Gut Flora, Disease and Obesity

---the other 200 posts---

The health of your gut flora (the interacting trillions of bacteria of a couple of hundred different species that make up the pound of bacteria that you carry primarily in your large intestines) is more important than your genetics to your overall health.  Thus, your health is a result of diet, gut flora adapted to your diet and exercise.  Everything else, your genetic risks, environmental toxins, etc. are of only minor impact.

I am trying to paint the big picture of how the food that you eat and your gut flora interact to determine your health, by which I mean whether you get sick, become obese and/or bloat with gas.

Health Depends on Gut Flora

If you are healthy, you have a couple of hundred different species of bacteria that help you to digest the protein, fats and carbs that you eat in meat and vegetables.  Your body easily digests protein and fats in meat, fish, eggs and dairy, because enzymes to digest them are present in your stomach and small intestines.  The only carbs that your body can digest are some simple sugars and starch.  The rest of the polysaccharides present in plants cannot be digested without the help of bacteria.  The polysaccharides that your gut flora can digest are fermentable, soluble fiber, e.g. resistant starch, pectin, inulin, arabinogalactan, xylans, beta-glucan, etc.  If you can’t digest soluble fiber, because you have damaged gut flora, dysbiosis, and are missing essential bacterial species normally found in a healthy gut, then the soluble fiber just passes through as insoluble fiber and readily dehydrates into hard, constipated stools.  Partial digestion due to just a few missing bacterial species produces the symptoms of food intolerances.  

Constipation Results from Dysbiosis

The bottom line is that the volume of healthy, soft, firm stools is made up of gut flora that digested dietary soluble fiber and converted it into more bacteria.  If you eat more soluble fiber, this food for your gut flora, will produce proportionately more bowel movements.

Gut Flora Guide Immune System Development

Most of cells of your immune system are in the lining of your gut and there are particular species of gut bacteria directly involved in the development of immune cells that have different functions as they spread throughout your body.  Some of these cells are aggressive and attack pathogens, while others make sure that the aggression doesn’t get out of control and cause autoimmune diseases or allergies.

Gut Flora Divided into Groups to Show Involvement in Disease

Recent studies have demonstrated the role of gut bacteria in producing nutrients, vitamins and neurotransmitters.  To highlight the essential role of gut flora in disease, I have divided the hundreds of species of gut bacteria into groups to illustrate their direct involvement in development of the immune system and regulation of the flow of dietary nutrients involved in obesity.  A recent study shows that an infection can produce a change in gut flora associated with marshaling additional fatty acid nutrients for the host instead of just producing more gut flora.  Chronic change of gut flora in this way leads to obesity.  Other types of dysbiosis contribute to infections, cancer, autoimmune disease, allergies, food intolerances, gas and bloating.

Group A Bacteria  Provide Aggressive Immunity

There are several dozen species of bacteria in healthy gut flora, including the filamentous bacteria, that trigger the development of the aggressive part of your immune system that attacks pathogens, and kills cells of your body that are infected with viruses or are cancerous.  Most antibiotics don’t permanently damage this group of bacteria, so after a course of antibiotics you can usually still stop infections.  Excessive suppression of aggressive immunity contributes to cancer.

Group B Bacteria Provide Suppressive Immunity

There are dozens of other species of bacteria, including Clostridia, that control the development of the suppressive half of your immune system that produces immune cells, such as regulatory T cells, Tregs, that stop the aggressive cells of your immune system from attacking your own cells and innocuous things such as food and pollen.  Many common antibiotics damage these species of bacteria and are thought to contribute to the development of autoimmune diseases and allergies.  Inflammatory bowel disease is characterized by a simplified gut flora with only half the healthy number of bacterial species.  Resistant starch preferentially feeds these bacteria to enhance suppressive immunity and in some individuals cure autoimmune disease.

Group C Bacteria Convert Soluble Fiber to Short Chain Fatty Acids (SCFA)

The fermentable soluble fiber in your diet is typically from vegetables and it is converted by the largest and most diverse group of bacterial species into short chain fatty acids.  Each different plant polysaccharide, and there are hundreds, requires many enzymes for complete digestion to the simple molecules used by the bacteria to make its own proteins, fats and polysaccharides.  Absence of bacteria that are specialized for the digestion of particular polysaccharides or other dietary components can disrupt gut flora and cause digestive disturbances that are experienced as food intolerances (also confused with food allergies that are rare.)  Some of the bacterial species convert polysaccharides into butyric acid and other short chain fatty acids that are the major source of energy for cells that form the lining of the intestines.  These SCFAs are also a major food source for other gut bacteria.

Group D Bacteria Convert SCFAs to Fecal Bacteria to Produce Bulk of Bowel Movements

In healthy people, the SCFAs produced by gut flora feed the intestines and the remainder produced in the large bowel is converted into more gut bacteria, which forms soft stools.  Antibiotics typically damage these bacteria and result in constipation.  These bacteria are typically more sensitive to antibiotics than those that digest the soluble fiber and produce SCFAs, so the excess SCFAs pass into the blood stream and contribute to obesity instead of stools.  Lean mice with gut flora exchanged from obese mice, become obese.  Cattle are fed antibiotics to enhance the conversion of corn polysaccharides into SCFAs and body fat prior to slaughter.

Group E Bacteria convert Soluble Fiber to Methane and Hydrogen, Bloat

Increased volume of the intestines, bloating, results from conversion of soluble fiber into methane, hydrogen and carbon dioxide gases.  Some of this gas is absorbed into the blood and can pass from the large intestines, through the blood, and back to the stomach and small intestines.  Helicobacter pylori, the cause of stomach ulcers and gastric cancer, can utilize hydrogen from the blood as an energy source.

In Summary:

A+B+C+D = healthy, normal weight

A+C+D = normal weight, autoimmunity and allergies

B+C+D = normal weight, susceptibility to cancer, chronic Lyme disease, food poisoning

A+B = normal weight, constipated

A+B+C = obese, constipated

A+B+D = normal weight, food intolerances

A+B+C+E = obese, constipated, bloated

Cure for Dysbiosis and Associated Diseases is Repair of Gut Flora

The excitement about the use of resistant starch (RS) and probiotics with Clostridia and other soil bacteria to reverse the symptoms of autoimmune diseases is based on the ability to repair gut flora damaged by poor nutrition and antibiotics.  Low carbohydrate diets that do not provide soluble fiber to feed gut flora lead to dysbiosis and chronic diseases.  Resistant starch, as the name suggests, passes on to the colon by avoiding digestion with amylases in the small intestines and acts as a soluble fiber to feed gut flora in the colon.  Clostridia convert the RS to sugars and SCFAs usable by other gut flora.  Note that some species of Clostridia produce toxins and it is these pathogens that take over in hospitals after the healthy species are killed off with antibiotics.  Fecal transplants are the best treatment for these hospital acquired infections. 

 I have discussed the role of hygiene, muddy veggies, fermented foods, etc. in several other posts on repair of gut flora.  

Complete repair of gut dysbiosis is possible, but it requires more than just changes in diet and dairy probiotics, as typically recommended erroneously by the medical industry.

Health is dependent on:

1. an Anti-Inflammatory Diet,
2. gut flora adapted to your diet
3. exercise and
4. adequate sleep

The rest (genetics, vegan vs. paleo, environmental toxins, organic veggies, GMOs, etc.) are minor contributors, less than 10% in aggregate, to overall health.

ref.

Gut microbiota composition correlates with changes in body fat content due to weightloss 

Dr. Oz Diet and Gut Flora Myths

….All 190 posts here….

I just watched a Dr. Oz program on health myths, including corrections, such as recognition of the high fructose content of agave syrup (especially bad for diabetics.)  So I thought I would go ahead and correct some of the perspectives on his show that I don't think are supported by biomedical research.

The Big Truth about Diet and Gut Flora

Health results primarily from a matched Diet AND Gut Flora, with minor contributions by exercise, personal genetics, environmental toxins, etc.  You can eat the extremes of just meat or only vegetables or any mixture and be healthy, as long as your gut flora is made up of about two hundred different species of bacteria that can fully digest the soluble fiber in your diet.  Health requires a gut flora adapted to your diet.  Those bacteria, the gut flora, produce all of your needed vitamins, eliminate constipation, block inflammation and control the development of your immune system, which takes place in the lining of your intestines in response to gut bacteria.

Assorted Health Truths

Truth:  Saturated fats are healthy, but polyunsaturated omega-6 vegetable oils are inflammatory.  Oz can't bring himself to read the literature and acknowledge the heart benefits of saturated fats and meat.

Truth:  Soluble fiber, e.g. pectin in fruit or inulin in leeks or chondroitin in meat, is healthy food for gut flora, but insoluble fiber, such as in whole grains is a scam and just sucks out micronutrients.  Oz could really help the public by explaining that the hundreds of different polysaccharides produced by plants, i.e. soluble fiber, are digested by hundreds of different enzymes in gut flora.  Gut flora digest soluble fiber into sugars that are converted into short chain fatty acids that feed intestinal cells.

Truth:  GMOs have been studied intensively, are relatively boring and healthy, but organically grown veggies have not been shown to provide any additional health benefits over conventional.  Oz adheres to a very political line and attacks GMOs without any reasoned arguments and touts organic veggies without reference to supporting research.

Truth:  Grass grown beef has healthier fats with more omega-3 oils, but omega-3 plant oils, such as ALA in flax, provide only minor benefits and can't substitute for the long chain DHA and EPA in fish/algae oil.  Oz keeps pushing flax seed even though the benefits are minimal and the problems of high insoluble fiber have not been tested.

Truth:  Constipation is a sign of unhealthy gut flora and can lead to autoimmune disease, allergy or food intolerance, but laxatives such as magnesium only fix the symptoms and not the missing essential gut bacteria.  Oz is really confused about constipation and focuses on dehydration rather than the bacterial content of stools.

Truth:  Antibiotics may be essential for surgery or life threatening bacterial diseases, but antibiotic-damaged gut flora must be repaired (not just probiotics) or the immune system will be compromised.  Antibiotics are major contributors to autoimmune disease and I don't think that Oz realizes the damage that he starts or continues by not repairing gut flora after he repairs hearts.

Truth:  Dairy probiotics, e.g. Lactobacillus or Acidophilus, can provide a quick fix for some functions of gut flora, but these limited probiotic bacteria do not survive in the gut and do not substitute for normal gut bacteria.  I think that Oz still sends his patients home with yogurt after heavy antibiotic treatment and leaves his patients with damaged gut flora and long term disease risk.

Truth:  An Anti-Inflammatory Diet can reduce sources of inflammation that is the foundation for cancer, autoimmunity, allergy and most diseases, but adding new bacteria (not dairy probiotics) through social contacts and live fermented foods is essential for a healthy gut and immune system.

Truth:  All needed vitamins are supplied by healthy gut flora (as biofilm chemical signals) and healthy people do not benefit from multivitamin supplements, but people with damaged gut flora, e.g. because of antibiotic use or autoimmune disease, may require specific vitamins.

Truth:  Antioxidants are just plant defense chemicals, i.e. plant antibiotics, that are unimportant in general health, but they may alter gut flora in unpredictable ways.  Oz likes all antioxidants, but can't explain why these generally toxic chemicals are not used by plants as antioxidants.

Truth:  All of the vitamin D that we need is supplied by minimal skin exposure to sunlight, but most Americans are vitamin D deficient, because chronic inflammation blocks solar production of vitamin D in the skin.  Oz doesn't seem to understand the role of inflammation in vitamin D deficiency.

Truth:  We don't need Grains and other sources of starch, but grains also typically cause health problems, e.g. sensitivity, intolerance or celiac, for most people and can cause inflammation of the gut and disruption of the gut flora that can lead to autoimmune diseases.  Most thyroid disease and back problems are autoimmune diseases that start with celiac.  Oz still promotes whole grains even though added bran lowers nutritional quality and many people are healthier without grains.  He also seems to ignore the relationship between grain, antibiotics and autoimmune disease.

Truth:  Breakfast is not a necessary meal and there are health benefits to lengthening the time between the last and first meal of the day, but if breakfast is eaten, it should be low in sugar and starch, i.e. avoid cereal, since cereal causes a severe spike in insulin when eaten after a fast.  Breakfast makes you hungry, because even protein in the morning will raise insulin and cause an eventual abrupt drop in blood sugar that is experienced as hunger.  Why does Oz believe in breakfast?

Truth:  Food intolerances and allergies (rare) are due to missing species of gut bacteria, but these eating problems cannot be fixed by diet alone, since new bacteria (other than dairy probiotics) must be eaten.  Dairy probiotics are only useful to cure lactose intolerance.

Truth:  Hygiene should be minimal, because most people repair damaged gut flora due to antibiotics, for example, by intimate contact with friends and pets.  Antimicrobial soaps and sterile home surfaces prevent gut flora repair, because the vast majority of bacteria killed by hygiene are beneficial.  Appropriate hygiene is a real problem for Oz and he is obsessed with closing toilet covers.

Truth:  Cardiovascular disease starts with inflammation and is aggravated by fat deposits, but statins and lowered serum cholesterol only reduce heart attack risk, because statins have a weak side effect of lowering inflammation.  Diet changes and repair of gut flora, e.g. my Anti-Inflammatory Diet, fish oil supplements and wild fermented foods, are much more effective at reducing inflammation and curing cardiovascular disease without the severe risks of statins.  Oz is slowly becoming skeptical of statins, but still hasn't read the research literature critically.

Truth:  Poor health and most diseases have only minor genetic risk factors, but diet and gut flora are "inherited" directly and shared by the whole family.  When your doctor asks what diseases run in your family, she is asking about your shared gut flora.  Oz still gives the impression that genes are significant in disease and for example asks audience members if relatives have had heart disease.  He should tell them to repair their gut flora!

Summary Diet Truths

Truth:  There is nothing magic about healthy foods.  All that is needed are protein (meat, fish, eggs, dairy, beans, etc.; plant and animal proteins are equivalent), fats (from leaf and meat, not omega-6-rich seeds) and soluble fiber (to feed gut flora) from their original sources to retain naturally abundant micronutrients (vitamins, except C, are usually unimportant.)  That is my Anti-Inflammatory Diet and supplements should not be needed.  Natural, local foods are healthy, but there are no super foods and exotic does not mean better.  Variety does not compensate for low quality.  Your gut flora needs time to adjust, especially to new soluble fiber, so just change foods with the seasons, not daily, and make sure that you are sampling new bacteria in live fermented foods to make your gut community adaptable.

Dr. Oz’s Pain: Constipation and Bursitis

Dr. Oz has complained several times about his constipation and the pain he feels in his shoulders during surgery.  He has recommended numerous treatments.  Since I feel a friendly affection toward Mehmet after talking/shouting at his image on the screen for hours, I think that I should give him some advice to relieve his pain.

Hot, Cold, Topical Treatments Are Effective, but Don’t Penetrate Themselves

Dr. Oz keeps talking about how various topical applications penetrate the skin.  He has even recommended the use of an electrical system to carry pain relieving steroids into his tissue by what looks to be electrophoresis.  This is dubious.  I would recommend that he stick to the topical chemicals, e.g. capsaicin, menthol, that target the hot and cold sensors of the superficial layers of the skin and result in deep penetrating nerve signals that trigger anti-inflammatory responses in the underlying bursa.

Constipation Is Caused by Damaged Gut Flora or Dysbiosis

Dr. Oz, like most physicians, does not usually explain the causes of diseases, such as bursitis.  Unfortunately, when he tries to explain problems, such as constipation, he overlooks important aspects of the problem for a facile physical model.  In the case of bursitis, it is important to realize that the patient, Dr. Oz, is also constipated.  Constipation can be aggravated by dehydration or “holding it”, but in Dr. Oz’s case, the combination of bursitis, an autoimmune disease, with constipation (and gas) suggests the more complete explanation of dysbiosis or damaged gut flora.  Dysbiosis is what causes constipation, because bowel stools, poop, is mostly packed, hydrated bacteria that grow in the colon by digesting soluble fiber.  If you eat an apple a day, there is enough pectin and other plant polysaccharides, i.e. soluble fiber, to increase the volume of the stools to make one regular.  [Don’t be confused by the misconception promoted by Dr. Oz that the volume of stools results from insoluble fiber, such as in whole grains.  The husk part of whole grains is useless or unhealthy and grains in general are not needed for a healthy diet.]  

Flush Toilet Hero

Dr. Oz’s constipation suggests a damaged gut flora.  Since he is a physician, one would suspect that he has used antibiotics in the past few years and wiped out essential types of gut bacteria.  Dr. Oz probably followed his own advice and attempted to patch up his damaged gut flora with probiotics.  Unfortunately, as I have repeatedly explained, dairy probiotics don’t survive in the gut and cannot repair damaged gut flora.  But Dr. Oz is even harder on his gut flora.  He has recommended the use of colloidal silver throat spray when he has been exposed contagious germs.  Silver, although ineffective for its intended use, is very toxic to gut flora after it is swallowed.  Dr. Oz also subscribes to numerous approaches to house and body hygiene, which are probably occupational hazards for surgeons.  Hygiene is the enemy when it comes to ingesting bacteria lost to antibiotics.  The atomizing flush toilet is my gut flora hero for spreading contagious health.

Damaged Gut Flora = Damaged Immune System

Constipation is bad enough, but damaged gut flora can mean that some of the bacteria needed for the gut-based development of cells regulatory T-cells (Tregs) that keep the immune system under control, are missing.  Constipation can lead to deficient Tregs and that means a major predisposition to autoimmune disease and allergies.  [Fecal transplants cure autoimmune diseases and allergies.]  Antibiotics, silver, hygiene excesses and constipation suggest to me that Dr. Oz has been cruising toward some rude immunological sequelae.

Autoimmunity Results From Antibiotics, Dysbiosis and Compromised Tregs

Autoimmune diseases result when a trifecta of inflammation, compromised Tregs and appropriate antigens occurs.  Normally physical damage, such as abusive shoulder exercise, results in inflammation as the first step in healing.  The inflammation can rev up the immune cells in the local area of tissue damage and some of the proteins, such as lubricin, which lubricates the bursa, may have basic triplet amino acid sequences that lead to presentation to immune system cells.  But no antibodies against self tissues are produced, because the Tregs stop the process.  Healthy gut flora produce healthy Tregs and block autoimmunity.

Dr. Oz abuses his shoulder bursa during surgery, but it can’t heal properly, because he has damaged his gut flora and compromised his Tregs.  The result is the autoimmune bursitis from which he now suffers.  He can reduce the symptoms and inflammation with topical anti-inflammatory natural chemicals, but he needs to repair his gut flora to repair his Tregs and reduce autoimmunity.  In the mean time, he is contaminating his local environment, family and friends with his unhealthy bacteria.  I wonder if Dr. Oz’s friend, Dr. Mike Roizen also suffers from autoimmune diseases?

Prescription to Repair Gut Flora:  Anti-Inflammatory Diet, Soluble Fiber, Fermented Vegetables, Less Hygiene

KEEP YOUR TOOTH BRUSH NEAR THE OPEN TOILET 

Antibiotics, Gluten, Hashimoto's Thyroiditis and Baldness

My impression is that Hashimoto's is caused by a combination of an initial immune attack on the thyroid and incompetent regulatory T cells.  In most cases the immune attack on the thyroid is a secondary consequence of celiac/gluten intolerance, in which anti-transglutaminase antibodies attack transglutaminase bound to gluten in the intestines.  Transglutaminase  is an enzyme that is also produced by the thyroid (and hair follicles) and attack by celiac antibodies can enhance or inhibit thyroid hormone production (or baldness.)  Both Hashimoto's and celiac do not occur if the suppressive part of the immune system, i.e. regulatory T cells, is functioning.  

Antibiotics Compromise the Immune System

The major point here is that antibiotics disrupt normal bacterial biofilms that line the intestines and these healthy gut bacteria are required for development of regulatory T cells.  Compromise of Tregs leads to autoimmune diseases, e.g. celiac, Hashimoto’s and baldness, and also allergies.

Antigens/Allergens Have Basic Amino Acid Triplets

The antigens targeted in autoimmune diseases, e.g. tTG, anti-nuclear, TPO, and allergies form an obvious pattern.  All of these antigens and allergens have simple amino acid sequences (rare patches of three basic/positively charged amino acids) that enhance their presentation to the immune system to produce antibodies.  Nuclear proteins, for example, are frequent autoantigens and most of these proteins interact with nucleic acids (negatively charged) and have predictable patches of positively charged amino acids (arginine and lysine).  Other common autoantigens have basic amino acid (arg/lys) patches, because they interact with phospholipids (also negatively charged.)  Proteins with basic patches, e.g. HIV-TAT or heparanase, are also readily transported into cells and nuclei.  Peptides with these sequences are produced by action of stomach enzymes on proteins, e.g. milk lactoferrin, and are antimicrobial.

Allergies / Autoimmune Diseases Are a Predictable Consequence of Antibiotics

Doctors treat with antibiotics, but they fail to repair damage that they cause to gut flora.  The gut flora of most patients treated with antibiotics, especially those who are most fastidiously hygienic, never fully recover.  Constipation is a common symptom of severe dysbiosis and related immunoincompetence.  Probiotics are gut flora bandaids and do not survive as components of gut flora.

Gut bacteria are also needed for development of the aggressive part of the immune system.  Thus, autoimmune diseases can be treated with even more intense use of antibiotics, that will eliminate the rest of the immune system.  Since all vitamins are produced by gut flora as quorum sensing signals, antibiotics can also produce the exotic symptoms of vitamin deficiencies.

Antibiotics are essential to many therapeutic approaches, e.g. surgical procedures or therapy for chronic Lyme disease, but they must be used responsibly and treated patients must be subsequently tested to ensure a repaired gut flora and a functional immune system have been reestablished after antibiotics.  Long term antibiotic use needs special attention, e.g. deliberate Repair of Gut Flora or a fecal transplant.

Thus, I think that it is most likely that ever increasing antibiotic exposure and processed foods, coupled with obsessive hygiene have led to crippled gut flora (as observed in the simplified gut microbiomes of Americans), a net decline in suppressive Tregs and the observed increase of autoimmunity and allergies.  The competence of the immune system may be a major determinant in the course of infection with a pathogen that can produce chronic infections.

Vitamin C, Guinea Pigs, Limeys and Gut Worms

Scurvy and the Need for Vitamin C

Old timey sailors got the symptoms of scurvy, defective collagen and connective tissue, presumably because they stopped eating leafy greens that contained the needed vitamin C, aka ascorbic acid.  Primates/humans and guinea pigs are among the few animals that lack the ability to make their own ascorbic acid and therefore must eat a diet with a minimum amount of the vitamin to avoid a deficiency disease.  This is the conventional wisdom partially based on observation and experiment, but also founded on conjecture.

Parasitic Gut Worms Were the Natural Source of Vitamin C

I don't believe that vitamins are essential ingredients of a healthy diet, but rather I contend that all of the necessary nutritional chemicals are produced by the microorganisms of the gut.  I have previously discussed the gut flora (bacteria and fungi) as the source of most vitamins.  I wish to expand vitamin production to include gut fauna (animals).  I think that it is likely that intestinal worms are the historically natural source of human vitamin C.

Gut Bacteria Control the Development of the Immune System

The human gut actively communicates with the biofilms of bacteria and fungi that form a lining for the healthy gut.  The aggressive cells of the immune system that attack invading pathogens, develop in response to chemical signals from filamentous gut bacteria, and the suppressive cells of the other half of the immune system, which prevents attack on innocuous food antigens (to avoid allergies) or the human body itself (autoimmunity), develop in response to Clostridium ssp.  Thus, the immune system can be highly compromised, if the gut flora bacteria are damaged, e.g. by antibiotics.

Vitamins are Signaling Chemicals of Gut Biofilms

The communities of bacteria in gut biofilms are self-regulating by exchanging chemicals called quorum sensing signaling molecules.  Different species of bacteria and fungi in the biofilms produce and detect different chemical signals.  Since the biofilms are in intimate contact with the cells that line the gut and absorb dietary nutrients, it is not surprising that the biofilm signaling molecules are also absorbed by intestine cells.  Many of these biofilm signal molecules are vitamins, e.g. the B vitamins.  Gut bacteria are the natural source of most vitamins and healthy gut flora eliminates the need for eating vitamins in food or supplements.  Vitamin deficiencies are a symptom of a damaged gut flora.  Antibiotics and vitamin supplements can damage healthy gut biofilms.

Dietary Soluble Fiber Feeds Gut Flora

The human gut flora consists of a couple of hundred different species of bacteria in each person.  Those bacteria in aggregate can produce about a hundred thousand different proteins that focus on the digestion of food molecules that the upper gut cannot digest and absorb.  Since the upper gut can only digest proteins, fats and starch/sugars, that means that the gut flora eat the rest, undigested plant/animal polysaccharides.  Soluble fiber is the plant polysaccharides, e.g. inulin and pectin, that are digested and feed the gut flora.  The undigested polysaccharides include cellulose.  Lignin and some other plant polymers also pass through the gut and are eliminated.  The undigested stuff is called insoluble fiber and it also has bound phytate, which drags some metals such as zinc out with it.  That is why insoluble fiber, such as wheat bran, is not nutritious or healthy.  Insoluble fiber is also a minor contributor to the bulk of stools, which are made up predominately of the gut bacteria that have grown on soluble fiber.

Sea Voyages Damage Gut Organisms

The hundred of different species of bacteria in the gut change in proportions to adapt to different foods in each meal.  If the diet is fairly constant, then the diversity of the population gradually increases, just as the diversity of species in a tropical rain forest is greater than in a temperate forest.  This also explains why gut flora diversity is far less in the USA than in other parts of the world.  Americans are encouraged to eat diverse diets in the search for vitamins and superfoods.  Each dramatic change in diet makes it hard for the gut flora to adapt and the remaining bacteria are those that are generalists.  It might also be expected that early sailors who changed their diets dramatically when they went to sea, ended up with a highly compromised ship-board gut flora (and fauna.)

The Perils of Hygiene

I have a fascination for stories involving the potential of rampaging tigers.  Images of a tiger attempting to drag a hunter from his seat on an elephant or the need of a colleague to employ an armed bodyguard when capturing crabs from Malaysian Mangrove roots at night, linger in my imagination.  I still think about the report of Wallace guarding his derrière while collecting beetles in Bukit Timah, Singapore, in “The Malay Archipelago.”  Humans tend to be incompatible with lions and tigers and bears, and we wipe them out.  We do the same with bacteria, fungi and worms.  We wash our hands, flush the toilet, use hand sanitizers, kill weeds, spray pesticides, grow meticulous lawns/crops, dose ourselves with antibiotics and cleanse.  We are free of the threat of tigers, but we failed to see what else was lost during their extermination.

Probiotics Don’t Fix the Damage of Antibiotics

Antibiotics ravage gut flora.  It is no surprise that a course of antibiotics frequently leads to diarrhea or constipation, since normal stools require normal gut flora.  What is surprising is that physicians, e.g. Dr. Oz, seem to think that antibiotic decimated gut flora can be fixed with probiotics.  Sure, probiotics can provide a temporary bandaid, since Lactobacilli that would normally live on milk in the gut of newborns, are able to provide most of the functions of an adult gut flora.  But probiotics don’t survive in the adult gut and probiotics to not repair damaged gut flora.

Changes to Gut Flora are Permanent, Unless....

Gut bacteria are like wolves in Idaho.  If you don’t bring in new wolves and stop hunting them, you never again have wolves in the wilderness.  If you don’t bring in new bacteria and feed them, damaged gut flora does not repair.  Antibiotic treatment that wipes out the bacteria needed for development of the suppressive immune system will lead to autoimmune disease.  However, repairing the gut flora by flushing in new bacteria (fecal transplant) or gradually reintroducing new diverse bacteria with fermented foods, can also reverse autoimmune diseases as the immune system is repaired.

Parasitic Worms Were Lost at Sea

We think that vitamin C is only provided by plants that we eat, because we didn’t notice what was lost when we cleaned out the worms that typically inhabit the human gut.  Who would have thought that those inconvenient creatures were there for our own good?  We unknowingly compensated for the lost vitamin C production of the worms by incorporating foods rich in vitamin C in our diets.  Shipboard diets that eliminated bowel worms were augmented with limes rich in ascorbic acid.

Guinea Pigs Also Need Worms

It is interesting to note that the experimental animal used to replicate human nutritional requirements for vitamin C is the guinea pig, which is one of the few animals (in addition to bats and primates) that doesn’t make its own.  It is also interesting that guinea pigs (and bats?) commonly have intestinal worms that have to be purged from their bowels before they are used in the lab. 

Gut Flora and Fauna Provide Vitamins

My bottom line is that a normal, healthy gut contains all of the bacteria, fungi and worms to supply all of the needed vitamins.  I do, however, think that dietary vitamin C is a good replacement for one function of intestinal worms, even though I will be watching for other benefits ( Helminth therapy?) that were lost with the removal of these parasites.

Some points:

•   Many vitamins are signal molecules for gut biofilm quorum sensing.
•   Intestinal worms are the typical source for human vitamin C.
•   Vitamin D is a hormone produced in the skin in response to sunlight.
•   Vitamin supplements are unnecessary (problem?), if gut flora and fauna are healthy.
•   Modern diets and hygiene eliminate gut parasites, so food needs to supply vitamin C.
•   Chronic inflammation consumes vitamin C and eliminates production of vitamin D.

Contagious Health

Healthy gut flora: bacteria from family, friends, Fido and food provide the foundation for the complex microbial community of the intestines, which controls the immune system.  Antibiotics and hygiene are detrimental to gut flora and health.

Gut Flora Are Complex

Recent studies of the gut flora, e.g. the human gut biome, show that each individual maintains more than 150 different species of bacteria.  Worldwide, that means that about a thousand different bacterial species are common residents of the human gut and together those gut bacteria use more than 1 million different genes.  Many of those genes code for the enzymes used by gut bacteria to digest plant polysaccharides, i.e. soluble fiber.

Hygiene Isolates People from Healthy Sources of Gut Flora

Every time we speak, we release a mist of bacteria from our lungs, mouth and GI tract.  These bacteria are on our skin, clothes and personal items, and provide a source of the bacteria that make us healthy.  Parents and older siblings pass these bacteria on to younger children.  These donated bacteria are essential for the development of a healthy immune system and children growing up with healthy relatives and exposed to soil bacteria via pets, farm animals, etc. are healthier than children who are more isolated.  

In this sense, hygiene is unhealthy, because an individual is isolated from new sources of bacteria that could replace those lost by limited diets, antibiotics, etc.  Otherwise, health is contagious, since gut bacteria from healthy individuals can spread among the population.  Washing hands and food is unnatural and unhealthy.

Few Bacteria Make You Sick, but Many Are Essential for Good Health

Food intolerance can result from “good” family hygiene, limited diets and exposure to antibiotics.  A common intolerance results from the absence of bacteria that produce an enzyme to digest dairy lactose, i.e. lactose intolerance.  Lactose intolerance can be readily cured by eating a dairy product, such as yogurt, that contains both lactose and live bacteria (probiotics) that can digest the lactose.  Simply eating moderate amounts of live yogurt daily for a couple of weeks resupplies the gut flora with bacteria that can digest lactose, and the intolerance is gone.

Soluble Fibers Are Plant Polysaccharides that Are Digestible by Bacterial Enzymes

Humans only produce enzymes to digest one polysaccharide, starch.  All of the other hundreds of polysaccharides present in plants are only digestible by bacterial (and fungal) enzymes of the gut flora.  If the bacteria and enzymes needed to fully digest a particular food polysaccharide are absent, then digestive problems ensue and the polysaccharide can act as a laxative.  Continual eating of the problem food with a new source of diverse bacteria, e.g. lightly rinsed vegetables right from the garden, then the gut flora will incorporate new bacteria that can digest the problem polysaccharide and the gut is happy.  

Soluble fiber feeds the gut bacteria that convert it into short chain fatty acids that nourish the colon. Constipation results from the absence of the bacteria needed to digest dietary fiber and to produce the large volume of bacteria that make up well hydrated stools. 

Gut Bacteria Are Needed for Healthy Immunity

Cells of the human immune system are stored predominantly in the lining of the intestines.  Intensive study of the interaction of the gut bacteria with the gut has revealed that both the aggressive half of the immune system that attacks pathogens and the suppressive half that protects the body itself from attack, develop in the gut in response to particular types of bacteria.  Thus, the absence of one type of bacteria can cripple responses to infection, while other bacteria are needed to block autoimmune diseases and allergies.  Most diseases are caused by disruption of the normal interactions between gut bacteria and the immune cells developing in the gut.

Antibiotics Lead to Autoimmunity

Antibiotics have dramatic and lasting impact on gut flora.  Cattle treated with antibiotics and a high carbohydrate diet have an altered metabolism (obesity) that leads to rapid fat accumulation in their tissues.  This is good for making tasty beef, but the same approach in people produces the suite of diseases in affluent societies.  

Children treated with an antibiotic for a simple ear infection, are much more likely to return to pediatricians for treatments of subsequent obesity, infections and diseases.  Compromised gut flora can take years to return to normal function after antibiotic treatment.  Loss of the appendix, which is the normal source of bacteria to replenish gut flora after diarrhea, results in an increased risk of abnormal gut flora and numerous autoimmune diseases.  It is likely that most autoimmune diseases are preceded by prior treatment with antibiotics that disrupted normal gut flora and permanently altered the immune system.

Interventions to Treat Disease:  the Anti-Inflammatory Diet and Fecal Transplants

It should be obvious that a disrupted or unhealthy gut flora will compromise the immune system and contribute to disease.  Treatment of diseases is complicated by the use of drugs that also impact the gut flora and produce additional side effects.  An alternative approach would be to support the healthy gut flora and normal development of the gut immune system.  As always, the answer is a supportive diet and a source of gut bacteria.  The diet is obviously the Anti-Inflammatory Diet that provides support for almost anything that ails you.  Probiotics are not retained in the gut, but they can contribute a few of the genes needed for a healthy gut flora. The source of bacteria for a  healthy gut flora may range from minimally washed garden vegetables, to the more aggressive total replacement of gut flora with a fecal transplant from a healthy donor.