbials/anti-parasitics). This is particularly imperative for those with reactive hypoglycemia and BG crashes when they go longer than 3-4 hours between meals.

Proposed Causes of Dysbiosis of the Microbiota
Round, Mazmanian 2009
Source: PDF

Gut Feelings?

This is the final step in our 7-Step SIBO series!  Thank you for joining Tim Steele (aka tatertot) and I on this fantastic discussion and opening conversations about our wonderous and fascinating GUT AND OUR MICROCRITTERS!

Has everyone seen Tim's GUTS OF STEELE and assayed via 16S PCR amplification at the American Gut Project???

• Resistant Starch: American Gut Project Real Results And Comparison (Very Big News) -- Free the Animal Post

By now, I hope you have an appreciation for the impact and difference one single organ as simple as the gut can affect our overall health, longevity, digestion and day-to-day brain function.  More importantly, we dream that you feel more confident in identifying, addressing and fixing some of these intestinal issues.

I believe it is truly challenging to deal with all the modern factors that are the proposed causes of dysbiosis of the microbiota (see above)
-- low-grade gut infections (microbial overgrowths, parasites, etc)
-- unbalanced health and immune systems (lack of commensals -- Bifido, SFB, and soil based organisms)
-- our unique genetic vulnerabilities (e.g. HLA DQ2.5 for celiac; HLA B27 for alkylosing spondylitis)
-- lifestyle (lack of dirt exposures, stress, diet, sedentary atrophy, lack of sleep, livestock/dairy grade antibiotics, disjointed relationship with soil and farming)
-- early colonization of pathobionts (birth in hospitals, lack of breastfeeding, compromised maternal biota sources, toxic formula)
-- medical and dental practices (mercury amalgams, vaccines, antibiotics, hyperhygiene)

NO WONDER WE GET GI-F*KCRD
SO QUICKLY SO EASILY

Estimated Surface Area
of the
Small Intestines

Main Problem with the Small Intestines: GINORMOUS SURFACE AREA

Our small intestines are like head size -- very variable in size!  As we grow, our small intestines grow as we age just like our height or head size. Much is perhaps determined by nutrition by mom and factors after birth.  Our small intestines vary from 5 to 10 meters (average 6-7 m) -- 3-6 times our height.  Indeed by surface area, our small intestines trump even our skin for being the largest organ.

In comparison, the large intestines is only a fraction of the length of the small intestines at  ~1.5 m.

Unfortunately I believe this predisposes us mammals to inherent problems as we frequently encounter digestive disruptors such as all the ones listed above.  These factors in our post-modern industrial neolithic age bombard us from pre-birth, birth and upwards.

I'm grateful that we have simple strategies and technology to address all of the gut disruptors -- fermented foods, whole grains/tubers/legumes, RS, potato starch prebiotics, soil based probiotics, diet, yoga, functional medicine lab testing GDX 2200 stool, ONE organic acids, Am Gut, uBIOME, etc.

Small Intestines: 5-10 meters (~15- 30 feet)
Large Intestine: 1.5 meter (~5 feet)
Source: NYU EDU SIBO

Stressors, Coz We R Not Zebras

Mental stress directly impacts our gut function.  The vagal nerve (see below) innervates our organs including the gut from head to tail.  This nerve controls calm, cool, rest, repose and digestion.  Look how the connections go between our brain to our gut, neat?  80% of our serotonin, the happy transmitter, are generated here.  Melatonin, our sleep hormone, is then produced from serotonin. What is the first sign of stress?  Insomnia, no wonder.

Who doesn't have stress? Widespread cortisol dysregulation is documented in teenagers (Dr. Briffa).

Vagal Nerve Innervations: Head to Tail (Butt)
Source: Medscape

Gut Brain Adrenal Axis

What are the variety of stressors the human body experience?

Gut
 --Sources of stress: gluten, pathogenic organisms, viruses, yeasts, dysbiosis, not enough gastric acid, lack of commensals, refined not-whole-foods, GMO food

Adrenal Glands
--Sources of stress: mental, physical, traumatic, intrauterine

Brain
--Sources of stress: perceived, mental, fear, lack of trust, heightened super senses (hear, smell, touch, feel, taste, sense), future fears, past fears



Effects of Stress Breaks the Gut

Stress (cortisol) breaks open our gut, makes the TJs (tight junctions) leaky, and abruptly even changes our gut flora to more pathogenic populations while reducing the numbers of the good flora like Bifido.  Read more about the gut-breaking effects on the Gut-Brain-Axis HERE.

Let's take surgery as an example (top diagram).  Being cut open by a surgical knife, bleeding, opening arteries and veins are one of the most stressful procedures a person may endure.  With any minor or major stressor, the adrenal glands must put out cortisol and adrenaline. With major trauma (surgery) or mental stressor, buckets of cortisol are secreted to maintain homeostasis, blood glucose, heart rate, blood pressure, hormones, etc.

In different gut disorders and SIBO, slightly variable nervous system effects are observed.  Some conditions are more 'turned up' by the sympathetic nervous system (SNS/adrenaline/cortisol) than others.  Some conditions are more deficient or defective in the parasympathetic nervous system (PSNS/calm/oxytocin) than others.

How do you balance?



Adrenal Botanicals and Yoga

In both clinical practice and in studies, certain rhizomes, tubers, and herbs are shown to buffer and balance the function of the adrenal glands.  Recently Robb Wolf and Chris Kresser talked about adrenal function.  Prior animal pharm ADRENAL posts. The funniest physician on adrenal and hormone health is DR. SARA GOTTFRIED!  Love love love this grrrrrl.

My favorite brand of adrenal support is by Gaia Adrenal Health but many exist.  What works for you?  How do you know when your adrenals are f*kcered?  How do you fix it? Does your physician ignore it?

Yoga -- for me yoga is the best tool for putting the SNS to rest and to bring the PSNS back to up to snuff. I don't know why it works!  There are studies but none explain the deep, contemplative, and restorative properties that I get when I'm regularly doing yoga. If you are in adrenal dysregulation, I'd highly suggest considering avoiding ALL Bikram and other extreme activities. The high heat and extreme form (90 minutes of high intensity sweating) is actually super detrimental for marginally functioning adrenals.

Bionic Adrenals
By Yoga
Source: HERE

Stress

Other ways to tell if you're 'stressed' is FINGERPRINTS (hat tip: D'adamo).  Our height of our fingerprint ridges may reflect our gut health microvilli height.  We are aware that sometimes skin damage reflects gut damage and bacterial/fungal translocation and their respective toxins  (acne, rosacea, psoriasis (and here), eczema, etc).  More damage, flatter villi, flatter fingerprints, different whorl and loop patterns.

In celiac, with severe SIBO, see the white lines and flatness of the ridges? On a gluten-free diet, these improve.

Figure 2 (white lines on gluten/celiac) versus
Figure 3 (diminished white lines on gluten-free diet)
Source: David TJ et al, 1970

References

Small intestinal length: a factor essential for gut adaptation.
Weaver LT, Austin S, Cole TJ.
Gut. 1991 Nov;32(11):1321-3.

The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease.  PDF free.
Collins SM, Bercik P.
Gastroenterology. 2009 May;136(6):2003-14.

Therapeutic considerations of L-glutamine: a review of the literature.
Miller AL.
Altern Med Rev. 1999 Aug;4(4):239-48.

Magnesium sulfate protects against the bioenergetic consequences of chronic glutamate receptor stimulation.
Clerc P, Young CA, Bordt EA, Grigore AM, Fiskum G, Polster BM.
PLoS One. 2013 Nov 13;8(11):e79982.

Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans by a mast cell-dependent mechanism.
Vanuytsel T, van Wanrooy S, Vanheel H, Vanormelingen C, Verschueren S, Houben E, Salim Rasoel S, Tóth J, Holvoet L, Farré R, Van Oudenhove L, Boeckxstaens G, Verbeke K, Tack J.
Gut. 2013 Oct 23.

A cross sectional study of dermatoglyphics and dental caries in Bengalee children.
Sengupta AB, Bazmi BA, Sarkar S, Kar S, Ghosh C, Mubtasum H.
J Indian Soc Pedod Prev Dent. 2013 Oct-Dec;31(4):245-8.

Dermatoglyphics in patients with dental caries: a study on 1250 individuals.
Abhilash PR, Divyashree R, Patil SG, Gupta M, Chandrasekar T, Karthikeyan R.
J Contemp Dent Pract. 2012 May 1;13(3):266-74.

The relation of bruxism and dermatoglyphics.
Polat MH, Azak A, Evlioglu G, Malkondu OK, Atasu M.
J Clin Pediatr Dent. 2000 Spring;24(3):191-4.

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #6 Avoid allergenic foods (corn, soy, gluten/wheat, dairy, nuts, egg whites, etc). Avoid GMO products and livestock/poultry fed GMO crops (corn, soy, etc)

Photo credit: Heritage J. Nature, 2004.

HOW TO CURE SIBO/SIFO, Small Intestinal Bacterial/Fungal Overgrowth
(protocol)

Step #6 
Avoid allergenic foods (corn, soy, gluten/wheat, dairy, nuts, egg whites, etc)
Avoid GMO products and livestock/poultry fed GMO crops (corn, soy, etc) 




The worst offenders to your gut are allergens and things that shouldn't be eaten in the first place. Wheat, vegetable and seed oils, and chemical food additives are not fit for human consumption on a continuing basis! Once you've healed sufficiently, you may get away with eating Tiramisu and deep fried, breaded fish but until your gut is as tight as a nuns ass

Also, what's sauce for the goose is not always sauce for the gander! One person may do just fine eating corn, nuts, eggs, etc... but another may have terrible allergies.

From: LeakyGut website:

An allergy denotes an abnormal reaction by our immune system to bodily contact with foreign substances that would normally be harmless.

There are said to be four types of allergic response. Type I, which causes immediate reactions such as restricted breathing, asthma, anaphylactic shock is the most well known, but effects a minority of the population.

Leaky gut and food allergies often co-exist, food allergies or hypersensitivities can increase intestinal permeability, causing an immune response and provoking further inflammatory reactions throughout the body.

When someone initially comes into contact with an allergen, B lymphocytes (a type of white blood cell) produce antibodies to attack the perceived threat. There are five types of antibodies called immunoglobulins. IgG, IgM, IgA and IgD protect us by attaching to foreign particles making it easier for other immune cells to destroy them. IgE antibodies are responsible for allergic reactions. Everybody has IgE antibodies but an allergic person produces high levels of IgE antibodies to attack the allergens.

The IgE antibodies bind to mast cells (resident cells of connective tissues containing allergy mediators) and basophils (a type of white blood cell containing allergy mediators) located in human tissue. The next time the person comes into contact with the allergen the mast cells and basophils will release potent chemical mediators such as histamine causing an allergic reaction.

Typical allergic responses are: runny nose, itchy eyes, wheezing diarrhoea, swelling, vomiting, restricted airways, eczema, hives. Type I allergies can also cause anaphylaxis and even death. The most common substances to cause Type I allergies are: medicines, dog and cat fur, dust mites, mould, pollen, bee stings, but other substances can also cause reactions such as: certain fruits, perfumes, smoke, nuts and other food or environmental substances.

Without boring you to death, please, please take into account any allergies you may have to the foods you eat! This is one of those things you will need to seek a doctor's advice on if you think you may have an allergy--don't spin your wheels, get tested!

GMO's

The fear of genetically modified organisms in our food supply may be media driven, and it may also be impossible to avoid, but I think there is enough evidence that someone with a really bad gut should seek out ways to avoid GMO foods. It's not that hard when it comes to grains...corn, soy, and wheat are nearly all to be suspected of being a GMO--so don't eat them! Other things like sugar, rice, and potatoes may also be grown from GMO seed and it is almost impossible to know when buying them.

I will admit that I didn’t know much about the GMO connection to gut health before writing this. Embarrassingly, my first Google search turned up this amazing article on Horizontal Gene Transfer, that said [GRACE: Dude, that's funny]:

“Horizontal Gene Transfer. Does horizontal gene transfer (HGT) between DNA from consumed GMO corn and corn products to our gut microbiota occur? Another emphatic YES. How do you reverse it if your microbiota is transformed? I wish I knew... Bacteria and fungi live in biofilms and exchange DNA within the matrix. Like a meme gone viral. Evidence for both DNA and lectin proteins from GMO Bt corn has been found in animals and humans that consume Bt corn. The DNA was found to survive and persist for a long time in the gut/rumen.

Every pesticide corporation has a GMO Bt corn brand. Bt is a lectin (like gluten) and disrupts intestinal epithelium in susceptible victims which can lead to gut dysbiosis and/or death. It was very effective pesticide in the beginning.

Rootworms and other pests have rapidly shown field resistance to nearly every brand -- Syngenta's Agrisure and Monsatan's YieldGuard. Dupont/Dow's Herculex has not as much, therefore Monsatan has reported they are planning to incorporate Herculex to synthesize TWO TOXINS into their new SmartStax corn -- in an attempt to overcome inherent field resistance. GMO is brilliant, no?”

“Recently pesticides from Bt GMO crops were found in 80% of fetuses and 93% of adults (healthy pregnant) randomly tested in one Canadian study (Aris and Leblanc, Reproductive Toxicology, 2011). This herbicide is used as a topical spray as well genetically spliced into the DNA of GMO crops with promoters for high-copy amplification and expression of of a bacterial toxin bacillus thuringiensis (Bt). Bt toxin is also known as Cry1Ab protein. It is a gut specific delta-endotoxin which exerts toxicity through increasing larvae/insect intestinal permeability causing the death of crop pests like leaf- and needle-feeding caterpillars (lepidopteran insects --butterflies, moths), beetles (coleoptera--weevils, ladybugs, beetles), and the larvae (e.g. babies) of leaf-beetles. It has been designed to be toxic to mosquitoes (dipteran)now. Fun, no?

Has lateral transfer of Bt DNA to our gut bacteria and microbial communities already occurred (or at least the unborn and adult Canadians in Aris and Leblanc's study)? Are we transformed? Mutant gut-hybrids of GMO experiments gone awry?
Like advising pregnant moms to avoid fish and seafood to minimize exposure to bioaccumulation of mercury and other pollutants, the American Academy of Environment Medicine (AAEM) issued a GM Foods Position Paper on May 8, 2009 for everyone to avoid all GMO foods in their diets. Why such adamant recommendations for exclusive GM-free diet prescriptions?”

This incredibly insightful author goes on to describe a study in which GMO pesticides were shown to alter the microflora of mice

“In 1998 two scientists fed mice for two weeks potatoes (a) soaked for 30min in a dilute suspension of harvested Bt toxin (from bacterial spores grown in the lab; 1 g/L concentration), (b) transgenic Bt potatoes, and (c) control potatoes. Mild structural changes in the microvilli of the ileum of the transgenic GMO Bt potatoes were seen in. However in the Bt delta-endotoxin soaked potato-fed mice, the ileum changes were quite substantially greater in scale -- '...basal lamina along the base of the enterocytes was damaged at several foci. Several disrupted microvilli appeared in association with variable-shaped cytoplasmic fragments.' The authors further report 'in the group of mice fed on the delta -endotoxin-treated potatoes, the Paneth cells of the crypts of Lieberku¨hn were highly activated and contained a large number of secretory granules. These cells are believed to have an important role in the activation of phagocytes and controlling the bacterial flora of the gut (Ariza et al., 1996; Fawcett, 1997). They contain elevated levels of lysozyme in their large eosinophilic secretory granules, an enzyme capable of digesting bacterial cells walls, and antibacterial peptides called cryptdins (Junqueira et al., 1998). Ouellette (1997) revealed that Paneth cell secretory products seem to contribute both to innate immunity of the crypt lumen and to defining the apical environment of neighboring cells....The antimicrobial polypeptides of the Paneth cell secretory products kill a wide range of organisms, including bacteria, fungi, viruses and tumor cells (Aley et al., 1995).' Lysozymes are 'cutters' -- they cleave and cut things, for instance, tumour/cancer cells and cell walls of pathogens that take a ride in our food.
Damage to the ileum and small intestines can lead to changes in microbial population and the disorder known as SIBO (small intestinal bowel overgrowth). An expanding body of knowledge links SIBO with nearly every chronic systemic and skin disease seen in outpatient medicine.

Bt toxin appears to induce self-digestion -- (increased Paneth cell and lysozymal activity) and damage from the inside out. Lovely! And it is present in unborn children and adults.”

Read more: Geneticist David Suzuki Says Humans “Are Part Of A Massive Experiment”
 Hat tip: Todd LePine

Do dietary lectins cause disease?
Freed DL.
BMJ. 1999 Apr 17;318(7190):1023-4.

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #5 Exercise low-moderate intensity one hour daily continuously (10,000 steps) to move the gut/peristalsis and overcome broken myenteric musculo-neuro junctions

EHP Sept 2013 (Modified)
The Environment Within: Exploring the Role of the Gut Microbiome in Health and Disease

Step #5. Exercise low-moderate intensity one hour daily continuously (10,000 steps) to move the gut/peristalsis and overcome broken myenteric musculo-neuro junctions

Dr. BG's 7-Steps Paleo* Gastro IQ SIBO Protocol

HOW TO CURE SIBO, SMALL BOWEL INTESTINAL OVERGROWTH

1. Fermented veggies made the ancient way with organic dirt-covered vegetables, ex. kraut, kvass, kim chee, kefir, etc. Read Sandor Katz.
2. Ancient heirloom potatoes, tubers, roots that are low glycemic index (or high if good insulin sensitivity) and ancient heirloom grains, legumes, lentils/dal that are low glycemic index (or high if good insulin sensitivity), prepared the ancient way (soaked, fermented, etc)
3. Soil-based probiotic 1-2 daily if not severely immune compromised (Bacillus licheniformis, Clostridium butyricum, etc)
4. Two versions of 'bionic fiber' to heal the gut...
VERSION A: Green banana flour 1-3 Tbs + Raw PS (potato starch) + high ORAC green powder in 2 cups water

VERSION B: Raw PS (potato starch) 1-3 Tbs + Psyllium (if not allergic) 1 Tbs + high ORAC green powder (I like Amazing Grass, LOL) in 2 cups plenty of water

Step #5:  WALK

Now, where have we heard that before.  Sounds a lot like the Primal Blueprint!  If anyone here doesn't know who Mark Sisson and Grok are, now is the time to meet them.  Mark Sisson came up with his Primal Blueprint as a way for the average person to implement a paleo diet in a personalized way that works for anyone from beginner to elite athlete.  One of the first things you will learn when you start reading the Primal Blueprint is that you don't need to kill yourself running mile after mile.  Walking steadily at a slow pace is the much preferred route to health and happiness.  

Grace says to walk 10,000 steps and then recommends you do it in an hour . . . hmmmmm.  I think her pedometer was broken that day or she was buzzing on lattes, because 10,000 steps is 5 miles by most accounts!  But that's OK, we'll give her that one!  The takeaway is that you need to get up and get moving.  Walk as much as you can.  Don't have an hour to spare, take four 15 minute walks, three 20 minute walks, heck--take 10 six-minute walks!  Just get walking.  Walking is a great way to keep your intestines limber and healthy.  If you have a sedentary desk job, it's even more important that you get up during the day and WALK.  Tell your boss you took up smoking, then follow the smokers to the smoke shack and do laps around the parking lot while they shorten their lives.  

According to this article, "As far back as the late 1950s, a study found that people with sedentary jobs (bus drivers) were twice as likely as those with active jobs (mailmen) to develop cardiovascular disease. More recently, extended daily TV watching and time on the computer-which, like desk jobs, involve long periods of time sitting still-have been linked to a greater risk of metabolic syndrome, a constellation of health problems that can lead to diabetes and heart disease."  

Here is a great website for all things walking related if you need some motivation to get started, but seriously, just walk.  Get some comfortable shoes and walk.  If you are a busy mom chasing kids or a factory worker who is on your feet all day, you probably have the walking part covered, but still, a nice leisurely stroll can be very relaxing and a great way to get outside.  

Wasn't that easy!



 Are you wondering what is peristalsis and myenteric musculo-neuro junctions? Let me expand....


There are two main ways that food and mucus material in the small intestines move along the gut (1) peristalsis and (2) MMC, myenteric migrating complex.  Peristalsis is the weak, wiggly movement propagated by the smooth muscle lining the intestinal tract.  The myenteric migrating complex on the other hand is powerful and strong, starting from the stomach and vibrating like a heart beat or pacemaker through the small intestines in pulses throughout the day every 90 to 120 minutes.  These are known as 'housekeeping waves'.  It is also described as 'a band of neural excitation that travels slowly across the stomach and intestines.' The movement quickly shuttles along the contents, mucous, bacteria and fungi out of the small intestines to the large intestines when we are fasting and through out the day.  Usually the MMC rhythmic contractions are painless and unnoticed, but for those with IBS or other bowel inflammation, sometimes these are uncomfortable or painful.

The presence of food actually temporarily decreases the MMC propulsive action because the gut needs to slow down for food to be thoroughly digested and absorbed in the small intestine, no? So it is no wonder that high-bolus insulin doses (which mimic eating) will stop the MMC. Guess what subgroup has poor functioning guts, SIBO and MMC? Type 2 diabetes and obese individuals where the MMC is less functional secondary to high insulin levels.  Additionally when the BG (blood glucoses) have been pathologically elevated for decades, damage to the nerves that regulate the small intestines can happen and this is known as autonomic neuropathy.  The result is abnormal peristalsis, spontaneous contractions, and reduced tightness of the sphincters which grip and prevent intestinal contents from escaping to places they shouldn't (like backward in heartburn/stomach contents or with feces).  Part of the charm of exercise is that all of these gut motility issues can be improved or even reversed with routine, regular exercise which improves insulin sensitivity, strengthens smooth muscle, improves the pacemakers of all of organs and calms the nervous system that regulates every organ.

Did you know our small intestines are innervated by 100 million neurons, as many as the spinal cord (Gershon 'The Second Brain')?  Therefore innervations to the small intestines can become 'broken' from various conditions which will lead to higher degrees of small intestinal bacterial/fungal overgrowth (aka SIBO/SIFO -- hat tip Keith Bell). Additionally hormone changes and structural tissue damage may also 'break' the sweeping motions that naturally occur in the small intestines leading to pseudoobstructions and SIBO (see HERE for complete list including hypothyroidism, diabetes, autoimmune diseases (celiac), viral damage (CMV, Epstein Barr, herpes zoster), drugs (verapamil, diltiazem)).

Exercise may not entirely erase damage to our second brain in the our guts but it can potently improve inflammation at the intestinal level and condition and strengthen the smooth muscle that control the contractions of the gut (peristalsis, MMC).

When I had CFS (Chronic Fatigue Syndrome) and nearly bed-bound, I couldn't walk a block, let alone 5 miles. If you haven't the capability to walk or jog far, start low and go slow. Consider starting with hydrotherapy or swimming (no gravity) gently at first for only 10 minutes daily and gradually build to tolerance.


Citations

Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels.
Queipo-Ortuño MI, et al.
PLoS One. 2013 May 28;8(5):e65465.

Habitual exercise program protects murine intestinal, skeletal, and cardiac muscles against aging.
Rosa EF, Silva AC, Ihara SS, Mora OA, Aboulafia J, Nouailhetas VL.
J Appl Physiol (1985). 2005 Oct;99(4):1569-75.

Freewheel training decreases pro- and increases anti-inflammatory cytokine expression in mouse intestinal lymphocytes.
Hoffman-Goetz L, Pervaiz N, Packer N, Guan J.
Brain Behav Immun. 2010 Oct;24(7):1105-15.

Exercise attenuates PCB-induced changes in the mouse gut microbiome.
Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M.
Environ Health Perspect. 2013 Jun;121(6):725-30.

Reflux oesophagitis in adult coeliac disease: beneficial effect of a gluten free diet.
Cuomo A, Romano M, Rocco A, Budillon G, Del Vecchio Blanco C, Nardone G.
Gut. 2003 Apr;52(4):514-7.

Small intestinal bacterial overgrowth: a comprehensive review.
Dukowicz AC, Lacy BE, Levine GM.
Gastroenterol Hepatol (N Y). 2007 Feb;3(2):112-22.

Gut peristalsis is governed by a multitude of cooperating mechanisms.
Huizinga JD, Lammers WJ.
Am J Physiol Gastrointest Liver Physiol. 2009 Jan;296(1):G1-8.

Chronic intestinal pseudo-obstruction: assessment and management.
Connor FL, Di Lorenzo C.
Gastroenterology. 2006 Feb;130(2 Suppl 1):S29-36.

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #4 Eat BIONIC FIBER

Cooked Resistant Starch Type 3 From Rice, Roots, Beans,
Lentils, GF Ancient Grains = BIONIC FIBER
Credit: Harry Flint et al, Nature, 2012.

Dr. Grace's Bionic Fiber for Your Gut:  Step #4

VERSION A: Inulin-FOS 1-2 TBS + Psyllium (if not allergic) 1 TBS + high ORAC green powder (I like Amazing Grass, LOL) in 2 cups water

VERSION B [Fat-Blaster]:  Inulin-FOS 1-2 TBS + Acacia Gum 1 TBS (or Green banana flour 1 TBS) + high ORAC green powder in 2 cups water

VERSION C [Amped Up Bionic Fiber]:  INULIN-FOS 1 TBS + ACACIA FIBER 1 TBS + Psyllium (if not allergic) 1 TBS  +  high ORAC green powder (I like Amazing Grass or Raw Reserve) in 2 cups of plenty water

Optional, add 1 tsp of one or several of below (rotate for variety and diversity):

• Pectin
• Modified Citrus Pectin
• Chorella
• Arabinogalactan
• Glucomannan (MAX: 1/4 to 1/2 tsp with 2 cups water)
• Oat Bran (Trader Joe's; Bob's Red Mill)
• GOS (UK Bimuno)
• FOS-rich Organic Yacon Syrup
• Green Banana Flour (oligos-inulin+RS2), Green Plantain Flour (oligos-inulin+RS2)
• fresh ground Flaxseed
• Baobab Hadza Fruit fiber

Resistant Starch Type III: Cooked-Crystallized Starch Is Evolutionarily Correct

The best, ancestral resistant starch for long-term health, leanness and modern, disruptive lifestyles is RS3, cooked-cooled resistant starch. The crystals that form upon cooling make up a dense, DNA-like configuration that our gut flora love; they have adored and have specialized preference for RS3 for millions of years since our hominid ancestors discovered FIRE. In epidemiological studies, RS3 in ancestrally prepared food protects against diabetes, inflammation, diseases of aging and colorectal cancer. 

Read more about the legumes, roasted heirloom tubers and gluten-free grains that are rich in RS3. A broad spectrum of fiber produces the best diversity and robustness in our gut flora populations:

• Foods rich in Cooked Resistant Starch RS3
  

Whole Real Food	100g = ~ ½ cup	Inulin-Oligosaccharide Content	RS3 Content
Chicory root	100g	41g	0
Jerusalem artichoke	100g	18g	0
Dandelion greens	100g	13g	0
Onion (raw)	100g	4g	0
Yacon syrup, 2 TBS	2 TBS	10-14g	0
Garlic (raw)	25g	3g	0
Cowpea, White Lupin	100g	5g	4g
Lentils, Chickpeas, Hummus	100g	4g	2-4g
Pinto Beans (cooked/cooled)	100g	3g	10g
Purple Potato (roasted/cooled)	100g	na	15-19g
Yams (boiled/cooled)	100g	na	6-8g
Potato (boiled/cooled)	100g	na	3-7g
Rice (cooked/cooled)	100g	na	1-2g
Long grain Rice (cooked/cool)	100g	na	2-3g
Sushi Rice (cooked/cool)	100g	na	3-4g

NEW RELATED POSTS:

• Sorry. Resistant Starch (Raw) is Unlikely to Miraculously Cause Weight Loss and Body Fat Loss
• Cooked RS3 Trumps Raw RS3; They are vastly different
• Peering into Four uBiome Stool Analyses (Part 1): Benefits of BIONIC FIBER; Emergence of Toxin-secreting Clostridium Botulinum and Loss of Over 1/3 of Gut Diversity and Species With 'Raw Bob's Red Mill Potato Starch'

RAW RESISTANCE STARCH TYPE 2 CONTRAINDICATIONS/ADVERSE EFFECTS:

• Part 1: Don't Take Raw Resistant Starch Alone and Other Precautions; RS2 Needs to Be Taken With Other Fiber To Spread Fermentation Completely Across the Entire Colon
• Part 2: Real Food Resistant Starch (RS3) Trumps High-Dose Potato Starch Diet To Expand the Lean and Immunoprotective Core Microbiota (Roseburia, Eubacteria, F. prausnitzii, Bifidobacteria)
• Part 3: Don't Take Resistant Starch If You Have Moderate to Severe Irritable Bowel Syndrome (IBS) Temporarily
• Part 4: Don't Eat Raw Resistant Starch (RS2) If Pre-Cancerous or Cancerous for Colorectal Cancer, Temporarily
• Part 5: Don't Take Raw Potato Starch (RPS) Temporarily If You Have an Autoimmune Disorder

RAW RESISTANCE STARCH TYPE 2 TRIGGERS ADVERSE GUT MICROBIOTA EFFECTS:

• Part I: Bifidobacteria longum, Roseburia, F. prausnitzii (and Akkermansia) Made Us Human (NONE OF THESE EAT RAW POTATO STARCH) NSFW
• Part II: HADZA GUTS HAVE THE ANCESTRAL CORE MICROBIOTA IN ABUNDANCE; High Dose RAW Starch Can Suppress Bifidobacteria, Roseburia, F. prausnitzii That Make Us Human
• Part III: PALEO MAG HOT TONY FEDERICO HAS THE ANCESTRAL CORE MICROBIOTA IN ABUNDANCE; Citizen Science; Cautions with RPS-RUMPS; High Dose RAW Starch Appears to Suppress Christensenella, Akkermansia, and B longum That Make Us LEAN
• Part IV: High Dose Potato Starch Can Make You Fatter, Insulin Resistant, Feed Vipers in Your UPPER GUT If You Are MISSING Bifidobacteria longum and Akkermansia mucinophila, aka SAD Microbial Fingerprint  NSFW
• Part V: High Dose Potato Starch Can Make You Fatter, Insulin Resistant By Lowering GLP-1 AND ESPECIALLY If You Are Missing  Bifidobacteria longum and Akkermansia mucinophila, aka SAD Microbial Fingerprint (NSWF)
• Part VI: Lose Weight, Body Fat, Improve Blood Glucoses and Insulin Sensitivity; Repair the Gut Flora That Potato Starch (Raw RS2) Damages

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #3 Eat Soil-Based Probiotics

Step #3:  Soil-based probiotic 1-2 daily if not severely immune compromised (Prescript Assist, Bacillus licheniformis, Clostridium butyricum, etc)

Or eat soil-based organisms (SBOs) from ancestrally prepared fermented foods: KOREAN PEPPER PASTE (GOCHUJANG), Thai shrimp paste, natto, fermented black beans, etc.

See prior animal pharm: Kochujang, [B licheniformis, B subtilis] fermented soybean-based red pepper paste, decreases visceral fat and improves blood lipid profiles in overweight adults

B pumilus

Today we'd like to talk about step 3 in Dr. BG's 7-Steps Paleo* Gastro IQ SIBO Protocol.  I came here as a bit of a know-it-all on resistant starch [RS3 from legumes, lentils, whole GF grains and roasted heirloom tubers/roots], but quickly realized that while RS3 was somewhat of a missing-link on a paleo diet, soil-based organisms (SBOs) are missing even more-so.  Luckily, combining RS and SBOs is the quickest route to restoring harmony in the gut.  In a few email exchanges with Dr. BG, she mentioned SBOs several times.  I was totally unfamiliar with the term.   I thought to myself, 'wow--she is so dumb, she can't even spell 'SIBO'.  Boy was I in for a surprise!  After sending me 200 links to read, I quickly became a believer in Soil Based Organisms.  

Also known as Homeostatic Soil Organisms (HSOs), these microbes have been flying under the radar for decades.  All throughout our evolutionary history, SBOs were there with us.  When we started cleverly sanitizing our hands, sterilizing our eating utensils, and homogenizing everything we ate SBOs were no longer our faithful ally.  

L plantarium

Soil Based Organisms are microbes which normally live in dirt, but can also live happily in our digestive tract.  Approximately 30 different strains have been successfully isolated and are commonly put into probiotic supplements.  There are hundreds of articles available concerning SBOs, but most of them are advertisements from the supplement industry designed to sell you their favorite formulations.  I managed to find a few papers that were reviewed by the National Institute of Health such as this one on SBOs and Immune Function.  The article describes using SBOs to successfully treat Chronic Fatigue System and cancers and they had "...proven successful in restarting the immune systems of persons with allergies, lung cancer and TB."  

A clinical study was done with 25 sufferers of IBS using a commercial SBO probiotic.  The study concluded: " This study identified 3 subsyndromic factors of IBS: general ill feelings/nausea, indigestion/flatulence, and colitis. In this methodologically oriented double-blind study in patients with IBS, combined probiotic-prebiotic treatment with Prescript-Assist was associated with significant reductions in these factors."  

I looked at the formulations of several SBO supplements recommended by Dr. BG and found they all contained a variety of microbes.  The first one I looked at is called Probiotic-3 from iHerb.  It contains Streptococcus faecalis, Clostridium butyricum, and Bacillus mesentericus.  Each one of these are well known probiotics found in the soil and in humans and convey protective properties when in the human digestive tract.  

S faecalis

WHOA!  HOLD ON...Dr. BG wants us to swallow a pill containing Streptococcus faecalis?  [Grace: YESSSS]  It's commonly found in 'diseased teeth needing or having had root canal treatment' and 'Some diseases caused E. Faecalis are endocarditis..., urinary tract infections, pneumonia or meningitis.'  WTF?  Well, it turns out that this microbe is also a powerful 'lactic acid [producing ] bacteria and it can help reduce symptoms when a person is lactose intolerant. The products created with this bacteria are useful for clearing diarrhea and for stimulating the immune system. Products fermented with this bacteria help to balance the intestinal microflora.'  Almost every one of the SBOs has a similar story!  OK, maybe Dr. BG is not totally crazy, but the jury is still out.   [Grace: Demented, no debate~!]

(NOTE: this is not an advertisement!)



Click the links to learn more:

Bifidobacteria and Lactobacillus are some of our most ancient enviromental and soil based microflora that our ancestors co-evolved with.

• FloraMend (L. gasseri, B. longum, B. bifidum) ~ B. longum is one of the 7 ANCESTRAL CORE MICROBIOTA
• Delpro™ Super powered Russian Lactobacillus
• Renew Life/Ultimate Flora [Critical Colon] BIFIDO MAX
• Baby Jarro-Dophilus powder (1 tsp = 2.4 grams GOS) does contains dairy/soy
• Klaire Therabiotic Factor 4 (no dairy)
• Theralac lactobacilli and bifidobacteria
• PURE probiotics with Bifidobacteria longum and lactobacilli

Lactobacillus acidophilus	Lactobacillus casei	Bifidobacterium longum
Lactobacillus rhamnosus	Lactobacillus brevis	Bacillus subtilis
Lactobacillus salivarius	Bifidobacterium bifidum	Saccharomyces boulardii
Lactobacillus plantarum	Bifidobacterium breve
Lactobacillus paracasei	Bifidobacterium lactis

If anyone is as interested in gut microbes as Dr. BG and I, please click each link above...these are links that I personally searched for, they were not hand-fed to me by manufacturer.   For instance, the link on Lactobacillus paracasei will lead you to an article by the American Society for Microbiology concerning this microbe and it's relationship to mucosal immune response.  I will leave it to you to look into these, as each one alone could fill several blogs!

Here is the takeaway for this blog:  If you are severely immune-compromised, do not take any probiotics.  They are alive or spores (except for the killed ones). Like a live (attenuated) vaccine, probiotics are contraindicated in a severely immune-compromised individual, someone on or after chemo/radiation, low WBC or suppressed bone marrow.

If not, and you want to treat SIBO or just improve your gut microbiome, consider taking supplements like these in your therapeutic plan along with RS3-rich foods and Bionic Fiber (version A, B, C):  

Prescript Assist
AOR Probiotic-3
FloraBalance
Body Biotic 
Primal Defense
MegaSpore (practitioners' offices only)
Primal Flora


There is no magic in using these brands, but the supplement you choose should  have a similar composition.  These supplements don't need to be taken for life, just until you kick-start your gut flora--when properly fed, these microbes will set up shop and help keep you healthy and happy.  Proper feeding of microbes relies on resistant starch and some other prebiotics we will talk about next...