The Immune - Digestive System Connection 
By Walter Sorochan Emeritus Professor San Diego State University

Posted March 03, 2012; updated February 4, 2022.  Disclaimer  The information presented here is for informative and educational purposes only and is not intended as curative or prescriptive advice.


You are on an airplane and half of the passengers are sneezing and coughing.  Malicious microbes are on the prowl!  Will you be one of their victims?

airplane_cabin sneeze

Or one of the lucky ones who manages to escape?  That depends in part on the microbial balance in your gastrointestinal tract. 

Dr. John Harvey Kellogg said over a century ago that “90% of diseases are due to improper functioning of the colon.”

2011:“The potential of beneficial microbes appears to be limitless” and that “this symbiotic relationship between the human body and microbes [is] a gold mine of potential therapies for a number of illnesses.”   Heather: immunological research

sick feeling We don't understand why we just don't feel right or good ---- instead we often feel sick or uncomfortable.  Doctors often prescribe medications that do not make us feel better.  Many of us may feel uncomfortable but not sick with serious symptoms. We continue living with this 'not feeling good' slight sick condition that we often refer to as "my gut feeling!

Such long term feelings of discomfort have continued to be a mystery until now. New research is providing a few more answers as to what causes us to feel bad or uncomfortable.   Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active.  Tlaskalová: role of gut microbes in diseases 2011 The new medical-health buzz is about the connection between the digestive system, the immune system and bacteria.  Human frontiers Listen 2011

This article summarizes information with supporting references about these connections that can cause us to be sick or healthy. Author Sorochan has tried to simplify the complex microbial and bio-chemical information, making it easier for average persons to understand the emerging research information.

We understand getting sick from outside our body, like getting a virus that causes flu or a chemical toxin; or we can get sick from the inside, like an organ not functioning properly. But what we were not aware is that feelings of discomfort and illness may be related to the bacteria in our digestive system. We can get sick from the the wrong kind of bacteria or when the proper balance of good and bad bacteria in the body is disrupted. You may find a very good and easy to understand article by two medical doctors, Kay Judge and Maxine Barish-Wreden, from Sacramento, California, about how obesity may be linked to the bacteria in our gut. Article by Judge: gut germs linked to obesity 2013 is no longer active.

Researchers since 2000 have discovered that there are over 400 good and bad bacteria living in the large intestine or colon. If the normal balance of 80 - 85% good and 15 - 20 % bad bacteria is disrupted, then the bad bacteria multiply and can cause many of our illnesses and diseases. Today, most of us show the reverse ratio; therefore, it’s no coincidence that the incidences of chronic and degenerative diseases have multiplied dramatically since World War II. Common everyday symptoms of not feeling good [ intestinal dis-balance of bacteria ] are bloating, abdominal cramping, constipation and diarrhea.

The good news is that changes to the mix of microbes in the digestive tract have already successfully treated disorders and illnesses like leaky gut syndrome, stomach ulcers, inflammatory bowel disease and Crohn's disease.

The Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO) stated in 2003 that there is adequate scientific evidence to indicate that there is potential for probiotic foods to provide health benefits and that specific strains are safe for human use.  Reid: Probiotic uses in medicine 2003

'Feel Bad' tummyFeeling sick has been assumed to be interpreted by the brain.  But new research has discovered that there is a second brain in the digestive system that not only interprets sickness but also is the real home of the immune system. 

When the immune system and the gastrointestinal system are not functioning properly, you begin to see signs and symptoms of illness–all sorts of illness [ everything from depression to skin rashes to eczema to asthma to autism to headaches to cancer ].   Levy: Dysbiosis & immune system 2017

Many articles on the internet, attached to advertisements that sell probiotics, make claims that the immune system originates in the digestive system. These articles lack references to back up these claims. The articles state that anywhere from 60% to 80% of the immune system is in the digestive system as a way to validate their products and to lure readers to buy various "fix the digestive system" supplemental products. Although the claims are correct, these claims are usually undocumented by marketers and lack scientific medical evidence and references.

Author Sorochan searched the internet for original research supporting the claims that the gastrointestinal tract is the home of the immune system. The most compelling evidence comes from Dr. Michael D. Gershon, chairman of the Department of anatomy and cell biology at Columbia University, in his book "The Second Brain," published in 1999.  Book by Gershon: The second brain is no longer active.

brain2  Immune system linked to digestive system: 

The bulk of evidence is based on the research by Dr. Michael D. Gershon and over 100 researchers Zimmer: How Microbes Defend us  who are studying brain-gut connections in the relatively new field of neurogastroenterology.  Their list of findings are supported by a number of observations: 

    bugangel5  There is a brain in the bowel! Hurley: brain2
    bugangel5  "Enteric nervous system" is located in the sheaths of tissue lining the esophagus, stomach, small intestine and colon.
    bugangel5  We have more nerve cells in the GI tract than in all the rest of our peripheral nervous system.  Article by Gershon: The second brain is no longer active.
    bugangel5  "The enteric nervous system uses more than 30 neurotransmitters, just like the brain, and in fact 95 percent of the body's serotonin is found in the bowels." Hadhazy: Gershon GI tract & immunity Angier: 95% serotonin in gut Gut-brain signalling
    bugangel5  Second brain [ in colon ] mediates the body's immune response.  Hadhazy: Gershon GI tract & immunity  Jung: Peyer's Patches  Article by Wenner: researching gut bacteria is no longer active.  Hurley: brain2
    bugangel5  The gut has now been found to contain at least seven different receptors that respond to serotonin.  Article by Gershon: The second brain is no longe active.
    bugangel5  Peyer’s Patches  are the immune sensors of the intestine; are lymphoid follicles located in the wall of the lowest portion of the small intestine. What do Patches do: Initiate immune response by monitoring for bacteria.  They 1) destroy bacteria, preventing them from entering the bloodstream. 2) they generate memory lymphocytes for long term immunity. They are a part of the collection of lymphoid tissues called MALT, mucosa-associated lymphatic tissue found in the lowest portion of the small intestine and the ileumJung: Peyer's Patches Peyer's Patch
    bugangel5  The second brain mediates the body's immune response; after all, at least 70 percent of our immune system is aimed at the gut to expel and kill foreign invaders. Hadhazy: Gershon GI tract & immunity  Article by Wenner: researching gut bacteria is no longer active.
    bugangel5  About 70% of the body's immune system is found in the digestive tract. The GALT(gut associated lymph tissue) is made up of several types of lymphoid tissue that store immune cells, such as T and B lymphocytes, that carry out attacks and defend against pathogens [Germs/ Antigens]. Article by Gershon: The second brain is no longer active.  Jung: Peyer's Patches
    bugangel5  The GI tract has both direct and indirect effects on immune function and the resulting ability to ward off disease. Bushman: bacteria die  Directly, the lining of the intestine is protected by a local immune system called gut-associated lymphoid tissue (GALT). Because GALT is the largest lymph system in the human body, the digestive tract has the most profound effect on overall immunity among all the internal organs. Indirectly, the GI tract contains hundreds of bacterial species in the large intestine that are both beneficial and harmful to the body. The balance of these bacteria in the gut is also a very important factor in the intestine’s defense system against disease. Each of us has natural made bacteriocidins or highly specific “antibiotics” that can do better healing than commercial antibiotics.
    bugangel5  Scientists were shocked to learn that about 90 percent of the fibers in the primary visceral nerve, the vagus, carry information from the gut to the brain and not the other way around. Hadhazy: Gershon GI tract & immunity 
    bugangel5  Serotonin from the gut, on the other hand, keeps bone-making in check: it suppresses the osteoblasts from making fresh bone, but to the caustic osteoclasts it says neither yea nor nay. In experiments with severely osteoporotic mice and rats, the researchers showed that if they used a drug to cut the rodents’ production of gut serotonin by only 40 percent, they freed up the animals’ osteoblastic carpenters so well that the most hollowed-out skeletons were restored to a sturdy state of brand-new. Angier: 95% serotonin in gut
    bugangel5  "cross-talk" between bacteria in our gut and our brain plays an important role in the development of psychiatric illness, intestinal diseases and probably other health problems as well including obesity." Foster: Real gut  Article by Wenner: researching gut bacteria is no longer active.  Bushman: bacteria die
    bugangel5  Disable certain viruses: Bacillus subtilis and Bacillus lichenformis. In studies conducted in Germany at the University of Berlin’s Max-Volmer Institute, both were shown to inactivate human immunodeficiency, herpes simplex (HSV-1 and HSV-2), simian immunodeficiency, feline calicivirus, murine encephalomyocarditis, and other lipid envelope viruses—along with mycoplasmas, fungi and bacteria. They do so by producing a potent chemical called surfactin, a detergent-like substance that dissolves the lipid membranes of lipid envelope viruses, thereby rendering them completely inactivated.   Kunst: sample of genome sequence 1997

This new field of neurogastroenterologyis supported by the relationships observed between healthy and diseased persons.  Article by Fasano intestinal disease is no longer active.  Giovanni: Irritable bowl syndrome  Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active.   Article by Cohen: Smarr gut check 2012 is no longer active.

Indeed medical research now recognizes many previous diseases and disorders as originating in the gastrointestinal tract or GI tract. Wu: gut bacteria causing autimmune arthritis Human frontiers Listen 2011  Tlaskalová: role of gut microbes in diseases 2011  The headquarters of the immune system is the gastrointestinal tract. Since approximately 90% of known pathogens enter the body through the gastrointestinal tract, it makes sense that the vast majority of the immune system would be located here.

 General Discussion: 

The links between colon bacteria and diseases are more apparent today than 20 years ago. Ng: probiotic advancements 2009  Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active.  Human frontiers Listen 2011  Tlaskalová: role of gut microbes in diseases 2011 Most persons dismiss bacteria in the large colon as human waste.  With a few exceptions, even many medical doctors do not perceive that there is a link between bacteria in the gut and our well-being.

Although we now have much more information about bacteria-gut linkage at this time, the cause-effect is not so clear.  In order to study a microbe, it has been historically crucial to be able to isolate it and study it in the lab.  Although the microbes we live with may not cause disease, they are very tricky bugs. They are usually very difficult to isolate and most difficult to grow in the lab. One explanation for this is that the microbial species living inside our bodies are part of a complex ecosystem that we do not fully understand yet; making it incredibly difficult to recreate in the lab and study. But numerous researchers have agreed on a strategy of how to study these tricky microbes in the body.  They decided to make a list or catalogue microbes found in all parts of the body. Once they have identified the microbes as in the digestive system, then they can begin to study the cause-effect of each microbe to a specific human disease and disorder.

With this plan in mind, researchers began identifying the numerous microbes in the digestive system.   Article by Heather: immunological research is no longer active.   George Weinstock of Washington University in St. Louis, Peer Bork of European Molecular Biology Laboratory [EMBL] in Heidelberg, Germany  Manimozhiyan-Bork: 3 types bacteria 2011  Bork: Bacterial balance & health   and colleagues at the Beijing Genomics Institute at Shenzhen, China, Bork: Bacterial balance & health   established a reference gene set for the human gut microbiome – a catalogue of the microbe genes present in the human gut.  The human microbiome project has been enhanced by the USA Human Microbiome Project (HMP) resources; that includes 600 microbial reference genomes, 70 million 16S sequences, 700 metagenomes, and 60 million predicted genes from healthy adult microbiomes. Proctor: USA Human Microbiome Project 2011   Microbiome studies of specific diseases and future research directions are also discussed. Human frontiers Listen 2011   The catalogue of microbes identifies microbes, their genome, characteristics and habitat.

Such research allowed Robert Holt, Holt: bacteria linked colon cancer  a senior scientist at the British Columbia Cancer Agency Genome Sciences Center, and his group of researchers to recently find hundreds of times more Fusobacteria in cancer cells than in normal, healthy cells.  Holt and his team further found that other types of bacteria that typically live in the gut are depleted in colon cancer tissues. It’s the first time that Fusobacterium has been linked to cancer.   ut, with no knowledge of Dr. Holt’s results, Dr. Matthew Meyerson and his colleagues at the Dana-Farber Cancer Institute in Boston found the same thing. And while Dr. Holt’s patients were from Canada, Dr. Meyerson’s were from people in the United States, Vietnam and Barcelona, and Spain. All had the bacteria in far greater abundance in their tumors than in normal colon cells.  Park: bacteria- cancer link   Another human microbe, papillomavirus, or HPV, is behind many cases of cervical cancer.   These are links and not causes of cancer.  

bact family Another early study helping to uncover the mystery of the connection between bacteria in the colon and diseases has been the research led by Peer Bork’s group at the European Molecular Biology Laboratory in Germany. Bork: Bacterial balance & health  They discovered that humans can be classified based on three distinct gut microbiomes. Manimozhiyan-Bork: 3 types bacteria 2011   Heather: immunological research The research team analyzed genomic data obtained from human fecal matter (the least invasive (and least glamorous) method to analyze bacteria living in your guts) derived from people living in Denmark, France, Italy, Spain, Canada Japan and the U.S. and discovered that three different clusters could be distinguished such that regardless of sex, weight, height, age or geographic location, the balance of gut bacteria could be separated into 3 different groups --- each differing in the bacterial contents that lived in their gut. Article by Heather: immunological research is no longer active.

gut types sc daily apr 20 2011Bacterial populations found in the gastrointestinal system fall into three distinct ecosystem classes [ illustrated on left ]:  Jones: 3 types of gut

     Type 1 mostly Bacteroides fragilis
     Type 2 mostly Preveotella & few Bacteroides
     Type 3 mostly Ruminococcus clostridia

These types live in the human gut and were strongly associated with diet.  Protein and animal fat diet was linked to Bacteroides genus, carbohydrates, lacking meat and vegetarian diet was linked to Prevotella genus and alcohol diet was linked to Ruminococcus. Bushman: bacteria diet   Recent research also suggests that each person’s internal ecosystem of friendly bacteria is unique, [ biochemical individuality ] and can influence our neurology and mental states, including the development of our brains during infancy.  Keep in mind that this information is preliminary and based on a small sample of the population and is subject to change with more update information.

our-zeroeth-birthday-present The above summary of recent research into gastro microbes gives one a brief picture of how fast scientists are progressing in attempts to better understand the links between microbes and disease.   But we really have to start with the microbial status of a new born child in order to understand how colon bacteria work. When babies are born, their immune systems are immature and inexperienced. As they come in contact with the outside world of microbes, food particles, and other substances, their immune systems learn how to differentiate “friend” from “foe.” They also learn how to effectively eliminate harmful substances [pathogens, toxins, etc.] from the body.  Problems arise when a baby’s immune system is not allowed to develop in a natural microbial environment [ e.g. kids playing in the dirt ].   Levy: Dysbiosis & immune system 2017

Within the first few months of an infant’s life, the gastrointestinal tract goes from being completely sterile [in the womb] to becoming colonized by hundreds, perhaps even thousands, of different types of microorganisms. These colonies of microorganisms are critical to immune system development, and to fundamental biological processes such as digestion, nutrient assimilation, as well as detoxification. The microorganisms in the gastrointestinal tract play a critical role in immune system function.   Levy: Dysbiosis & immune system 2017

Good germs in the gut can fix a broken - sick human body. Ng: probiotic advancements 2009  Good bacteria are known to provide essential “building blocks” for the human immune system, especially with regard to regulatory functions [the parts that keep the immune system “in check”]. A lack of these essential building blocks can result in an immune system that cannot shut itself off, and can treat benign substances as “invaders.”  Scientists have been aware for some time that disruptions to the development of the critical colonies of microorganisms in the gut can lead to a variety of immune system dysfunctions.   Levy: Dysbiosis & immune system 2017

gut-population Focusing on the bacteria in the gut to fix the feel-sick problems makes sense for several reasons.  Bacteria make up much of us.  If you compare the number of human cells versus bacterial cells that each of us contains, we are more bacterial than we are human. Of all the cells in our body, we are about 10% human and 90% bacterial. If you compare the number of human genes in our body to bacterial genes, we are 1% human and 99% bacterial. All of these bacteria that we carry around weigh an average of 2 to 5 pounds. Other microorganisms that can inhabit the gut include yeasts, parasites, viruses, and protozoans. The primary roles of “healthy” intestinal microorganisms include metabolism, defense, and regulation of the immune system. The metabolic functions of good germs include (but are not limited to) vitamin synthesis, fermentation of carbohydrates, and energy production. Good germs are also necessary to protect the gastrointestinal tract from pathogenic invaders by producing bacteriocidins or highly specific “antibiotics” and by competing with pathogenic organisms for food and space.   Levy: Dysbiosis & immune system 2017

The immune systems of children [ and adults ] with autism, ADHD, celiac disease, asthma, and many other conditions do not working properly. The symptoms experienced by children with chronic illnesses can be linked directly to an improperly functioning immune system. For example, medical researchers have found that some of the symptoms associated with disorders like autism may stem, in part, from autoimmunity. Autoimmunity is a term used to describe what happens when an individual’s immune system attacks its own cells and tissues. Some children with autism, for instance, have auto-antibodies [ or antibodies ]  against their own brain cells. The hypothesis is that the child’s immune system is attacking cells in the brain and causing inflammation in the brain. Autoimmunity is one of many forms of immune dysregulation.  Levy: Dysbiosis & immune system 2017

Children with other conditions like celiac disease [ a serious autoimmune condition where a child cannot tolerate wheat or gluten ] have immune systems that have learned to attack intestinal cells, especially in the presence of wheat or gluten.

Fortunately, it is only recently that we have become aware of the symbiotic lifestyle between bacteria and humans.  In 2005, the Nobel Prize for Physiology and Medicine was awarded to Australian Physicians/Microbiologists, Robin Warren and Barry Marshall. Warren and Marshall discovered “the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease.” One crucial key in unlocking the mystery of how good bacteria prevent disease is that the solution to some human diseases does not reside solely within the human body [host] but rather within the microbial environment.” Heather: immunological research

It is this kind of information that has excited hundreds of scientists to further study the many bacteria in the human gut and how these may cause diseases and/or maintain health.  The human gut catalogue is already speeding up the advent of an emerging medicinal research on the linkages between gut microbes and immunity and wellbeing.  Zimmer: How Microbes Defend us  Bork: Bacterial balance & health  Although the linkage may be an early association it may not identify the cause [ as yet ].  This is the cautionary approach taken by two medical doctors, Upadhyay and Moudgal, in their limited and incomplete  2012 review of probiotics.  Upadhyay: Probiotics review 2012  This opinion is contradicted by Reid and his researchers:  "Based upon the evidence to 2003, future advances with single- and multiple-strain therapies are on the horizon for the management of a number of debilitating and even fatal conditions."  Reid: Probiotic uses in medicine 2003  Likewise, The Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO) have stated that there was adequate scientific evidence in 2003 to indicate that there is potential for probiotic foods to provide health benefits and that specific strains are safe for human use.  Reid: Probiotic uses in medicine 2003

Besides finding new links between the many microbes in our digestive system and our health, scientists are also finding that many diseases are accompanied by dramatic changes in the makeup of our inner ecosystems. Besides discovering microbes in the lungs,  The Imperial College, London, UK., team also discovered that people with asthma have a different collection of microbes than healthy people and that obese people also have a different set of species in their guts than people of normal weight.   Zimmer: How Microbes Defend us  Changing the bacteria in obese persons could enhance the growth of good bacteria that normalize body weight. 

 Linking bacteria to diseases and disorders 

There is a lot of evidence that bacteria are linked to diseases, disorders and immunity.  Below are a few such examples:

Immune system is not an organ. There is no specific organ called the "immune organ." The immune system is a collaborative effort by the entire body to maintain the blood in a "clean" state; the result is immunity --- that is to say; an ability by the body to protect itself from foreign invasion by organisms or substances that might compromise it. Immune theory & dig sys A few examples of bacteria linked to the immune system:

Intake of the probiotic strains Lactobacillus plantarum HEAL 9 (DSM 15312) and Lactobacillus paracasei 8700:2 (DSM 13434) reduces the risk of acquiring common cold infections.  Berggren: probiotics strengthen immunity 2010

L. rhamnosus boosts phagocytic activity. The destruction of foreign invaders and other harmful matter by phagocytes can be increased by three times their normal activity. Circulating antibodies have been shown to increase by six to eight times their normal levels after introduction of L. rhamnosus. Probiotic bacteria & your health

Dr. Luc Deschepper, M.D., recently treated 1,500 patients with B. laterosporus for illnesses related to suppressed immune system function. The micro organism produced such significant improvement in symptoms that his patients now demand the special B. laterosporus supplement he used in the study. One reason for its surprising effectiveness against immune related illnesses may be its strong antibiotic qualities.  Probiotic bacteria & your health

Research shows B. subtilis to be one of the most important immune system stimulators of all the transient micro organisms. It is remarkable for its ability to activate the body's immune defense, as well as its ability to stimulate the proliferation of crucial lymphocytes. Probiotic bacteria & your health

Cancer:  Evidence is mounting that microbes are linked to cancer. Castellarin: Fusobacterium link to colon cancer 2011  Park: bacteria- cancer link 2011   Porter: controlling leukemia 2011  Some genera of bacteria, such as Bacteroides and Clostridium, have been associated with an increase in tumor growth rate, while other genera, such as Lactobacillus and Bifidobacteria, are known to prevent tumor formation. Bifidobacteria longum has also been found to substantially inhibit the formation of colon and mammary gland tumors in laboratory animals caused by nitrosamines, common dietary mutagens found in browned or charred food. Although no claims can be made for curing colon cancer, certain strains of friendly bacteria have indeed been documented in animal studies to have anti-tumor properties.  Wikipedia: Gut flora

According to David B. Hughes and Dallas G. Hoover of the University of Delaware, bifidobacteria have the ability to remove cancer forming elements or the enzymes that lead to their formation. Writing in the April 1991 issue of Food Technology, Hughes and Hoover reported animal studies demonstrating bifidobacteria longum's ability to protect against the formation of liver tumors related to pathogenic microbes in the intestine. Probiotic bacteria & your health

Collaborative research by Robert Holt and his associates at the British Columbia Cancer Agency Genome Sciences Center, and Dr. Matthew Meyerson and his colleagues at the Dana-Farber Cancer Institute in Boston, found hundreds of times more Fusobacteria in cancer cells than in normal, healthy ones.  Castellarin: Fusobacterium link to colon cancer 2011  Park: bacteria- cancer link 2011

Perhaps the most exciting way probiotics can help fight cancer is through its ability to promote health in people undergoing chemotherapy or radiation treatments. In 2006, Russian researchers reported the ability of probiotic called Acilact to improve the health of mice when exposed to ionizing radiation and chemotherapy. The probiotics reduced the ability of bad microbes from invading the intestinal tract.  Probiotics reduce pro-carconogenic enzymes and produce short chain fatty acids which create a healthy pH colon which, in turn, can lower cancer risk. Article by Tannis: probiotic rescue is no longer active.

Allergies: Scientific evidence also shows that ingesting foods containing probiotics can also lessen symptoms of lactose intolerance and reduce the occurrence of allergy in susceptible people. Article by Kalliomaki: probiotic help allergy is no longer active  Gill: Probiotics and human health  Coleman: Probiotics skin care and Beauty   Dunn: soap kills good bacteria Article by Ewers: Book Inflammation is no longer available.

Obesity: There is a relationship between the brain, colon bacteria and obesity.   Kotnturek: Brain-Gut axis  Article by Judge: gut germs linked to obesity 2013 is no longer active.

  • Firmicutes observed link in lean persons

  • Bacteroidetes can be observed in obese individuals.   Wikipedia: Gut flora  Article by Alleyne: Probiotics help lose weight is no longer active.

Arterial stiffness:  A study conducted in 2007 using milk fermented with Lactobacillus helveticus (L. helveticus) provided evidence that milk fermented with this probiotic significantly improved the arterial stiffness of those involved in the study. Other studies conducted using milk fermented with L. helveticus indicate that this probiotic not only helps with arterial stiffness but also supports bone mineral density and increases calcium absorption in postmenopausal women.

Rheumatoid Arthritis: The microbe Prevotellaceae in both oral and intestinal locations is linked with certain predisposed individuals who may develop auto-inflammatory disease. Article by Scher: RA & microbes is no longer active. Article by Ewers: Inflammation is no longe active.  Article by Reinberg: Rheumatoid Arthritis is no longer active.  Wu: gut bacteria causing autimmune arthritis 2010  Mazmanian: microbe symbiosis factor prevents

Multiple Sclerosis:   "Precisely which bacteria are involved in the emergence of multiple sclerosis remains unclear; possibly clostridiums."   Max Planck Institute: gut flora & MS

Vitamin synthesis:  You can cut your risks from most major diseases by 50 to 80 percent. All you have to do is get enough D. Some researchers have labeled vitamin D as a natural flu vaccine! [ It also means we can significantly reduce both health care costs and the staggering national deficit by taking a few simple steps. ] Article by Null: Vit D triggers immunity 2010 is no longer active.

Japanese researchers have shown in 1984 that bifidobacteria longum, bifidum and breve are substantial producers of vital B vitamins and vitamin C. Tlaskalová: role of gut microbes in diseases 2011  That gut bacteria can synthesize vitamin C refutes the medical dogma that humans cannot make it.

Lactobacilli acidophilus is responsible for the production of vitamin K which helps blood to clot and helps build strong bones. New research suggests that vitamin K deficiency may be a crucial factor in predisposing the body to the onset of osteoporosis.  Bentley: Vit K synthesis pdf format

Depression:  medications meant to cause chemical changes in the mind often provoke GI issues as a side effect. Yadav: serotonin like to osteroporosis  Psychiatrists are looking to the link between bacteria in the gut and serotonin to help alleviate depression.  Foster: Real gut

Osteoporosis:  gut-derived serotonin (GDS) inhibits bone formation and may interfere with osteoporosis.  Hadhazy: Gershon GI tract & immunity  Yadav: serotonin link to osteroporosis 2010

Acid Reflux or GERD:  GERD or Gastroesophageal Reflux Disease

According to Zhiheng Pei, MD, PhD, of NYU Langone Medical Center in New York City, and colleagues, this disorder is associated with large-scale changes in the microbes that populate the esophagus. This study found that esophageal disease is associated with large-scale changes in the microbes that colonize the esophagus, although it is not yet clear whether the effect is a cause or an effect of GERD.

The changes are sufficiently clear that they define a normal “microbiome” and one that is more than 15 times more likely to be found in people with esophagitis or Barrett’s esophagus. The normal microbiome — dubbed Type I — is dominated by a Streptococcus species.

Pei said in a statement. “But if changes in the bacterial population do indeed cause reflux, it may be possible to design new therapies with antibiotics, probiotic bacteria, or prebiotics.” The finding is an important addition to the small number of studies that have tried to characterize gastrointestinal microbes, according to Sebastian Suerbaum, MD, of the Hannover Medical School in Hannover, Germany.  Article by Smith: GERD linked to mirobe is no longer active.  The study was supported by the National Cancer Institute, the National Institute for Allergy and Infectious Diseases, and the Department of Veterans Affairs. 

Researchers are also discovering new ways that the immune second brain in the digestive system works. Additional findings Article by Seattle SCCA: autoimmune diseases is no longer active. between the interactions of the gut and the brain are also helping to explore revolutionary treatments of auto-immune diseases and disorders like asthma,  skin disorders like eczema or acne Coleman: Probiotics skin care and Beauty, autism Hurley: brain2, constipation, inflammatory bowel disease Ng: probiotic advancements 2009, leaky gut, celiac, Alzheimer's disease, Myasthenia Gravis, Rheumatoid arthritis Wu: gut bacteria causing autimmune arthritis  Article by Reinberg: Rheumatoid Arthritis is no longer active., lupus, weight lose Article by Alleyne: Probiotics help lose weightis no longer active., Type 1 Diabetes Mellitus Dryden: diabetes may start in intestines, Raynaud’s phenomenon, Addison's disease, thymus gland disorders, Hirschprung's disease chronic diseases Article by Stevenson: antibiotics cause chronic diseases 2011 is no longer active., psoriasis and frequent respiratory infections, asthma Zimmer: How Microbes Defend us, bronchitis, chronic rhinitis, post-nasal drip, nasal voice, sinus congestions, and allergies Gill: Probiotics and human health. The primarily chronic respiratory conditions indicate a weakened immune system because of disbacteriosis. They usually appear after a routine respiratory infection that was treated with antibiotics, which in turn damage intestinal flora. Indeed, many of these difficult to treat disorders are now suspected to be part of the gut-immune system and not as separate host entities.  Such thinking changes prospective treatment modalities and especially the use of anti-biotics.

 "The probable cause of much autoimmune disease must be the indiscriminate use of antibiotics!"  Article by Stevenson: antibiotics cause chronic diseases 2011 is no longer active.



The good and friendly bacteria, or probiotics, in the large intestine are essential to good health. It is in the GI tract that good bacteria help the body systems work. Most of these bacteria live harmoniously with us. We give the bacteria a place to live and they return the favor to us by maintaining order and keeping harmful bacteria and other invaders from disrupting the digestive system. [ illustration on right  Andrews: Probiotic food ]. Healthy intestinal bacteria or probiotics, are the infantry soldiers of your digestive army.   Market Research: boosting immunity   Pearl: immune-dif connection

The GI tract keeps microorganisms under control by an extensive immune system that is able to ward off diseases and disorders.  Wiki: intestinal tract But it does so only when there is a balance between good and bad bacteria. Directly, the lining of the intestine is protected by the largest local immune system called gut-associated lymphoid tissue (GALT).

The GI tract is the home of the gut-brain that does many other things beside immunity. For example, it helps balance hunger and satiety, or the sense of being full, communicating those states to the big brain. It tells the big brain that "I'm full!"  More research on the topic of satiety and obesity may provide better therapy for obese persons. Another example is the gut-brain housing 95 % of the serotonin; where it acts as a neurotransmitter and a signaling mechanism to trigger digestion.  Brown: Gershon second brain  Pych Today: second brain

 Mystery links: 

Why do so many persons feel mystery illnesses or discomfort and just feeling sick?  Much of this mystery appears related to good bacteria not keeping the bad guys in check, thereby causing a weakened immune system!  Bacterial imbalance may be caused by many factors: Levy: Dysbiosis & immune system 2017   Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active  Drug interactions  Gill: Probiotics and human health  Article Ewers: Biik Inflammation is no longer active.

  • Excessive Stress – long term mental and emotional
  • Poor Diet like excess meats and sugar desserts
  • Carbonated beverages, especially sugared sodas
  • Artificial Sweeteners
  • Lack of Beneficial Bacteria (Probiotics) in Colon
  • Use of antibiotics without a life-threatening or limb-threatening situation
  • Use of foods that are contaminated with antibiotics and antibiotic residues, mainly factory farmed animal foods
  • Exposure to chemical toxins like bromide pesticide and fluoride in water
  • Drinking chlorinated water decreases beneficial bacteria in the intestine.
  • Swimming in chlorinated swimming pool, kills all bacteria
  • Eating foods and beverages that have sugar or other concentrated sweeteners
  • Regular consumption of refined and processed foods like cookies, chips, pastries, and prepackaged goods
  • Regular consumption of alcohol
  • Not chewing your food until liquid
  • Use of steroids like prednisone and hydrocortisone
  • Use of antacids and other acid-inhibiting drugs
  • Use of laxatives
  • Use of birth control pills

It is apparent from a glance at the above list that many of our behaviors and good intentions disrupt the bacterial balance in the digestive system. Our lifestyle often  compromises our immune system. Article by Mazmanian: symbiosis health and disease is no longer active.  Pearl: immune-dig connection  Article by Ewers: Inflammation is no longer active.

 So how can you restore your broken immune system? 

This is a tricky fix as there may be many factors contributing to the bacterial disbalance at the same time. Not only do we need to restore the good and bad bacteria inside our body but also control the environment outside us. Doing both at the same time can muddy the progress of the fix and can be counterproductive.  Buying the hype advertized probiotics and ingesting same may not be the best way to fix a broken immune system!   Levy: Dysbiosis & immune system 2017

So lets start with the food you eat and try to restore the good and bad guys in the gut and thereby restore at least part of our immune system. Most of us will probably have more control of the internal body ecosystem than our external environment.

Providing nutrition for good bacteria is essential to a healthy digestive system. It is also important for all parts and systems of the body to get the appropriate nutrients like vitamins, minerals, amino acids [proteins], as well as the carbohydrates and fats that are needed for normal body metabolism. Otherwise the body cannot function as designed and we should recognize this as disease rather than as nutritional dysfunction; therefore such disease is correctable. Article by Null: Vit D triggers immunity is no longer active.  The body needs ALL essential nutrients [ co-factors ] to be present as a package to enhance good gastrointestinal tract health. Several of these include much overlooked vitamins A, B-complex, C and D and micro and macro minerals.  Vitamin D and magnesium act as turn on/off switches in many body systems, including DNA-RNA metabolic processes.  Article by Null: Vit D triggers immunity is no longer active.

"You are what you eat!" But it is more than just what you gulp down. Are the vitamins, minerals, complex carbohydrates, fats and amino acids absorbed or assimilated into the blood stream? Assimilation makes the difference whether you are healthy or sick. This aspect of eating is ignored! You really don't know whether the amount of a vitamin or mineral, as specified in the label, is really absorbed into your blood stream!

People who love to eat what is referred to as comfort food --- like milk shakes, soft drinks, white breads, white pastas, cookies, sweets, fries and hamburgers, promote the growth of disease-causing bacteria.  Article by Walker: Cure for Crohns Disease is no longer active.  Article by Ewers: Inflammation is no longer active. Then too, the balance of bacteria in the gastrointestinal tract is most commonly disrupted by antibiotic usage, excessive sugar consumption, stress, exposure to toxic chemicals and drinking chlorinated water.

Researchers also have found that altered levels of acidity and alkalinity in the gastrointestinal tract will change the ecology of the bowel environment, and thereby affect the type, quantity and behavior of micro organisms found there. For example, a diet consisting chiefly of processed foods can dramatically alter the vital acid/alkaline balance of the intestinal tract. Such an imbalance can lead to a dramatic overgrowth of unwanted and extremely harmful microorganisms.

A diet high in red meats or rich, fatty foods will dramatically alter the acid/alkaline balance of the intestines, leading to the overgrowth of disease causing, putrefactive bacteria that eventually overcome the beneficial bacteria and open the door to an onset of serious health problems.  Mayo Clinic: Probiotic bacteria & your health

You can find more good information by clicking on nutrients.

 Controlling Environmental toxins:    Many industrial uses of chemicals, while well intended and economical, cause silent incubating health problems in humans. Sorochan: Silent Pandemic of Environmental Pollutants Classic example of this are the misuse of bromides as a pesticide in agriculture and industry, the use of chlorine to purify water and the use of fluorine in water to prevent dental caries. Iodine: halogen robbers While perhaps doing good on the one hand, on the other hand these three halogens create nutritional-health crises by interfering with much needed iodine absorption. So much so, that the majority of people in North America are critically deficient in iodine.

Beside eating good food to restore the gut bacteria, we need to drink safe water and avoid exposure to chlorine. Chlorinating water in the water purification system kills bacteria in the water but the chlorine remains in the drinking water. Drinking home water allows the chlorine to kill good and bad bacteria in the gut. We need to minimize exposure to chlorine by showering and swimming without contacting chlorine.  The implication is that we need to purify water using safer microbial-water treatment processes other than chlorine.

halogens2 What's wrong with chlorine?  After all, chlorine kills bacteria!  Chlorine, along with other poisonous halogen chemicals, also has destructive and devastating affect on our immune system. Halogens kill the good bacteria in our colon. Bromide, fluoride and chlorine disable our ability to use iodine, an essential halogen nutrient for all body cells; further weakening our immune system.  Iodine as an essential nutrient can be displaced in the food chain by most active bromide compounds used as pesticides in agricultural crops, then by fluorides in drinking water, used to prevent dental decay and then by chlorine in chlorinated drinking water; in that hierarchial order. When iodine is replaced by the more active halogens [ referred to as goitrogens which interfere with iodine utilization ] the body absorbs less iodine and the population is then at increased risk to goiter and other diseases and disorders --- including silent and ignored health problems. Abraham: Orthiodinesupplementation  Goitrogenic Foods to avoid eating  Cooking process deactivates most of the goitrogenic compounds in foods.

That we should avoid using antibiotics should be obvious by now. Medical doctors should also prescribe probiotics along with the antibiotic for some time afterward to restore the gut flora.

The above discussion about fixing your broken immune system and restoring the balance of good and bad bacteria is very brief. You can find more information in the references below and on the internet.

 Finding good probiotics can be a problem. 

Finding documented information about supplemental probiotics is difficult and often impossible.  Article by Dash: Criteria for Probiotics is no longer active.  Article by Fitzpatrick: probiotic survey Canada is no longer active. The reasons for this should be obvious. Research about colon bacteria and how the many different species [ genera ] function is in its infancy. Just what is the research link between microbial strains and affect on the human body? Although scientists have begun to identify the good and bad guys in the GIT, they are at the same time trying to verify the link between bacteria, disease and health and also determine whether certain bacteria cause a disease [effect]. Research is escalading faster than scientists can present it to the public in words that the public understands. Consequently, there is very little transparency about probiotics information and comprehensible, documented research that simple folk can use as a guide. How can there be "real" standards for selecting probiotic products that work when the microbial scientists are in the early stages of unraveling the gut flora? Yet that is what some marketers selling probiotics, with good intentions, have tried to do.

So it should not be surprising that the astute consumer is bewildered about probiotics. How does one make an informed decision about probiotics when reference to background information about different microbes is difficult or impossible to find? This is an information vacuum.  On the one hand, probiotic product marketers make unsupported claims about the benefits of probiotics. Many of the products currently on the market are not clearly tied to research documenting beneficial effects. On the other hand, researchers need to translate technical microbe information into simple easy to understand terms! Just simple words and readily available probiotic information on the internet would be a help! We also need a probiotic information clearing center!

Many supplements state on the label how many billions of probiotics they contain but actually labels are slightly missing the point. For example, given the right probiotic foods, those bacteria will multiply many times over in just a few days.  Hence, one may not have to continue ingesting probiotic supplements for a month or longer.

Another issue is to provide the variety of species or genera of good bacteria. If you don’t have an ‘original’, you can’t make copies.

But first the most crucial issue is getting these live bacteria past the acid stomach which can kill them off, and into the intestine where they can do their job. This is not as simple as it sounds. Many potential probiotic bacteria are killed off long before they ever reach the large intestine. Indeed, implicit in the definition of a probiotic is that it should be a bacterium from a strain proven to survive transit through the gut and proven to have a beneficial effect in the large intestine, in clinical trials. Such documented information is lacking in commercials and labels.

Lacking good independent probiotic information makes buying supplemental probiotcs a problem! You don't know if the brand you buy will really work. You also don't know whether the probiotics you ingest ever reach their destination. At this time, there is no monitoring test to determine this. The label product information and claims espoused by marketers is usually not supported by documentation. In a 2003 study, Belgian researchers examined the probiotic bacteria of 25 dairy products and 30 powdered products that were used as nutritional supplements. And the results were stunning! More than a third of the powdered products contained no living bacteria whatsoever - unlike the dairy products, which contained up to a billion living microorganisms per milliliter. In identifying the bacteria, the researchers found that only 13 % of the products contained all bacteria types included on the label. Meanwhile, in one third of all the products, the researchers found other bacteria not listed on the label. Belgian research 2008  The message from this Belgian research is that you need to do your homework on the probiotic you intend to buy.

In spite of the short-comings about probiotics, most probiotics should be safe to take.

Having a good guide to help you purchase probiotics would be helpful. But even such general guides, like Mercola's website, are difficult to follow and understand.  Article by Dash: Criteria for Probiotics is no longer active. These well intended guides read more like personal opinions than scientific documents.

 What to Expect when you take probiotics 

You may initially feel gassy or bloated when you first start taking probiotics. This is usually caused by the die-off of harmful bacteria. The bloating typically goes away after a few days. Drinking enough water, consuming adequate fiber, a healthy diet and bowel regularity really helps you purge properly and limit this die-off effect. If bloating and gas continue or are severe, you may benefit from a colon cleanse. Consult your medical therapist for this help.

Remember, if the probiotic supplement does not contain proper probiotic strains, right potency, right formula, is not living bacteria and is not acid and bile resistant, it will offer no health benefits.

Once you are eating the right foods it is generally possible to maintain a healthy bacterial balance in your gut without the use of probiotics.

 Summary: Good Immune Health 

This article summarizes the emerging research about the body connections between gastrointestinal bacteria and body systems, immunity and how we can stay healthy!

We have known for a long time that we need a strong immune system to have good health. The real medical revolution happening now is the awareness that the gastrointestinal tract is the home of the immune system Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active. and that colon bacteria can prevent illness and diseases. Although scientists have discovered linkages between bacteria and diseases, they are just beginning to determine whether bacteria cause diseases.

Would you believe that approximately 80 to 90% of diseases originate in the digestive system? A properly functioning digestive system is key to the overall health of your body. It is your digestive system that helps you to assimilate nutrients, houses a majority of the immune cells and the enteric nervous system, and helps you to rid toxic wastes from the body. If your digestive system is not doing its job, it can make you feel bad, feel uncomfortable and even sick.

Medical science is now in a new research era of investigating the links between bacteria in the gut and diseases, the links between the brain or central nervous system and the digestive, lymphatic and immune systems. Their findings will change the way medicine is practiced, how psychiatrists will deal with many mental and physical health problems and how we eat. Article by Cohen:gut check is no longer active. Reid: Probiotic uses in medicine 2003  Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active.  There is evidence that prescribing the good germs [ probiotics ] and not drugs can help to treat many disorders and prevent diseases. [ This type of unorthodox thinking and therapy may contradict conventional medical practice. ] Article by Stevenson: antibiotics cause chronic diseases 2011 is no longer active.

A major contradiction to fixing the bacterial balance in the gut are the outdated and irresponsible uses of toxic chemicals in industry, agriculture, public health and health care fields. A critical example is current use of halogens: chlorine in purifying drinking and swimming water, fluoride in drinking water to prevent tooth decay and bromide in food pesticides. These halogens destroy our body's ability to use the essential mineral iodine; thereby making us more prone to being chronically sick. Using these halogens is like continuously shooting oneself in the foot! It keeps us in a perpetual state of really being sick!

This article review brings together much of the on-going research about personal microbiomes. In order for new information about body systems, immunity and bacteria to be implemented, we need a new revolution in industry, medicine and public health. Out-dated public health practices like chlorinating drinking water need to be replaced by available technology that does not disrupt iodine utilization. Replacing halogens can become economical through infrastructure projects like upgrading municipal water treatment plants that replace chlorination with oxygenation or other technology; and replacing bromides in insecticides. Medical school curricula need to be updated! Practicing doctors need to go to seminars to update their knowledge skills. The real need is the 'political will' that values human health over making money.

Each of us has natural made bacteriocidins or highly specific “antibiotics”synthesized in the GIT that can do better healing than commercial antibiotics.


A-gold, "A Gut-Full of Probiotics for Your Neurological Well-Being," The Wiley Life Sciences Blog, December 09, 2011.  Article by A-gold: probiotics is no longer active.

Andrews Ryan, "All About Probiotics," Precision Nutrition, May 3, 2010.  Andrews: Probiotic food

Angier Natalie, "Job Description Grows for Our Utility Hormone, The New York Times, May 2, 2011.   Article by Angier: 95% serotonin in gut is no longer active.

Alleyne Richard ,"A probiotic drink a day helps women lose weight after giving birth," The Telegraph, May 08, 2009.   Article by Alleyne: Probiotics help lose weight is no longer active.   "Researchers found that women who took the food supplement during and after pregnancy saw a bigger reduction in both their waistline and overall body fat."

Arumugam Manimozhiyan and others, "Enterotypes of the human gut microbiome," Nature May 12,2011, 473,174–180.   Arumugam: gut bacteria

Bentley R., and R Meganathan, "Biosynthesis of vitamin K (menaquinone) in bacteria," Microbiol Rev. September, 1982 ; 46(3): 241–280.   Bentley: Vit K synthesis  Bentley: Vit K synthesis pdf format

Berggren A, Lazou Ahrén I, Larsson N, Önning G., "Randomised, double-blind and placebo-controlled study using new probiotic lactobacilli for strengthening the body immune defence against viral infections," Eur J Nutr. 2011 Apr;50(3):203-10.   Berggren: probiotics strengthen immunity

Bork Peer, "Bacterial balance that keeps us healthy," Biology & Nature, March 4, 2010.   Bork: Bacterial balance & health

Bravoa Javier A., Paul Forsytheb,c, Marianne V. Chewb, Emily Escaravageb, Hélène M. Savignaca, Timothy G. Dinana, John Bienenstockb, and John F. Cryana, "Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve," PNAS, August 29, 2011.  Eating probiotic bacteria changes behaviour in mice. Bravoa: probiotic bacteria changes behaviour

Brochu, E., “Bacillus in Prophylaxy and Therapeutics," Clinical literature and references, Rosell Institute, Inc., Montreal, Canada.

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Campbell Barry, Brain-gut axis.   Campbell: slides

Castellarin Mauro,René L. Warren,J. Douglas Freeman, Lisa Dreolini, Martin Krzywinski, Jaclyn Strauss, Rebecca Barnes, Peter Watson, Emma Allen-Vercoe, Richard A. Moore1, and Robert A. Holt, "Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma," Genome Research, October 18, 2011.  Castellarin: Fusobacterium link to colon cancer 2011  "An estimated 15% or more of the cancer burden worldwide is attributable to known infectious agents."

Christensen Margaret, "Understanding Gastrointestinal health - What Are My “Gut Feelings” Telling Me?" Christian Center for Whole Life Health.   Article by Christensen: GI health is no longer active.

Cohen Jon, "The Patient of the Future," Technology Review, March/April 2012.  Article by Cohen: SPatient of future 2012 is no longer active.  Internet pioneer Larry Smarr's quest to quantify everything about his health led him to a startling discovery, an unusual partnership with his doctor, and more control over his life. "I have no doubt this is the future of medicine, but I have no idea how to get there from here," says gastroenterologist at UCSD, William Sandborn. Smarr directs the California Institute for Telecommunications and Information Technology in La Jolla, Ca..  Article by Smarr: UT Newpaper story is no longer active.

Cohen Sheldon, William J. Doyle, Cuneyt M. Alper, Denise Janicki-Deverts,  "Sleep Habits and Susceptibility to the Common Cold," Arch Intern Med. 2009;169(1):62-67.  Carnige Mellon University. Cohen: Sleep & colds  Cohen: Sleep & colds

Coleman Claire, "Probiotic beauty: They're the bugs that boost digestion - but can they also clean up your skin?" Mailonline, April 20, 2009.   Coleman: Probiotics skin care and Beauty

Probiotic beauty --- clean up your skin? Although as a concept it’s still in the early stages, the idea is that probiotics (beneficial bacteria) and prebiotics (essential fuel for the beneficial bacteria) can help improve the balance of bacteria in your skin, in the same way they are known to improve the balance of bacteria in your digestive system.  Research published in the British Journal of Dermatology suggested that eczema and the associated itching improved after patients were treated with a probiotic cream. And, just this month, the Journal of Dermatological Science devoted coverage to a small study that seemed to show that, using prebiotics, it is possible to reduce the levels of acne-causing bacteria without harming the good bacteria.

Dash S.K., "Selection Criteria for Probiotics," Presented at XXXVII Dairy Industry Conference, February 7-9, 2009, Kala Academy, Panjim, Goa.   Article by Dash: Criteria for Probiotics is no longer active. 

Dryden Jim, "Diabetes may start in the intestines, research suggests," Journal Cell Host & Microbe, February 15, 2012.   Dryden: diabetes may start in intestines   Their research suggests that problems controlling blood sugar — the hallmark of diabetes — may begin in the intestines. “When people become resistant to insulin, as happens when they gain weight, FAS doesn’t work properly, which causes inflammation that, in turn, can lead to diabetes.” Fatty acid synthase (FAS) in the intestine. FAS, an enzyme crucial for the production of lipids, is regulated by insulin, and people with diabetes have defects in FAS.

Dunn Rob, "Scientists Discover That Antimicrobial Wipes and Soaps May Be Making You (and Society) Sick," Scientific American, July 5, 2011.  Dunn: soap kills good bacteria  "But what do antibiotic wipes and soaps do? Amazingly, no one really knows."

Ewers Keesha, "What Contributes to a “Pro-Inflammatory” Lifestyle?" Fern Life center, January 24th, 2012.  Article by Ewers: Inflammation is no longer active.   causes: e.g.  1. High Sugar Foods: You immune system is suppressed for 2-4 hours after ingesting it

Fasano Alessio and Terez Shea-Donohue, " Mechanisms of disease: the role of intestinal barrier function in the pathogenesis of gatrointestinal autoimmune diseases," Nature Clinical Practice Gastroenterology & Hepatology, September 2005, Vol 2, No 9.  Article by Fasano intestinal disease is no longer active.

Fitzpatrick K.C., "Probiotics discussion paper." Health Canada, March 2005.   Article by Fitzpatrick: probiotic survey Canada is no longer active.

Foster Jane, "'Knowing It In Your Gut' Is Real, Researchers Find," Integral Options cafe, March 28, 2011.   Foster: Real gut  
Researchers at McMaster University discovered that the "cross-talk" between bacteria in our gut and our brain plays an important role in the development of psychiatric illness, intestinal diseases and probably other health problems as well including obesity. "The wave of the future is full of opportunity as we think about how microbiota or bacteria influence the brain and how the bi-directional communication of the body and the brain influence metabolic disorders, such as obesity and diabetes," says Jane Foster, associate professor in the Department of Psychiatry and Behavioural Neurosciences of the Michael G. DeGroote School of Medicine.

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Gill HS, Guarner F. "Probiotics and human health: a clinical perspective," Postgraduate Medical Journal, 2004;80(947):516–526.  Gill: Probiotics and human health

Guilliams Thomas, "An Emerging Trend of High-Dose Probiotic Use in Clinical Practice," Mirintus, Dec. 15, 2011.  Article by Guilliams: Probiotic Use in Clinical Practice 2011 is no longer active.

Giovanni Barbara, Cesare Cremon, Giovanni Carini, Lara Bellacosa, Lisa Zecchi, Roberto De Giorgio, Roberto Corinaldesi, and Vincenzo Stanghellini, "The Immune System in Irritable Bowel Syndrome," J Neurogastroenterol Motil, October 17 2011, (4): 349–359.  Giovanni: Irritable bowl syndrome

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Goitrogens:  Goitrogenic foods are foods that interfere with iodine absorption. Goitrogens are common in vegetables: cabbage, brussels sprouts, broccoli, and cauliflower. However, warnings that these foods are the cause of hypothyroidism are probably exaggerated. First, the goitrogens are destroyed when these foods are cooked. Goitrogenic Foods to avoid eating

Guarner Francisco, and international review team, "Probiotics and prebiotics," World Gastroenterology Organisation, May 2008.  Article by Guarner: International review probiotics 2008 is no longer active.

Gut-brain signaling, The Citizen's Compendium.   Gut-brain signalling

Wikipwsia: Gut flora "Most bacteria belong to the genera Bacteroides, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, and Bifidobacterium.  Other genera, such as Escherichia and Lactobacillus, are present to a lesser extent.  Species from the genus Bacteroides alone constitute about 30% of all bacteria in the gut, suggesting that this genus is especially important in the functioning of the host. The currently known genera of fungi of the gut flora include Candida, Saccharomyces, Aspergillus, and Penicillium." Wikipedia: Gut flora

Hadhazy Adam, "Think Twice: How the Gut's "Second Brain" Influences Mood and Well-Being," Scientific American, February 12, 2010.  Hadhazy: Gershon GI tract & immunity   "95 percent of the body's serotonin is found in the bowels.

Heather,"Escaping Anergy: The Immunology Research Blog," August 5, 2011.   Article by Heather: immunological research is no longer active.

Hodes Steven, "Why Do We Feel Sick All the Time?" KAJAMA.  Article by Hodes: Feel Sick All the Time is no longer active.

Holt Robert, "Two Cancer Studies Find Bacterial Clue in Colon," NY Times, October 17, 2011, authored by GINA KOLATA.   Holt: bacteria linked colon cancer Published: "Fusobacteria were known before this, of course, but were thought of as microbes that mostly live in the mouth — they are often in plaque and are associated with periodontal disease. But there are also recent reports associating them with ulcerative colitis and Crohn’s disease."

Hughes D.B., and Hoover D. G., " Biofidobacteria: Their potential for use in American dairy products," Food Technology, April, 1991, 45, 74.  

Hurley Dan, "Your Backup Brain," Psychology Today, November 01, 2011 - last reviewed on January 02, 2012.  Hurley: brain2   There's a "second brain" in your stomach. It influences your mood, what you eat, the kinds of diseases you get, as well as the decisions you make. And you thought it was all in your head!

"Immunity Theory, The Immune System and Allergies: The Immune System, its Relation to Digestion and How to Support and Restore it." Amulex.  Immune theory & dig system

Jain K.K.,MD, [contributing editor] "Neurogastroenterology - Clinical summary," MedLink Neurology, July 29, 2011.  Article by Jain: Clinical summary is no longer active.

Jockers David, "Melatonin plays an important role in healthy digestive and immune function," Natural News, September 12, 2011.    Jockers: Sleep & immunity

Jones Nicola, "Gut study divides people into three types," Nature, April 20, 2011.   Jones: 3 types of gut   Bacterial populations fall into three distinct ecolosystem classes that could help to personalize medicine. Peer Bork, who led the study at EMBL: "our gut flora can settle into three different types of community -- three different ecosystems."

Peer Bork’s group at the European Molecular Biology Laboratory in Germany, discovered that humans can be classified based on three distinct gut microbiomes. The research team analyzed genomic data obtained from human fecal matter (the least invasive (and least glamorous) method to analyze bacteria living in your guts) derived from people living in Denmark, France, Italy, Spain, Japan and the U.S. and discovered that three different clusters could be distinguished such that irregardless of sex, weight, height, age or geographic location, the balance of gut bacteria could be separated into 3 different groups-each differing in the bacterial contents that lived in their gut.

Type 1 = Bacteroides fragilis; type 2 = Preveotella & few Bacteroides; and type 3 = Ruminococcus clostridia [linked to cancer but not causal]. 

People who were Type 1 had a different balance of gut bacteria than people in Type 2 or 3. Similar to bloodtypes, that is that all people can be classified into one of 4 groups based on if they express A, B, AB or O antigens on their red blood cells, Bork suggests that this new biological classification, enterotypes (named for the collection of bacteria that live in the gut that distinguish the three groups) may be used to better tailor diets, drug regimines and antibiotics for an individual based on his/her microbiome. For example, someone of Enterotype 1 may respond better to particular antibiotics or diets than someone who is Enterotype 2 or 3. However, this is still a hypothesis that requires more research, funding and public interest to better understand the differences between these enterotypes and whether specific enterotypes are found in other highly colonized areas of the body such as the urogenital tract and skin, and importantly: if different microbial environments in our bodies play a role in disease susceptibility or resistance.

Judge Kay, & Maxine Barish-wreden, "Obesity may be gut reaction," Harmful bacteria in intestine linked to many harmful conditions Union-Tribune, San Diego, January 29, 2013.   Article by Judge: gut germs linked to obesity 2013 is no longer active.

Jung Camille, Jean-Pierre Hugot, and Frédérick Barreau, "Peyer's Patches: The Immune Sensors of the Intestine," International Journal of Inflammation Volume 2010, Article ID 823710, 12 pages. July 11, 2010.   Jung: Peyer's Patches

Kalliomaki M., Salminen S., Arvilommi H., Kero P., Koskinen P., Isolauri E., "Probiotics in primary prevention of atopic disease: A randomized placebo-controlled trial," The Lancet, April 7, 2001; 357:1076-1079.  Article by Kalliomaki: probiotic help allergy is no longer active.

Kalman Douglas S, Howard I Schwartz, Patricia Alvarez, Samantha Feldman, John C Pezzullo and Diane R Krieger, "A prospective, randomized, double-blind, placebo-controlled parallel-group dual site trial to evaluate the effects of a Bacillus coagulans-based product on functional intestinal gas symptoms," BMC Gastroenterology  November 18, 2009, 9:85.   Artile by Kalman: intestinal gas is no longer active.  Conclusion: Bacillus coagulans-based product was effective in improving the quality of life and reducing gastrointestinal symptoms in adults with post prandial intestinal gas-related symptoms and no GI diagnoses.  Studies suggest that the probiotic Bacillus coagulans decreases the symptoms of abdominal pain and bloating in subjects with inflammatory bowel disease .

Kelly GS., "Larch arabinogalactan: clinical relevance of a novel immune-enhancing polysaccharide," Altern Med Rev.,  April 4, 1999, (2):96-103.   Kelly: probiotic preventing cancer

Kiani Leila, "Bugs in Our Guts—Not All Bacteria Are Bad: How Probiotics Keep Us Healthy," ProQuest, September 2006.   Article by Kiani: distribution - health effects microbes in gut is no longer active.

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Levy Maaayan, Aleksandra A Kolodziejczyk, Christoph A Thaiss, Eran Elinav, "Dysbiosis and the immune system," Nat Rev Immunol, 2017 Apr;17(4):219-232.  Levy: Dysbiosis & immune system 2017

Manimozhiyan Arumugam, others & Peer Bork, "Enterotypes of the human gut microbiome," Nature June 2011, 473,174–180.   Manimozhiyan-Bork: 3 types bacteria 2011   "we identify three robust clusters (referred to as enterotypes hereafter)"

Market Research, "Boosting immunity through digestion," Market   Market Research: boosting immunity

Martin Michelle, "Listen now Microbes," BBC radio 4, June 1,2011.   Human frontiers Listen 2011

New research has suggested that pathogenic microbes could be implicated in a whole host of diseases, including obesity, heart disease, cancer, Alzheimer's, arthritis and autism.

""We may find there are new links between the human microbiome and diseases that today we don't think of having any underlying microbial component," says Claire Fraser-Liggett, Director of the Institute for Genome Sciences at the University of Maryland.

The hope is that this research may pave the way for more personalised treatments which could help get our bacterial communities back on the right track.

Max Planck Institute of Neurobiology in Martinsried, Germany, "Natural intestinal flora involved in the emergence of multiple sclerosis," Max-Plank Gesellschaft, October 27, 2011.   Max Planck Institute: gut flora & MS   "Precisely which bacteria are involved in the emergence of multiple sclerosis remains unclear; possibly  clostridiums."

Mazmanian, SK., et al. “A microbial symbiosis factor prevents intestinal inflammatory disease,” Nature, 2008. 453:620-625. Mazmanian: microbe symbiosis factor prevents

Mazmanian Sarkis K., "Evolutionary Mechanisms of Host-Bacterial Symbiosis during Health and Disease," California Institute of Technology, October 10, 2010.  Article by Mazmanian: symbiosis health and disease is no longer active.  “The potential of beneficial microbes appears to be limitless” and that “this symbiotic relationship between the human body and microbes [is] a gold mine of potential therapies for a number of illnesses.”

Mercola J., "Beneficial Bacteria (Probiotics) May Halt Allergies In Babies,", April 14 2001   Article by Mercola: Allergies & probiotics is no longer active.

"Researchers in Finland used a type of bacteria found naturally in the gut -- called Lactobacillus GG (Lactobacillus rhamnosus), which is safe at an early age and effective in treatment of allergic inflammation and food allergy -- to try to prevent allergy development in at-risk infants.

Investigators gave a group of pregnant women probiotic capsules every day for a few weeks before their due dates. For 6 months after delivery, women who breast-fed continued on the probiotics, while bottle-fed infants were given the treatment directly. All of the babies were considered to be at high risk of developing allergies because a parent or sibling was affected.

By the age of 2 years, 35% of the children had developed allergic eczema, a condition in which the skin becomes irritated, red and itchy.

But children who had received probiotics were half as likely to develop the skin condition. This cut in eczema risk is the most spectacular, single result to come out of studies on preventing allergic disease. Exactly why friendly gut bacteria might protect against allergies is unclear, but the effect may be an "extension of the hygiene hypothesis."   Article by Kalliomaki: probiotic help allergy is no longer active.

Mercola J., "One Third of Probiotics 'Good Bacteria' Products, Like Acidophilus, Found to be Worthless,", July 11 2001.  Article by Mercola: 13 % good bacteria is no longer active.

Mercola J., "Wall Street Journal Gives BIG Thumbs Up to Good Bacteria,", January 31 2009.  Article by Mercola: immune sys 80% in GI tract is no longer active.

MetaHIT is a EURO funded project with affiliations to International Human Microbiome Consortium (IHMC).  Director Dusko.Ehrlich, "Metagenomics of the Human Intestinal Tract," Report August, 2011. Article by MetaHIT Report on intestinal tract is no longer active. MetaHIT is a project financed by the European Commission under the 7th FP program. The consortium gathers 13 partners from academia and industry, a total of 8 countries. Its total cost has been evaluated at more than 21,2 million € and the funding requested from the European Commission has been set with an upper limit of 11,4 million €. The project will last from January 1, 2008 until June 30, 2012.

Minocha Anil, "Probiotics for Preventive Health," Nutr Clin Pract APRIL-MAY 2009 vol. 24 no. 2 227-241.   Minocha: Probiotics & preventive health

Randomized, double-blind studies have provided evidence of the effectiveness of probiotics for preventing various diarrheal illnesses as well as allergic disorders. Evidence for their efficacy for use in the prevention and treatment of bacterial vaginosis and urinary tract infections is also mounting. In addition, probiotics may be useful for preventing respiratory infections, dental caries, necrotizing enterocolitis, and certain aspects of inflammatory bowel disease. Data also suggest that probiotics may promote good health in day care and work settings, and may enhance growth in healthy as well as ill and malnourished children.

Monastyrsky Konstantin, "Restoring Intestinal Flora,"  Monastyrsky: restoring good health “There are over 400 species of bacteria in the colon; bacteria make up 30%–50% of the total dry matter in the feces, or even 75% according to other calculation." Disbacterosis

National Cancer Institute, "Immune system," Article by NCI: immune sys is no longer active.

"New concept in old disease,"   Article about New concept in old disease is no longer active.

Ng SC, Hart AL, Kamm MA, Stagg AJ, Knight Sc., "Mechanisms of action of probiotics: recent advances," Inflamm Bowel Dis., February 15, 2009,(2):300-10.  Ng: probiotic advancements 2009

"In controlled clinical trials probiotic bacteria have demonstrated a benefit in treating gastrointestinal diseases, including infectious diarrhea in children, recurrent Clostridium difficile-induced infection, and some inflammatory bowel diseases. This evidence has led to the proof of principle that probiotic bacteria can be used as a therapeutic strategy to ameliorate human diseases. The precise mechanisms influencing the crosstalk between the microbe and the host remain unclear but there is growing evidence to suggest that the functioning of the immune system at both a systemic and a mucosal level can be modulated by bacteria in the gut."

Null Gary, "Vitamin D is essential for activating immune system function," Gary Null- Your Guide to Natural Health, December 3, 2010.   Article by Null: Vit D triggers immunity 2010 is no longer active.

Park Alice, "A Surprising Link Between Bacteria and Colon Cancer," Time HealthLand, October 18, 2011.   Park: bacteria- cancer link 2011

Pearl Seth, "The digestive immune system connection," Digestive Health Information Center,   Pearl: immune-dig connection

Porter David L., Bruce L. Levine, Michael Kalos, Adam Bagg and Carl H. June, "Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia," N Engl J Med 2011; 365:725-733, August 25, 2011.   Porter: controlling leukemia 2011

Primal Defense: Two of the soil organisms in Primal Defense are Bacillus subtilis and Bacillus lichenformis. In studies conducted in Germany at the University of Berlin’s Max-Volmer Institute, both were shown to inactivate human immunodeficiency, herpes simplex (HSV-1 and HSV-2), simian immunodeficiency, feline calicivirus, murine encephalomyocarditis, and other lipid envelope viruses—along with mycoplasmas, fungi and bacteria. They do so by producing a potent chemical called surfactin, a detergent-like substance that dissolves the lipid membranes of lipid envelope viruses, thereby rendering them completely inactivated. 

Probiotics means "for life." The joint Food and agriculture/World Health organization defines probiotics as "live microorganisms which, when administered in adequate amounts, confer a health benefit to the host."  Market Research: boosting immunity  Probiotics are not the same thing as prebiotics -- nondigestible food ingredients that selectively stimulate the growth and/or activity of beneficial microorganisms already in people's colons. When probiotics and prebiotics are mixed together, they form a synbiotic.

"Gut bacteria also: •help synthesize B and K vitamins •enhance gastrointestinal motility and function •enhance digestion and nutrient absorption •obstruct the growth of “bad bacteria” and other pathogens •help metabolize other plant compounds/drugs •produce short-chain fatty acids (SCFAs) and polyamines •produce coagulation and growth factors •produce cytokines (cell signaling molecules) •help regulate intestinal mucus secretion and ultilization •help regulate blood flow to the viscera."   All about probiotics

Proctor LM., "The Human Microbiome Project in 2011 and beyond," Cell Host Microbe. 2011 Oct 20;10(4):287-91.   Proctor: USA Human Microbiome Project 2011   Human frontiers Listen 2011

PT Staff, "Our Second Brain: The Stomach," Psychology Today, May 01, 1999.   Pych Today: second brain States that human stomach has neurotransmitters similar to the brain.

Reid Gregor, Jana Jass, M. Tom Sebulsky, and John K. McCormick, "Potential Uses of Probiotics in Clinical Practice," Clin Microbiol Rev. 2003 October; 16(4): 658–672.   Reid: Probiotic uses in medicine 2003

Reinberg Steven, "Stomach Bacteria Might Trigger Rheumatoid Arthritis," Bloomberg Businessweek Executive Health, June 17, 2010.   Article by Reinberg: Rheumatoid Arthritis is no longer active.

Report of a Joint FAO/WHO Expert consultation on evaluation of health and nutritional properties of probiotics in food including powdered milk with live lactic acid bacteria, Cordoba, Argentina, October 1-4, 2001.   Article about Report: evaluation probiotics is no longer active.

Reuter Gerhard, "The Lactobacillus and Bifidobacterium Microflora of the Human Intestine: Composition and Succession," Current Issues in Intestinal Microbiology 2001. 2(2): 43-53.  Article by Reuter: Microflora human intestine is no longer active.

Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, & Mazmanian SK., "The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota," Science 2011.  Round: microbe clonization 2011  The host immune system, via Toll-like receptor (TLR) recognition, can differentiate pathogenic and commensal bacteria. This landmark article for the first time determines how microorganisms tailor host immune cell activation in order to establish symbiotic colonization of determined niches in the gut in a mutualistic fashion.

Rubin Jordan, "Beyond Probiotics,"  Article by Rubin: Probiotic healing is no longer active.

Scher, Jose U., Ubeda, Carles, Pillinger, Michael H., Bretz, Walter, Buischi, Yvonne, Rosenthal, Pamela B., et al; Characteristic Oral and Intestinal Microbiota in Rheumatoid Arthritis (RA): A Trigger for Autoimmunity? [abstract]. Arthritis Rheum 2010;62 Suppl 10 :1390, DOI: 10.1002/art.29156.   Article by Scher: RA & microbes is no longer active.

Seattle Cancer Care Alliance (SCCA), "Autoimmune Diseases Facts."  Article by Seattle SCCA: autoimmune diseases is no longer active.

Serotinin & Sunlight: Low exposure to sunlight can deplete serotonin. Serotonin deficiency is related to Seasonal Affective Disorder, which includes feelings of sadness or depression during the winter months or in the evenings. Light plays a crucial role in serotonin production. Sunlight makes serotinin

Smith Michael, “Gerd linked to microbe changes,” Medpage Today, August 04, 2009.   Article by Smith: GERD linked to microbe is no longer active.   This study found that esophageal disease is associated with large-scale changes in the microbes that colonize the esophagus, although it is not yet clear whether the effect is a cause or an effect of GERD. The study was supported by the National Cancer Institute, the National Institute for Allergy and Infectious Diseases, and the Department of Veterans Affairs.

Stevenson Heidi, "New Study Reveals That Antibiotics Damage Our Immune System," GAIA Health, April 24, 2011.   Article by Stevenson: antibiotics cause chronic diseases 2011 is no longer active.

"The study concludes that the use of antibiotics must be causing chronic diseases." A new California Institute of Technology [Caltech] study has shown that our intestinal bacteria determine which bacteria are beneficial and which are pathogenic. Even more significantly, it is the gut bacteria that trigger an immune response, not the immune system itself. This indicates that science and medicine need to completely rethink the current view of how the immune system operates.

Taylor John R., and Mitchell, Deborah. The Wonder of Probiotics. New York, NY: St. Martin’s Press, 2007.   "recommends a supplement with at least five of twelve particular probiotic species. The first of those is Lactobacillus acidophilus DDS-1, the basis for any probiotic program. The others include Lactobacillus casei, Lactobacillus plantarum, Bifidobacteria bifidum, Bifidobacteria longum, Bacillus coagulans, Bifidobacteria infantis, Lactobacillus rhamnosus, Lactobacillus salviarius, Lactococcus lactis, Enterococcus faecium, and Streptococcus thermophilus."

Teraguchi, S, Ono , J . et al. "Vitamin production by Bifidobacteria originated from human intestine" [Thiamine , riboflavin , pyridoxine , niacin, folacin , vitamin B12, vitamin C] . Nippon Eiyo Shokuryo Gakkaishi [Journal of the Japanese Society of Nutrition and Food Science] 37(2): pp 157-164,1984 (language : Japanese with summary in English) "Research by Japanese scientists has demonstrated that vitamin C is generated from healthy human intestinal flora." Article by Teraguchi: Bifidobacteria makes vitamins is no longer active.   Article by Teraguchi: Vit from human bacteria is no longer active.

"Abstract:  Vitamin production by the strains of Bifidobacterium infantis, B. breve, B. bfidum, B. longum and B. adolescentis was studied. They accumulated vitamin B1, B2, B6, B12, C, nicotinic acid, folic acid and biotin intracellulary while they excreted vitamin B6, B12 and folic acid in the medium.

B. longum, B. breve and B. infantis exhibited an appreciable vitamin production. The production of vitamin B2 and B6 by B. longum was outstanding. B. breve and B. infantis respectively produced nicotinic acid and biotin to a higher concentration which was distinctive from the case of the other species. A significance of the intestinal Bifidobacteria, in vitamin nutrition in the host, was discussed.

Tlaskalová-Hogenová Helena, "Review: The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases," Cellular & Molecular Immunology, January 2011, 8, 110–120.   Tlaskalová: role of gut microbes in diseases 2011   "Although the most important findings in this fascinating field are still to come, it is clear that our bacterial companions affect our fates more than previously assumed."

UCSD  UCSD: lines defense

Upadhyay Nikhil and V. Moudgal, "Probiotics: A Review," February 2012 Journal of clinical outcomes management: JCOM 19(2):76-84  Upadhyay: Probiotics review 2012

Walker Morton, "Jordan Rubin's amazing journey, Cure for Crohn’s Disease, sickness to health,"  Article by Walker: Cure for Crohns Disease is no longer active.

HSO = Homeostatic Soil organisms: These are beneficial microbes found in pristine soils that are as necessary for health. Homeostatic soil organisms are super probiotics (the opposite of antibiotics). They restore balance to an autointoxicated gastrointestinal tract in a specific manner. Upon being swallowed, the HSOs™ activate and bring about gut restoration by attaching themselves to the intestinal mucosa. On the gut wall they reproduce to form colonies along the course of "receptor sites" which had previously been established by harmful bacteria and other pathological microorganisms. These pathogens are crowded out or eaten up by the probiotics so that symptoms of illness they had been producing tend to terminate eventually. The time factor for symptomatic healing is dependent upon the volume of pathogens lodged at the gut's receptor sites. No matter what the number of bad bacteria or other pathogens, HSOs™ implant themselves and bring about gut restoration.

Wenner Melinda, "Jeremy Nicholson's Gut Instincts: Researching Intestinal Bacteria," Scientific - June 17, 2008  Article by Wenner: researching gut bacteria is no longer active.

"The most well-known disease-causing gut organism is the bacterium Helicobacter pylori, which can trigger peptic ulcer. In the past few years, scientists have linked obesity to the relative abundance of two dominant intestinal bacterial phyla and found that dysfunctional intestinal bacteria are associated with nonalcoholic fatty liver disease, inflammatory bowel disease and some types of cancer. Nicholson even speculates that the organisms could play a role in neurological disorders, such as attention-deficit hyperactivity disorder, Tourette’s syndrome and autism. “We have some evidence now that shows that if you mess around with the gut microbes, you mess around with brain chemistry in major ways,”

Wikipedia, "Bifidobacterium."   Wiki: Bifidobacterium     Bifidobacteria are able to prevent or alleviate infectious diarrhea through their effects on the immune system and resistance to colonization by pathogens. There is some experimental evidence that certain bifidobacteria may actually protect the host from carcinogenic activity of intestinal flora. Bifidobacteria may exert protective intestinal actions through various mechanisms, and represent promising advances in the fields of prophylaxis and therapy. 

Bifidobacteria, called probiotics, are a natural part of the bacterial flora in the human body and have a symbiotic bacteria-host relationship with humans. B. longum promotes good digestion, boosts the immune system, and produces lactic and acetic acid that controls intestinal pH. These bacteria also inhibit the growth of Candida albicans, E. coli, and other bacteria that have more pathogenic qualities than Bifidobacteria.  Wiki microbes  

Species: B. angulatum; B. animalis; B. asteroides; B. bifidum; B. boum; B. breve; B. catenulatum; B. choerinum; B. coryneforme; B. cuniculi; B. dentium; B. gallicum; B. gallinarum; B indicum; B. longum; B. magnum; B. merycicum; B. minimum; B. pseudocatenulatum; B. pseudolongum; B. psychraerophilum; B. pullorum; B. ruminantium; B. saeculare; B. scardovii; B. simiae; B. subtile; B. thermacidophilum; B. thermophilum; B. urinalis; B. sp. Wiki microbes

Wikipedia, Immune system.  Wiki: immune system

Wikipedia   Wiki: intestinal tract

Wikipedia, "List of human diseases associated with infectious pathogens."   Wiki: List human disease linked pathogens

Wikipedia, "Payer's Patch."   Peyer's Patch 

Wong, Julia M. W., de Souza, Russell Kendall, Cyril W. C., Emam, Azadeh, Jenkins, David J. A., "Colonic Health: Fermentation and Short Chain Fatty Acids," Journal of Clinical Gastroenterology, March 2006 - Volume 40 - Issue 3 - pp 235-243.   Wong: fatty acids  The rate and amount of SCFA production depends on the species and amounts of microflora present in the colon, the substrate source and gut transit time.Butyrate has been studied for its role in nourishing the colonic mucosa and in the prevention of cancer of the colon.

Wu Hsin-Jung, Ivaylo I. Ivanov, Jaime Darce, Kimie Hattori, Tatsuichiro Shima, Yoshinori Umesaki, Dan R. Littman, Christophe Benoist, and Diane Mathis, "Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells," PubMed Central, June 25, 2010 issue of Immunity.   Wu: gut bacteria causing autimmune arthritis 2010

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, et al. , "Evolution of Symbiotic Bacteria in the Distal Human Intestine,"  PLOS Biology,  2007, 5(7): e156. doi:10.1371/journal.pbio.0050156.   Xu: evolution Symbiotic gut Bacteria

Yadav Vijay K, Santhanam Balaji, Padmanaban S Suresh, X Sherry Liu, Xin Lu, Zhishan Li, X Edward Guo, J John Mann, Anil K Balapure, Michael D Gershon, Rudraiah Medhamurthy, Marc Vidal, Gerard Karsenty & Patricia Ducy, "Pharmacological inhibition of gut-derived serotonin synthesis is a potential bone anabolic treatment for osteoporosis," Nature Medicine February 17, 2010, 16,308–312.   Yadav: serotonin link to osteroporosis 2010

Zimmer Carl, "How Microbes Defend and Define Us," New York Times, July 12, 2010.   Zimmer: How Microbes Defend us  "The Imperial College team that discovered microbes in the lungs, for example, also discovered that people with asthma have a different collection of microbes than healthy people. Obese people also have a different set of species in their guts than people of normal weight." and bacteriotherapy or fecal transplantation