Friday, March 14, 2014

Gut Microbiome Biohacking Basics; Mild Havoc? Or Unmitigated Upheaval?

Linkin Park
Roads Untraveled

Roads Untraveled?

More and more studies are pouring into our collective knowledge about the microcritters in our 'forgotten organ,' the humble gut. The latest making the rounds is a stunning article on how one of the first antibiotics created by Eli Lilly in the 1950s was used as a 'digestive aid' in livestock (like ?cocaine in COKE? or ?nicotine in tobacco once plugged by physicians or ?gliadin in modern hybridized wheat plugged by govt juggernauts) .They were used to put on fat and poundage to cattle and livestock by a 3-FOLD magnitude. In those war and post-war days, the population was skinny and desired 'fat'. In modern times, we've flipped. The majority are overweight/metabolically deranged and desire 'thin.'
Source: Big Tobacco led throat doctors to blow smoke (Stanford)

Do Antibiotics Make Us Fat?

"On the Point" with Tom Ashbrook has a new podcast that interviews the author of the new NY Times article linking agricultural use of antibiotics in animal feed decades ago with the new diabesity epidemic, Pagan Kennedy. Dr Ilseung Cho is also interviewed, gastroenterologist at NYU and gut microbiome researcher. Dr. Cho talks about the potential gut effects of antibiotics.

Dr Cho is from Marten Blaser's lab which recently concluded in their study "Infant Antibiotic Exposures and Early-Life Body Mass" that YES antibiotics are highly correlated to higher 'fatness' in babies who received antibiotics before age 6 months, and older as well but the effect was less consistent apparently after babies start to crawl around (Trasande et al 2013).

Clearly there are multiple factors that go into becoming fat. Clearly we have ignored the gut microbiome for too long. 100% of everyone that I know has had at least a single course of antibiotics if not double digits. As a child of a physician, I've had my share. For many fevers and sniffles, I got the 'pink liquid'. Partly I went into pharmacy believing that drugs were not only good, but life saving.

Can antibiotics actually be life altering and life stealing? Bringing on autoimmunity? Triggering UC, Crohn's and IBS? Ushering in the storms of autism, diabesity and allergies that are seem inescapable and epidemic? Before I had kids, I once had Shigella. It was awful and Cipro did cure it -- but did it impair my gut? Should I have taken measures to protect the commensal populations?

My oldest daughter was born ~14 years ago via emergency C-section. Despite breast feeding her, she had 2-3 months straight of inconsolable crying and colic (age ~6-9 months), endless ear infections (6-12 months), then later developing reactive asthma (1.5-10 until we started vitamin D) which required middle of the night treatments, nebulizers and urgent care visits. We have never had asthma in the 'family'. It certainly didn't appear 'genetic'. In hindsight, I suspected that her atopic hypersensitivities be related to many things not excluding the (lame gut) legacy that I handed to her, C-section birth and formula at age 6 - 18 months.
How important is the maternal microbiome bequeathed to the baby? Did my firstborn inherit a gut with major deficits secondary to the 15-20 courses of antibiotics during my life (which of course did save my life a few times, including a large third-degree burn)? In light of the new data emerging from 16S rRNA sequencing technology, all these questions are being illuminated and even answered.

ONE THE POINT PODCAST: Antibiotics and obesity. Whether it’s possible that antibiotics plump up humans the same way they do animals, livestock. American farmers commonly feed their livestock grain laced with antibiotics because it makes bigger animals. Heavier. Fatter. So what about the antibiotics we humans take – for the ear ache, the strep throat, the sinus infection. Could those make us heavier? Fatter? No one argues that diet and exercise – or lack of it – come first. But could antibiotics be a scale-tipping X-factor in American obesity?

From Tom’s Reading List
New York Times: The Fat Drug – “In the last decade, however, scrutiny of antibiotics has increased. Overuse of the drugs has led to the rise of antibiotic-resistant strains of bacteria — salmonella in factory farms and staph infections in hospitals. Researchers have also begun to suspect that it may shed light on the obesity epidemic.”
Mother Jones: Can Antibiotics Make You Fat? –”Are we being exposed to tiny levels of antibiotics through residues in the meat we eat—and are they altering our gut flora? It turns out that the Food and Drug Administration maintains tolerance limits for antibiotic residue levels, above which meat isn’t supposed to be released to the public.”
Nature: Antibiotics in early life alter the murine colonic microbiome and [INCREASE] adiposity – “Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we proposed that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities.”

Intro of our Gut Characters

Here is the line up. They originate from life -- mom, diet, foods, dust bunnies, soil exposures, pets, kissing, hugging, licking doorknobs, etc.

Source: Ch 2 The Commensal Microbiology of the GI Tract
Manson, Rauch, Gilmore 2008

Intro of Some of What Our Gut Characters Do [Caveat: If We've Got Them]

They eat and poop, and we eat their secretions (vitamins, amino acids, SCFA (short chain fatty acids)) and then poop then out. Half of our dry poop in weight is in fact them. Their DNA exceeds ours by 150-times. Basically their microbiome complements our human genome with 150-fold more genes. Our Homo sapien-derived double helixes don't alter (much, debatable here). Their's is contrastingly plastic. They can sweep up lactose digestion or antibiotic-resistant plasmids or DNA from their environment or via microbial-sex. In evolution, they appeared first and will likely appear last... "Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. (Thomas et al 2011)" When diet resource allocation or subpopulation neighbors shift, so do their gene expression. They shift to the diet provided. Additionally, they can control our gene expression. Bacteroidetes thetaiotamicron (one of our vital omnivorous commensal symbionts, Roberfroid et al 2010) has been shown to turn on/off over 400 genes in the host, thus altering molecular architecture and body functions (Heselmans et al 2005). Indeed, our microbes may maketh the man, woman and child (and all animals, insects, plants).

Your response to fiber, RS, g banana/plantain flour, potato starch, probiotics and food all depend on what is filling your zoo cages, the pre-existing microbiota. Do you have vipers or voles? Electric eels or earthworms? Is your apex predator for the ecosystem EXTINCT. Does excessive flatulence blow you to the moon and clear the room?
Source: Fermentation of non-digestible oligosaccharides by human colonic bacteria
Gibson et al, 1996


No one who lives in an industrialized country is exempt. Broad spectrum, potent, synthetic antimicrobials can permanently damage the gut characters originally present many new studies besides research from Cho and Blaser's work. Jansson et al discovered that for a single 7-day course of antibiotics, gut testing showed that even TWO YEARS OUT WTF, THE SYMBIOTIC GUT CHARACTERS WERE GONE. The former fingerprint and diversity were extinct. Diversity means resilience -- the ability to bounce back and be robust against inevitable changes, shifts and hurdles. Michael Pollan, author and eater of all things fibrous and fermented, stated that after a 'precautionary' course of amoxicillin antibiotics prior to oral dental surgery, his intestinal commensal populations plummeted. The healthy blooms disappeared (Prevotella), replaced by noxious Proteobacteria (NY Times, My Best Friends are Germs 2013). Antibiotics and their drug-resistant DNA are also found in feedlot poultry, pigs, cattle, dairy and eggs. It is hard to escape these chemicals even if your dental surgeon or pediatrician are not eager to whip out their blank Rx pads.

Why Do Antibiotics Do So Much Damage and Can Lead to SIBO/SIFO?

Here is our gut below -- the  intestines are long and when splayed open have a large surface area equivalent to a high-piled terry cloth towel as large as a tennis court. The small intestines are 6-8 meters and colon ~1.5m. The small intestines are significantly longer: 4-5-times longer than the colon. This is where disease can begin. The interface between the outside world and our immune system and blood supply are separated by a single layer of cells. Many microbes actually attach to the intestinal cells in the small intestines (eg SFB, segmented filamentous bacteria) and eat from our bodies directly. These are the same organisms recently shown to prevent or cure T1D model in rodents. Most of the other gut characters live in the interior of the tube (lumen) or in the slime (mucous) along the length of the whole intestines.

Functional Ecology of the Small and Large Intestines
Source: Martin F P et al., J Proteome Res 2009;8:3464–74

The Russians have studied bugs far longer and in a more integrative manner when compared to Pasteur or other micro-phobes. Some of our best probiotics (Natren), yogurt strains and gut-healing protocols (GAPS) are from Russia. Korshunov et al has been studying how gut microbes can be protected with Bifido and Lactobacillus probiotics after chemotherapeutic induced dysbacteriosis (antibiotics). His studies revealed that SIBO (small intestinal bacterial overgrowth) occurs almost instaneously. He didn't study the mycobiome but it's not unfathomable that SIFO (fungal overgrowths) occurred as well. The small intestines are vulnerable because the role of the microbes there is one of protection, immuno modulation and symbiosis. Once the ecosystem is perturbed, all health can change. Extraction of nutrients is just one single function of the small intestines. The immune system lines the entire gut from mouth to anus, and particularly in the small intestines the job is intimate and foremost. When the ecosystem is complete, our commensals + gut do the job of:
--maintaining tight junctions
--prevent permeability
--stopping breaching or bacterial/fungal translocation to other organs or blood
--allowing tolerance for other commensals (Toll receptors, toll='fantastic' in German)
--decreasing allergic reactions and hypersensitivities (asthma, eczema (Heisenbug), food intolerances (gluten/dairy -- me), sinuses (Richard N), etc)
--tagging pathogenic strains, protozoa and parasites as foreign invaders for elimination
--secreting antimicrobial peptides (AMPs) to limit the growth of unsavory characters (the commensals are the 'apex predators' of the gut ecology)
--modulating mood and behavior by facilitating neurotransmitter and hormone synthesis (HPA-thyroid-genitalia-GUT axis)
--other than the spleen and bone marrow, create immune cells necessary for host health

There are a ton of factors for dysbiosis and unbalanced microbiota -- but antibiotics seem to be at the core, like here and here. Without commensal symbionts guarding the gut due to potent pharmaceutical antibiotics, the minor population of pests and vermin strains are left alone and un-mitigated. When there is plenty of food around, they will bloom or double overnight (or sooner). Korshunov et all called this 'contamination of the small intestines,' in other words SIBO/SIFO. It is indeed a common clinical feature in modern medicine as new human gut microbiome studies are revealing, yet largely undiagnosed with no modern medical solutions. The 7 steps for the ultimate gut health restores the commensal populations to a level that allows the gut to recover stability, diversity and optimal health.
[Characteristics of experimental antibiotic-induced dysbacteriosis]. [Article in Russian]
Martynov AI, Grinevich AS, Korshunov VM, Pinegin BV. Zh Mikrobiol Epidemiol Immunobiol. 1982 Jan;(1):48-54. 
Changes in the microflora of the large and small intestines in mice and guinea pigs after the oral administration of canamycin (a hardly absorbable antibiotic) and ampiox (an easily absorbable antibiotic) in different doses. The administration of these antibiotics in different doses (therapeutic, subtherapeutic and over therapeutic) led to an increase in the number of opportunistic microorganisms and the contamination of the small intestine by these organisms. These changes were also well pronounced in guinea pigs, normally having no enterobacteria. After the administration of the antibiotics was stopped, opportunistic microorganisms were gradually eliminated from the small intestine. The rate of decontamination depended on the administered dose of the antibiotic: the higher the dose was the longer the process of the decontamination of the small intestine lasted. An increase in the amount of opportunistic microbes in the large intestine and the decontamination of the small intestine occurred simultaneously with the decrease in the amount of lactobacilli and bifidobacteria in both the small and large intestines.  

OTHER MICROBIOME KILLERS = Atkin's, VLC, Ketotic, Low-Fiber Diets

There are many ways to kill your gut besides antibiotics. Dietary changes make profound changes to the gut. Diet is in fact one of the primary drivers of diversity and populations in the gut. As we know with Darwin and his finches, diet drives evolution of morphology and anatomy. The main gut characters that produce the anti-inflammatory BUTYRIC ACID and other SCFAs are also the same ones often associated with longevity in centanarians, better health and less fraility (Roseburia, F prausnitzii, Ruminococci, Bifidobacteria). The preferred diet of these butyrate-producers is fiber + RS. These 2 groups: (1) Ruminococci (Clostridium cluster IV) and (2) Roseburia (Clostridium cluster XIVa) munch on mostly RS, not inulin, other fibers or meat (eg other a bacteria eats bacteria world LOL). They do not appear too diversified in their culinary palate, yet they comprise the great majority of gut characters in healthy, disease-free, cancer-free individuals. Ruminococcus bromii assists all of the other gut inhabitants by being an enthusiastic and primary degrader of resistant starches, making carb by-products that can be utilized by others lower in the ecosystem. When these 2 groups 'bloom' in the colon, gut pathogen populations go down, gut inflammation is reduced and even horrific diseases completely and 100% reverse in new research trials (C diff antibiotic-induced colitis, UC, IBS, autism, etc).

Butyrate drops precipitously with a low-carbohydrate, low fiber/RS diet in a study by Duncan et al 2007. The anti-inflammatory gut species took nosedives (see below) -- Roseburia, F prausnitzii, Ruminococci, and Bifidobacteria. Subsequently, butyrate in the stools became only 1/5 to 1/4 of the maintenance diet amount. Butyrate trended with Roseburia (Clostridium cluster XIVa) populations. The prime fuel (70-80%) for colonocytes is butyrate from microbial fermentation (the next best is glutamine from skeletal muscle, then glucose). An energy crisis occurs when they are not supplied well.

Human gut characters prefer and need indigestible carbohydrates. Indigestible to Homo sapien but digestible to microbial amylases and a consortium of enzymes that break down all configurations of fiber and RS starches down. These butyrate-producers are not as carnivorous as other species (Bacteroidetes). This is likely from millions or perhaps I suspect billions of years of co-evolution where our gut species took advantage of the environmental bounty and abundance of plant fibers. The biomass of earth is 75% plant carbohydrates;  microbes blanket the earth, air and water.


Source: Karen Scott PhD ROWETT SLIDES
Duncan et al (2007) AEM 73; 1073-1078

Wednesday, January 22, 2014

Two Case Studies -- Diarrhea-IBS and Constipation-IBS and GI Fx Stool Test: Overgrowth of Pathobiont Klebsiella, Fungi Rhodotorula and super-low commensal Clostridia

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

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...

Wednesday, January 8, 2014

More Nematodes, Soil Bacteria, and Glowing in the Dark Wounds Observed in the American Civil Wars

Why Some Civil War Soldiers Glowed in the Dark

Source: Mental_Floss
Hat tip: Keith Bell; Dr. D'Adamo

Below from Matt Soniak

[***the soil based organism SBO discussed here is found in Prescript Assist]

By the spring of 1862, a year into the American Civil War, Major General Ulysses S. Grant had pushed deep into Confederate territory along the Tennessee River. In early April, he was camped at Pittsburg Landing, near Shiloh, Tennessee, waiting for Maj. Gen. Don Carlos Buell’s army to meet up with him.

On the morning of April 6, Confederate troops based out of nearby Corinth, Mississippi, launched a surprise offensive against Grant’s troops, hoping to defeat them before the second army arrived. Grant’s men, augmented by the first arrivals from the Ohio, managed to hold some ground, though, and establish a battle line anchored with artillery. Fighting continued until after dark, and by the next morning, the full force of the Ohio had arrived and the Union outnumbered the Confederates by more than 10,000.

The Union troops began forcing the Confederates back, and while a counterattack stopped their advance it did not break their line. Eventually, the Southern commanders realized they could not win and fell back to Corinth until another offensive in August (for a more detailed explanation of the battle, see this animated history).

All told, the fighting at the Battle of Shiloh left more than 16,000 soldiers wounded and more 3,000 dead, and neither federal or Confederate medics were prepared for the carnage.

The bullet and bayonet wounds were bad enough on their own, but soldiers of the era were also prone to infections. Wounds contaminated by shrapnel or dirt became warm, moist refuges for bacteria, which could feast on a buffet of damaged tissue. After months marching and eating field rations on the battlefront, many soldiers’ immune systems were weakened and couldn’t fight off infection on their own. Even the army doctors couldn’t do much; microorganisms weren’t well understood and the germ theory of disease and antibiotics were still a few years away. Many soldiers died from infections that modern medicine would be able to nip in the bud.


Some of the Shiloh soldiers sat in the mud for two rainy days and nights waiting for the medics to get around to them. As dusk fell the first night, some of them noticed something very strange: their wounds were glowing, casting a faint light into the darkness of the battlefield. Even stranger, when the troops were eventually moved to field hospitals, those whose wounds glowed had a better survival rate and had their wounds heal more quickly and cleanly than their unilluminated brothers-in-arms. The seemingly protective effect of the mysterious light earned it the nickname “Angel’s Glow.”

In 2001, almost one hundred and forty years after the battle, seventeen-year-old Bill Martin was visiting the Shiloh battlefield with his family. When he heard about the glowing wounds, he asked his mom - a microbiologist at the USDA Agricultural Research Service who had studied luminescent bacteria that lived in soil - about it.

“So you know, he comes home and, 'Mom, you're working with a glowing bacteria. Could that have caused the glowing wounds?’” Martin told Science Netlinks. “And so, being a scientist, of course I said, ‘Well, you can do an experiment to find out.’”

And that’s just what Bill did.

He and his friend, Jon Curtis, did some research on both the bacteria and the conditions during the Battle of Shiloh. They learned that Photorhabdus luminescens, the bacteria that Bill’s mom studied and the one he thought might have something to do with the glowing wounds, live in the guts of parasitic worms called nematodes, and the two share a strange lifecycle. Nematodes hunt down insect larvae in the soil or on plant surfaces, burrow into their bodies, and take up residence in their blood vessels. There, they puke up the P. luminescens bacteria living inside them. Upon their release, the bacteria, which are bioluminescent and glow a soft blue, begin producing a number of chemicals that kill the insect host and suppress and kill all the other microorganisms already inside it. This leaves P. luminescens and their nematode partner to feed, grow and multiply without interruptions.

As the worms and the bacteria eat and eat and the insect corpse is more or less hollowed out, the nematode eats the bacteria. This isn’t a double cross, but part of the move to greener pastures. The bacteria re-colonize the nematode’s guts so they can hitch a ride as it bursts forth from the corpse in search of a new host.

The next meal shouldn’t be hard to find either, since P. luminescens already sent them an invitation to the party. Just before they got got back in their nematode taxi, P. luminescens were at critical mass in the insect corpse, and scientists think that that many glowing bacteria attract other insects to the body and make the nematode’s transition to a new host much easier.


Looking at historical records of the battle, Bill and Jon figured out that the weather and soil conditions were right for both P. luminescens and their nematode partners. Their lab experiments with the bacteria, however, showed that they couldn’t live at human body temperature, making the soldiers’ wounds an inhospitable environment. Then they realized what some country music fans already knew: Tennessee in the spring is green and cool. Nighttime temperatures in early April would have been low enough for the soldiers who were out there in the rain for two days to get hypothermia, lowering their body temperature and giving P. luminescens a good home.

Based on the evidence for P. luminescens’s presence at Shiloh and the reports of the strange glow, the boys concluded that the bacteria, along with the nematodes, got into the soldiers’ wounds from the soil. This not only turned their wounds into night lights, but may have saved their lives. The chemical cocktail that P. luminescens uses to clear out its competition probably helped kill off other pathogens that might have infected the soldiers’ wounds. Since neither P. luminescens nor its associated nematode species are very infectious to humans, they would have soon been cleaned out by the immune system themselves (which is not to say you should be self-medicating with bacteria; P. luminescens infections can occur, and can result in some nasty ulcers). The soldiers shouldn’t have been thanking the angels so much as the microorganisms.

As for Bill and Jon, their study earned them first place in team competition at the 2001 Intel International Science and Engineering Fair.

Thursday, January 2, 2014

Two C elegans Articles and Two Success Cases With The 7-Steps To Cure SIBO

Appears Just Like Human Dysbiosis/SIFO/SIBO
Worms need microbes too: microbiota, health
and aging in Caenorhabditis elegans
Cabreiro, Gems, 2013

Worms need microbes too: microbiota, health and aging in Caenorhabditis elegans.
Cabreiro F, Gems D.
EMBO Mol Med. 2013 Sep;5(9):1300-10.

Worms as Human Aging Models and Worm SIFO/SIBO

Humans are one of the highest form of eukaryotes and worms, the simplest, most elegant.  C. elegans nematodes have nearly the full suite of homolog nuclear receptors, IGF, insulin, and  AMPK pathways. They have a gut microbiota as well and mutualistic health of the microbiota mirrors their longevity.  Careiro and Gems discuss in the above article how bacterial proliferation of the nematode gut highly correlates with reduced immunity and aging.  While the relationship is mutualistic, both microbes and host benefit.  The microbes have a happy home, warmth and food.  For the worm host, the gains are immeasurable -- happy immunity, vitamins/minerals and longevity. One of the best growth media for C elegans is B subtilis, the soil based organism I talk a lot about. When growth media are switched out to bacteria which are less mutualistic (like pure E. coli), the nematodes have a very short life. Blockages of the lumen occur; worm constipation and something analogous to mammalian SIFO/SIBO.  When the media has a natural SBO like B subtilis, the nematodes thrive, have no signs of aging or bacterial proliferation and demonstrate notable worm longevity.  Any intervention in fact that prevents bacterial proliferation (SIFO/SIBO) extends lifespans they reveal.  Makes sense, no?

Two of my favorite probiotics contain B subtilis (Prescript Assist and AMD Syntol). Foods that contain B subtilis include any ancestrally prepared and fermented foods that include both protein and starch: gochujang, natto, fermented black bean sauce, Thai shrimp sauces, etc.

Prior Animal Pharm:

  • Cure SIBO Step #1 Eat Fermented Foods (Guest Post by Tim Steele 'Tater')
  • Korean Pepper Paste [B. subtilis etc] Burns Body Fat, Soil-Based Organisms (SBO), Gut Microbiota -- New Study 'Kochujang, fermented soybean-based red pepper paste, decreases visceral fat and improves blood lipid profiles in overweight adults'
  • Gut I.Q. and the Distal Gut Microbiome as a Driver of Health and Disease
  • Why We Are Sick and Fat: Calories In (SUPERORGANISM) = Calories Out (MICROBIOTA) + Calories Out (HUMAN) + HEAT*Fluxxx

Gut microbiota as a candidate for lifespan extension: an ecological/evolutionary perspective targeted on living organisms as metaorganisms.Ottaviani E, Ventura N, Mandrioli M, Candela M, Franchini A, Franceschi C.
Biogerontology. 2011 Dec;12(6):599-609.

Worms, Change in Hunter-Gatherer Existence and Extended Families

The second article discusses how in the Neolithic only 10,000 years ago, humans were faced with even more pathogens than ever by living in close quarters with both other humans and livestock.  Without a resilient immune system and evolving gene polymorphisms, we could not have survived.  "With the introduction of agriculture and animal husbandry, food resources became more abundant and constant and, for the first time in human history, the population size dramatically increased." The authors theorize that if it were not for improved immunity via the gut microbiota humans would not have been able to the endure the high antigenic and pathogen load.  I think this is true.  The lectins and phytates from dietary sources were one challenge and the pathogens like worms, malaria, plague, mites, and other fun things were yet another hurdle. Hemochromatosis, cystic fibrosis, increased salivary alpha-amylases might have been some of the adaptations that survived.

"The support of grandmothers in the nourishment of children allowed more pregnancies in the daughters, and thus a greater reproductive fitness."   Having two children myself, I can support their theory that post-menopausal female longevity was certainly favored for perhaps many reasons including processing grains (soaking, fermenting), preparing fermented vegetables and foods, farming and other tasks for feeding young, dependent children.  There were so many tired nights raising the little kiddies. Certainly, I would not have been able to survive the post-natal years without my children's grandparents from BOTH SIDES. LOL

"Furthermore, symbiont intestinal microorganisms provided a strategic fitness advantage for the human beings living the Neolithic agricultural revolution by protecting the host from pathogen colonization and enhancing the plasticity of the immune system. Finally, dietary change in the Neolithic agricultural societies due to agricultural practice likely induced a substantial re-adaptation of GM [gut microbiota], favouring microbial communities capable to ferment these new complex polysaccharides to short chain fatty acids (Hehemann et al. 2010)."

Who are your symbionts? Are they extinct? Do you respect them? Are you doing things that favor their growth?   Have you weeded? Seeded your gut microbiota? Feeding and breeding your symbionts in luxury and abundance?

Success Cases with SBO Probiotics and the 7-Steps
I'm grateful for Tim and Richard at FTA for starting the conversations on gut ecosystems, fiber and health optimization.  Thanks for directing people over here to the 7-Steps To Cure SIBO/SIFO.

Happy New Year to my kind readers~!!  Thank you for sharing your wonderful stories.  I love U and love hearing them all.

Case A: After 3 weeks of SBO + FIBER/RS + Gut Rehab -- Reversal of Sjogren's Auto-Antibodies (Chromatin, SSB-LA, ANA)
Anonymous was taking 3 months of PS but no changes until SBO probiotics were taken. In only 3 weeks with taking Primal Defense and Prescript Assist three times per day, she reported her autoimmune Sjogren's disease to be completely 100% 'cured'.  Three noxious auto-antibodies (SSB-LA, Chromatin, ANA) normalized or returned to near normal.
"My fingernails are clear and my cold fingers are gone. Oh, I didn't want to tell you this just yet. But my Sjogren's antibody (SSB-LA) turned negative last week! That's after being on the RS/Probiotics regimen for only 3 weeks! I was on RS since August, however. Also, one of the incipient lupus antibody that I tested positive (Chromatin) turned negative this time! My ANA is positive but with very low titer (1:40). That's the lowest I ever tested and even normal people test at that level. My rheumatologist will be confused!

If this holds up, and I'm hoping it does, I have cured an autoimmune disease. No symptoms and no antibody: that's a 100% cure. Not just remission. Being antibody-negative is not supposed to be possible, right? Whither molecular mimicry and eternal damnation, I mean, eternal autoimmune tissue attack? You mean, that's contolled by the microbiome, too? So much for Dr. Fassano and leaky gut (which I now realize seem to have been a foil ... it happens but the underlying condition seems to be gut dysbiosis and bacteria).

Wow, I gotta try this on my aunt who also has Sjogren's and my cousin who has Lupus. Thanks so much guys. This is not what modern medicine says is possible!"

Case B:  After SBO, Fermented Food + FIBER/RS + Gut Rehab -- Reversal of Pain, Poor Mood, and Fibromyalgia
From Alexander Hardy (Ajmhardy)
"Just thought I’d add to the noise here- I’ve had a set of health problems that differs from most people using RS on this site, namely persistent and intense anxiety, as well as adrenal and sleep problems due to going VLC for a few months. I’ve also had fibromyalgia for the past year now, and I could not get it to go away for the longest time. After reading Richard’s and Tim’s posts here, I added RS to my diet (which already included fermented foods, good meats, and lots of vegetables), and my symptoms have started to improve for the first time since I started feeling the pain.

They have not gone away completely yet, but my mood and the pain have gotten so much better that for the first time in a year, I completely forgot I had fibromyalgia yesterday for almost the entire day. I cannot thank you guys enough for putting in the tremendous amount of work that you do to spread the word about resistant starch... 

A note to anyone who may be reading this in hopes of helping their fibromyalgia- it took me a solid month of having dr bg.’s bionic RS and straight potato starch (total 8 TSP potato starch a day) to finally feel the pain subside, and I would guess it could take some people many months to get the same relief I got, depending on the state of their gut.

So don’t give up if this doesn’t work within a month, and make sure to include the things that I consumed before I added the potato starch- dulse (for iodine), vitamin d and K supplements, as well as N-acetylcysteine , sauerkraut, kimchi, gochujang, variety of greens and other veggies, sweet potatoes and potatoes, magnesium and zinc supplements, prescription assist, and fish oil pills."

--Ajmhardy // Dec 24, 2013 at 23:31

Wednesday, December 18, 2013

Crowd-Sourced Science n=4

Allan Folz's Gut Microbiome Study, n=4

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
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

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

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

Thursday, December 5, 2013

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???

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)


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)

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?

 --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

--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


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


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.

Saturday, November 30, 2013

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) (Guest Post: Tim/TATER)

Photo credit: Heritage J. Nature, 2004.

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

Guest Post: Tim Steele (aka Tatertot)

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 [GRACE: Tiramisu was delicious, thanks Tim! And my tight gut thank RS + SBOs!], you need to stay away from anything that resembles a Krispy Kreme donut!

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!


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?”

My second Google search turned up another amazing article by the same amazing author [GRACE:  TWICE FUNNY]…
“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 [GRACE: Thrice!]:
“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.”

[Thanks Tim~!! Read more: Geneticist David Suzuki Says Humans “Are Part Of A Massive Experiment” Hat tip: Todd LePine]

Do dietary lectins cause disease?
Freed DL.
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