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By Alice Abler
Over a century ago, Russian scientist Ilya Metchnikoff (aka Elie Metchnikov) began a life-altering study of a group of Bulgarian peasants. He was intrigued by their unusual longevity; despite primitive hygienic conditions, members of the group often lived to be a hundred years old. The mainstay of their diet was a soured milk product – something between buttermilk and yogurt – that was teeming with lactic acid bacteria. Metchnikoff opined that these microbes battled pathogenic, life-shortening bacteria in the gastrointestinal system.
Predating the current knowledge of the gut-brain connection, Metchnikoff developed a theory that the physiological changes associated with old age are due to poisoning of the body by the products of unfriendly bacteria in the gut. Aware that food can influence the makeup of the gut flora, he postulated: “The dependence of the intestinal microbes on the food makes it possible to adopt measures to modify the flora in our bodies and to replace the harmful microbes by useful microbes.”
Metchnikoff proposed that consuming fermented raw milk would allow beneficial bacteria to supplant the harmful organisms in the gut. To this end, he began the task of separating out and drying the lactic acid bacteria, which he called the “Bulgarian Bacillus” – now known as Lactobacillus delbrueckii subsp. Bulgaricus – so the soured milk product could be replicated outside its native land.
Metchnikoff tested his theory on himself, inoculating fresh milk with the lactic acid bacteria and drinking the fermented product on a daily basis, which benefited his health. After he won a Nobel Prize in physiology in 1908, his ideas spread far and wide, remaining quite popular until “modern” ideas of sterility and germ-free living changed the way we eat and drink. Today, however, the old idea of adding beneficial bacteria to our diets is regaining popularity – this time, with a new name: probiotics.
Functions of the microbiome
Although it’s still common to think of bacteria as unpleasant and unwanted, our bodies house thousands of distinct species, and the human microbiome (this collection of microbes) is crucial to our existence. Colonies of bacteria, along with some fungi and yeasts, are found in the mouth, sinuses, ears, genitals, and urinary and gastrointestinal systems, as well as on the skin, and each colony is specific to the part of the body in which it is found. These microbes actually outnumber our own cells by as much as ten to one.[3,4]
Today, we believe that the microbiome may be as important to human health as the genome. However, unlike the genome, we can change our microbiome. The potential of this goes far beyond what we currently understand, and studying the human microbiome – particularly the beneficial bacteria that reside in our gastrointestinal system – is rapidly becoming one of the most important scientific inquiries of this age.
The gut microbiota, the microbes living in our intestines, are responsible for numerous functions that are necessary for our good health. These functions can be grouped into three general areas:
- Metabolic processes (breakdown of food and its transformation into energy)
- Trophic processes (synthesis of vitamins and other vital nutrients)
- Protective processes (feeding and strengthening of the intestinal mucosal lining, which keeps ingested harmful pathogens from attaching to the walls of the intestines; and production of antimicrobial compounds that kill off those pathogens)
Metabolism: We have long understood that naturally occurring fiber in whole foods is helpful for regulating the passage of waste through the body, but we continue to discover other ways that such foods, in combination with the gut microbiota, keep the colon healthy. The gut microbes produce enzymes that aid in the fermentation of carbohydrates and enable the breakdown of fibrous materials that cannot be digested by the human body alone. The results of this important process include the production of short-chain fatty acids (SCFAs), some of which are absorbed into the bloodstream through the gut walls and transported to vital organs. Study of their many roles is ongoing, but it appears that SCFAs act as food for the mucosal lining, aid in the prevention of gastric disorders (for example, colitis, irritable bowel syndrome, and Crohn’s disease), regulate cholesterol synthesis, and protect against cancer and cardiovascular disease.
Trophism: Beneficial gut flora also manufacture nutrients for use within the body. Vitamins B1, B2, B3, B5, B12, and K2, along with folic acid and biotin, are all synthesized by the microbiota. Bacterial fermentation of carbohydrates in the large intestine yields significant amounts of lactic acid, which plays several important roles in the human gut. It is a fuel for mitochondria (the “engines” at the center of our cells), aids the immune system, and has even been found to inhibit colon cancer in both animal and in vitro studies.
Protection: The lactic and other acids produced by beneficial gut bacteria also reduce the pH of the gastrointestinal system, creating an acidic environment that is detrimental to many pathogens. In some cases, the pathogenic microbes die, but in most cases, they simply pass through without attaching to the intestinal walls. Their passage is facilitated if the intestines are healthy and robust, with a rich growth of cilia on the walls and a generous mucosal layer (nourished by helpful bacteria) that pathogens find difficult to penetrate. As pathogens pass through a properly functioning gut, they encounter active beneficial bacteria, which distinguish between harmful microbes and friendly flora. These pathogens are targeted by the beneficial bacteria and may be destroyed by antimicrobial compounds (bacteriocins) that they produce.
A delicate balance
When pathogens do manage to attach to the intestinal walls, a healthy immune system will kick in to suppress the intruders, a process in which inflammation plays a role. In moderation, inflammation can help the body’s healing processes and protect against invading pathogens. However, too much inflammation is associated with many of today’s chronic diseases – heart disease, diabetes, cancer, autoimmune disorders, and diseases of the bowel. An important part of avoiding excessive inflammation is to make sure the gut has a healthy balance of beneficial gut flora to pathogenic bacteria.
Unfortunately, in modern society, it’s all too easy to destroy that delicate balance. Experiencing excessive stress, being exposed to toxic chemicals within the home or in agriculture, eating fruits and vegetables treated with pesticides or herbicides, consuming meats and dairy products from animals treated with antibiotics, drinking chlorinated water, ingesting processed or sugary foods, and even aging can create an imbalance in the gastrointestinal system. However, as we will see, this imbalance can be rectified.
Probiotic treatment of disease
An imbalance of intestinal flora resulting in inflammation is related to a surprisingly broad range of intestinal disorders and chronic diseases. However, promising results from many recent studies have shown that increasing the amount of beneficial bacteria in the gut can reduce inflammation and lead to improvements in health.
Foodborne pathogens and friendly flora
Various diarrhea-causing bacteria, such as Clostridium difficile, are common in the digestive system. With a proper balance of intestinal bacteria, C. difficile does not cause problems. However, when the balance is disrupted and the population of beneficial bacteria is drastically reduced (most commonly by the use of antibiotics), the number of pathogenic microbes can increase enough to cause severe diarrhea.
Repopulating the gut with friendly flora – probiotic treatment – usually alleviates the symptoms of infection by C. difficile, salmonella (a common food-borne pathogen that causes diarrhea and nausea), and even rotaviruses (the most frequent cause of severe diarrhea in infants and young children). The use of such treatment could have far-reaching implications. According to the Food and Agriculture Organization of the United Nations (FAO), these treatable infections are responsible for millions of deaths each year in developing countries.
Constipation: Probiotic therapy to alleviate constipation has a long history of anecdotal success. For millennia, people have ingested fermented milk products to aid in regularity. Although studies on the topic are inconclusive, some results support this long-standing home remedy by indicating that probiotics may be helpful in cases of chronic or severe constipation.
Inflammatory bowel disease: Some studies illustrate that inflammatory bowel disease (a group of conditions that includes pouchitis, Crohn’s disease, and irritable bowel syndrome) may be caused or aggravated by alterations in the balance of gut flora. These findings indicate that probiotic therapy using combinations of bacterial strains may help remediate inflammatory bowel disease through modulation of the microflora.
One study found that people with ulcerative colitis had a much smaller population of bifidobacteria (one of the beneficial flora) – about 30 times smaller – than would be found in a typical healthy individual. Increasing the bifidobacteria levels via probiotic treatment brought on remarkable improvements. Probiotic treatment of patients with active ileo – colonic Crohn’s disease also had favorable results, and patients undergoing remission had higher levels of bifidobacteria than those who did not.
Helicobacter pylori is a microbe responsible for type B gastritis, peptic ulcers, and gastric cancer. This pathogen does not thrive in acidic environments, so organic acids formed by Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus bulgaricus, Pediococcus pentosaceus, and Bifidobacterium bifidus bacteria can inhibit its growth. They render the stomach environment inhospitable, reducing the occurrence of these conditions.
Cancer: Beyond gastric cancer, there is some preliminary evidence that beneficial microorganisms can prevent or delay the onset of other cancers. Some members of the gut microbiome can produce carcinogens (such as nitrosamines), but taking probiotics such as lactobacilli and bifidobacteria could theoretically modify the balance of flora favorably, thereby decreasing cancer risk. More research in this area is needed. However, studies have found evidence that cancer recurrences at other sites, such as the bladder, can be reduced by intestinal instillation of probiotics.[14,15]
Immunity: A healthy gut is the key to a healthy immune system, and probiotic modulation of host immunity is a very promising area for future study. Research has proven that certain bacteria in the gut influence immune system development, correcting deficiencies and increasing the numbers of healing cells. Although it is not yet known exactly how bacteria interact with the immune system, there is plenty of intriguing evidence showing that intestinal bacteria do bolster immunity.
Allergies: An allergic reaction is the body’s immune response to a substance that is perceived to be a pathogen. The results of several trials illustrate the potential for probiotics to modulate the immune response and prevent the onset of these reactions.
In one study, Lactobacillus rhamnosus GG was given to pregnant women for four weeks prior to delivery, and then was given for six months to their newborns, who were at high risk for allergy. This probiotic treatment resulted in a significant reduction in skin conditions such as eczema and atopic dermatitis.[17,18]
In other clinical studies with infants allergic to cow’s milk, atopic dermatitis was alleviated by ingestion of probiotic strains of lactobacillus and bifidobacteria. The positive results appear to be due to probiotic lactobacilli reversing intestinal permeability, promoting gut barrier function. This means that a proper balance of the microbiota helps keep the gut lining healthy, which prevents molecules of food matter from migrating out of the gastrointestinal tract and into other organs, where they provoke an immune-system response.
Cardiovascular disease: Scientists hypothesize that low levels of beneficial gut microbes in the obese may contribute to chronic low-grade inflammation related to cardiovascular disease. Moreover, probiotic lactobacilli and their metabolic byproducts seem to aid in prevention and therapy of various ischemic heart syndromes. Certain strains of lactobacillus also seem to reduce serum cholesterol, perhaps through deconjugation of bile salts by the production of bile salt hydrolase.
Arthritis: Probiotics have a positive effect on calcium metabolism and bone health. This is thought to be the result of improved absorption of minerals due to the production of SCFAs, increased expression of calcium-binding proteins, degradation of phytic acid, and other anti-arthritic effects. Probiotics also improve immune function, which can help reduce the severity of rheumatoid arthritis and other autoimmune diseases.
Kidney stones: People who are host to Oxalobacter formigenes, a beneficial gut bacteria, are much less likely to develop kidney stones than those whose gastrointestinal tracts lack that microbe. O. formigenes seems to break down calcium oxalate in the intestinal tract before it can move into the kidneys and form stones. In clinical studies, probiotic supplements containing lactic acid bacteria, including Lactobacillus acidophilus, Lactobacillus brevis, Streptococcus thermophilus, and Bifidobacteria infantis, reduced urinary oxalate excretion and helped prevent kidney stone formation.
Urogenital tract infections in women: Nearly all infections of the vagina and bladder (with the exception of sexually transmitted diseases) are caused by microorganisms that originate in the bowel. A preponderance of lactobacilli in the vagina is associated with vaginal health. Bacterial vaginosis is tied to the overgrowth of pathogenic bacteria, which under normal circumstances are subdued by a healthy community of lactobacilli. Disruption of the normal lactobacillus-rich vaginal flora is caused by broad-spectrum antibiotics, spermicides, hormonal imbalances, and poor diet.
Probiotic therapy may treat or prevent urogenital tract disorders. Yogurt with live cultures taken orally or vaginally is commonly recommended for prevention and treatment of candidal vaginitis, and oral probiotics that include L. acidophilus have seemed to help in clinical trials. Evidence suggests that probiotics containing lactobacilli can reduce recurrence of this condition.
Uropathogenic Escherichia coli originating in the bowel is responsible for up to 85 percent of urinary tract infections in women. Taking oral probiotics and using probiotic suppositories that create a lactobacillus barrier in the vagina help keep pathogens from traveling into the bladder, thereby blocking the infection process.
Depression: Gastrointestinal problems can play a role in depression, and their treatment with probiotics can have positive effects. Stress, a known risk factor for depression, causes an imbalance in the gastrointestinal microflora – with decreased lactobacillus and bifidobacteria – which can be corrected with the use of probiotics.
Gut bacteria may be able to alter brain neurochemistry, affect anxiety – and depression-related disorders, and play a role in regulating the central nervous system. Because the gut and the brain work in tandem, constipation and depression may be associated. Since healthy intestinal flora ensure regular elimination of human waste through stool formation, regular elimination may help alleviate depression.
Autism: The gut-brain connection can also play a role in autism spectrum disorders. There is a strong correlation between autism severity in children and degree of gastrointestinal problems, which is the focus of ongoing research.
Natasha Campbell-McBride, MD, a physician with degrees in both neurology and nutrition, believes that autism is largely caused by “toxicity, which is produced by the abnormal microbial mass in the digestive tract of the child, [and] establishes a link between the gut and the brain.” She has successfully treated hundreds of autistic children and adults, and her book Gut and Psychology Syndrome has helped many more sufferers through the process of rebuilding the proper balance of intestinal flora and healing the gut.
Establishing healthy flora
A fetus may have limited exposure to bacteria via the placenta, but the majority of the microbiome begins to form on the day of a baby’s birth. Ideally, the first flora to attach itself to a baby is the beneficial bacteria in the birth canal. Babies born via Caesarean section do not have this protection, which may explain why those babies seem to be more vulnerable to asthma, allergies, and infection. As an example, 64 to 82 percent of reported cases of methicillin-resistant Staphylococcus aureus (MRSA) infecting the skin of newborns, as recorded in Los Angeles County and Chicago in 2004, occurred in Caesarean-delivered infants.
The health of the mother’s flora is crucial to the future health of her infant. A breast-fed newborn begins to nurse almost immediately after birth, getting yet more friendly bacteria from the mother’s skin and her “first milk” – the bacteria – and nutrient-rich colostrum. Bifidobacteria dominate the fecal microbiota of healthy breast-fed infants whereas formula-fed infants have a wider range of organisms present, including bifidobacteria, bacteroidetes, clostridia, enterobacteria, and streptococci. At weaning, there are changes in the numbers and diversity of the gut microbes, and the microbiome gradually begins to resemble that of an adult.
Microbiome and early development
Research shows that young children who take antibiotics may be at greater risk of developing allergies and asthma, as the drugs decimate the original healthy microbiome, which seems to be more protective than one that is returned to proper balance later. This conclusion is supported by results of the Human Genome Project, which infer that specific probiotics may be introduced to infants to establish a flora that improves life-long health.
With this in mind, some have suggested that probiotic treatment in premature, low-birth-weight newborns can save their lives. These babies are often fed with artificial infant formula, which does not transfer any beneficial bacteria to their guts. Although antibiotics are often prescribed, administering probiotics can help colonize and develop a healthy microbiome in newborns, which can reduce the severity of necrotizing enterocolitis, the second most common cause of death among premature infants.
Killing off good bacteria
In our germophobic society, excessive prescription of antibiotics has created resistant strains of harmful bacteria, and we regularly have antibacterial soaps, wipes, and gels positioned for use in public spaces. Of course, these can be helpful under certain circumstances, but their everyday use can wreak havoc on our microbiome. Drinking chlorinated and fluoridated water also has a negative effect on gut flora. Radiation and chemotherapy kill both harmful and helpful bacteria. Oral contraceptives, meat and dairy products from animals treated with antibiotics, processed foods, excessive alcohol and caffeine, and soft drinks all contribute to gut dysbiosis.
Role of the appendix
Some research indicates that, although the appendix has long been thought to be a disposable vestigial organ, it may actually act as a “safe house” for the bacteria living in the gut. The stored bacteria would serve as a reserve to reinoculate the colon if needed. This backup system would be activated if the contents of the intestinal tract were purged, whether as a result of exposure to a pathogen or through artificial means. This theory explains how gut bacteria can repopulate after a bout of diarrhea, a course of antibiotics, or procedures such as colonoscopies, which disturb the microbial flora in the colon and can alter their balance.
The good news is that we can reverse the damage done to the microbiome through diet, lifestyle, and probiotic therapy. Using antibacterials and antibiotics only when necessary, and avoiding irradiated or processed food as well as chemicals that kill beneficial bacteria are important first steps.
Eating foods that contain natural probiotics helps rebuild and maintain a healthy microbiome. These foods include fermented vegetables and grain products (such as pickles, sauerkraut, tempeh, miso, natto, kimchi, and sourdough); fresh, raw milk and fermented, unpasteurized dairy products (yogurt, lassi, kumiss, and kefir); live vinegars; and lacto-fermented beverages (kombucha and beet kvass). Such foods have been diet staples in many cultures since the beginning of written history. It’s only in recent decades that naturally fermented foods have been replaced with denatured replicas – pickles made with distilled vinegar, sourdough made with processed yeast, and dairy products pasteurized to kill bacteria.
Today, we have access to what seems to be an innumerable variety of commercial probiotic formulas in tablet, capsule, powder, or liquid form, marketed for everything from improved oral health to relieving troublesome skin conditions. These preparations often contain specific beneficial strains of bacteria from the genera Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, and Bacillus as probiotic agents that are either taken on their own or added to a food.
More than 100 strains of beneficial bacteria may be found in fermented raw milk products, while commercial yogurt is typically made from pasteurized milk, in which much of the naturally occurring bacteria has been destroyed by heat. In the United States, the Food and Drug Administration requires that anything labeled yogurt must be pasteurized before culturing with Lactobacillus bulgaricus and Streptococcus thermophilus. With most brands, only a few types of beneficial bacteria are reintroduced after pasteurization.
Some yogurt products carry a “Live and Active Cultures” seal, which assures that they contain at least 100 million organisms per gram at the time of manufacture, and at least ten million at the end of the listed shelf life. Unfortunately, many commercial probiotic formulas only list the potency as of the production date, and there is no guarantee of what may remain after transportation and storage.
With any commercial probiotic product, it’s important that the microbial strains be listed on the label. That label should also disclose the recommended serving size and the number of microbes available at the time of manufacture and at the time of expiration. This number is often referred to in terms of “colony-forming units” (CFU), which indicates the amount of live bacteria that will multiply in the gut. The label should also have storage recommendations.
Most probiotics are sensitive to heat and environmental conditions, and should be stored in a cool, dark place, such as a refrigerator, for optimum longevity. However, some products are lyophilized (freeze-dried) to maintain viability, and these may not require refrigeration (although refrigeration can often extend shelf life). To best protect the active bacteria, follow any instructions on the product packaging. A reputable probiotic should have contact information on the label for consumers with questions.
Prebiotics are substances that aid in the colonization of probiotics. These indigestible carbohydrate compounds (complex carbohydrates or fiber), primarily oligosaccharides, pass through the gastrointestinal system but are not used by the host, instead feeding the flora in the gut.
Ideally, this process begins with a newborn’s first meal. Human milk contains specific oligosaccharides that are of no nutritional use to the baby, but they are far from useless. Researchers have found these sugars serve as prebiotics that feed Bifidobacterium longum subsp. infantis, a particular subspecies of bacteria that colonizes the gut of nursing newborns.
Like probiotics, prebiotics are found in nature and are also commercially available in capsules, powders, or enhanced food products. Jerusalem artichokes (sunchokes), chicory root, dandelion greens, grains, honey, yacon, bananas, and alliums (garlic and onions) are all natural sources of fructooligosaccharides (FOS), plant-based prebiotics that provide food for health-promoting lactobacilli and bifidobacteria.
A mixture that combines probiotics and prebiotics is called a synbiotic. The name alludes to synergism, underscoring the idea that the prebiotics and probiotics in a product work together in the gut. Some naturally fermented foods, especially fermented dairy products, contain a combination of friendly flora to populate the gut, and undigestible fiber that feeds the gut bacteria. Makers of synbiotics try to emulate this. Some commercial yogurt manufacturers, for example, create synbiotics by adding the prebiotic inulin to their probiotic products.
For the majority of people, the use of probiotics, prebiotics, and synbiotics is best viewed as an addition to a healthful lifestyle and balanced diet. Consumers often ingest these products with the goal of reducing their risk of disease and maximizing their good health through improving the health of their intestinal flora.
Foods containing beneficial bacteria have been important components of traditional diets since before written history. We still have much to learn about the wide range of benefits these foods provide, but their value is well established. As Metchnikoff and others learned long ago, adding these helpful bacteria to our diet can improve our health in extraordinary ways.
About the Author
Alice Abler is a health, food, and sustainable living writer with a background in art and design. She has lived in several countries, learning about the culture and the food, and now resides in Southern California, where she enjoys studying and incorporating age-old principles of permaculture and sustainability at her home. She is the Life and Health editor for Vision.org and maintains a website at ReNourishment.org.
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Six common probiotics
The study of beneficial bacteria and yeasts has given rise to a whole new category of supplements in the health marketplace – commercial probiotics. With so many products available today, it can be challenging to understand their differences. To this end, here is a list of six common types of probiotics and their roles in gastrointestinal health:
- Lactobacillus is a genus of bacteria that is very important for gut health. These microbes produce lactic acid as well as antibacterial, antiviral, antifungal, and antiseptic agents, all of which can render the gut inhospitable for pathogenic bacteria and prevent them from colonizing. Lactobacilli are important for the proper functioning of the immune system and the health of the mucosal gut lining. Certain species of lactobacillus have been isolated and used medicinally since the 1890s to restore normal microbial balance in the gut (Lactobacillus acidophilus), and since the early 1900s to treat urogenital infections. Throughout history, lactobacilli have been used to culture dairy products.
- Bifidobacterium is a strain of lactic-acid-producing bacteria that is abundant in breast milk. It is the most common bacteria in the infant gut, and lays the foundation for proper immune and gastrointestinal function. The amount of bifidobacteria in the gut decreases with age, but they remain the most abundant type of bacteria through adulthood. They synthesize amino acids, proteins, organic acids, vitamins K, B3, B6, B12, and folic acid, and assist in absorption of calcium, iron, and vitamin D.
- Saccharomyces is a family of yeasts used for treatment of diarrhea. In the 1920s, French scientist Henri Boulard observed that people in the Indo-China region chewed the skin of lychee and mangosteen fruits for this purpose, and he isolated from it a yeast strain called Saccharomyces boulardii that has been proven effective as a preventative and therapeutic agent for various gastrointestinal disorders. It is also an antagonist to Candida albicans, a pathogenic yeast responsible for a multitude of infections. Members of the Saccharomyces genus have been used for leavening bread for thousands of years, and for fermenting grains and fruits to make spirits. Saccharomyces and other fungi are traditionally used in cheesemaking.
- Streptococcus, another strain of lactic acid bacteria, normally lives in the bowel. Like lactobacilli, streptococci control pathogens by lowering pH and producing antibacterial substances such as hydrogen peroxide. They aid digestion by breaking down proteins and fermenting carbohydrates. Although some strains of these bacteria are pathogenic, others are commonly used in commercial products for alleviation and prevention of gastrointestinal disorders. Beneficial strains of streptococcus, such as S. salivarius and S. thermophilus, are commonly added to commercial yogurt and have shown to be effective in reducing reoccurrence of bacterial vaginosis and pouchitis.
- Enterococcus has certain similarities with Streptococcus, and there have been some difficulties in differentiating between the two genera. In 1984, based on DNA studies, a number of streptococcal species were reclassified as enterococci. Because of this, and because enterococci perform many of the same functions as streptococci, they are often not properly distinguished from each other on product labels.
- Bacillus subtilis is a type of soil bacterium. It is a spore-forming microbe that is resistant to intestinal acid, temperature extremes, and most antibiotics. This bacteria has antiviral, antifungal, and antibacterial properties, and secretes a substance that can function as a digestive enzyme. B. subtilis was used as a treatment for gastrointestinal disorders before the existence of sulfur-based antibiotics. It has strong immune-stimulating properties and is promoted as beneficial for allergies and autoimmune disorders. These soil bacteria are transient, meaning they do not colonize the gut but pass through and must be replaced via regular ingestion. In Asia, bacillus strains are traditionally used to ferment soybeans and to make natto.
– Alice Abler
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- Dixit K, Gandhi DN. Biotherapeutic properties of probiotic yeast Saccharomyces species in fermented dairy foods. Dairy Science and Food Technology. http://www.dairyscience.info/probiotics/105- biotherapeutic-probioticyeast.html. Published 2006. Accessed December 17, 2013.
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Published in the Price-Pottenger Journal of Health and Healing
Winter 2013 | Volume 37, Number 4
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