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Microbiome: All the bacteria, viruses and fungi in your body

Your Microbiome: All the Bacteria, Viruses, and Fungi that inhabit every body part

Modern technology is making it possible for medical scientists to analyze inhabitants of our bodies that most people would rather not know about. But the resulting information could one day possibly save your health or even your life.
I’m referring to the trillions of bacteria, viruses and fungi that inhabit virtually every body part, including these tissues once thought to be sterile. (Blood, cerebrospinal fluid, synovial fluid and many others were originally thought to be free of living organisms.) Together they make up the human microbiome and represent what is perhaps the most promising yet challenging task of modern medicine; determining the normal microscopic inhabitants of every organ and knowing how to restore the proper balance of organisms when it is disrupted.
Proof of principle, as scientists call it, has already been established for a sometime devastating intestinal infection by the bacterium Clostridium difficile. This infection, popularly called C. diff, often occurs when potent antibiotics wipe out the normal bacterial inhabitants of the gut that otherwise keep it in check.
When all else fails to clear up a recurrent C. diff infection, The US Food and Drug Administration has approved treatment with a fecal transplant from a healthy gut presumed to contain bacteria than can suppress C. diff activity. The treatment is highly effective, with a cure rate in excess of 90 per cent.
Under the auspices of the U.S. National Institute of Health, a large team of scientists is engaged in creating a “normal” microbiological road map for the following tissues: gastrointestinal tract, oral cavity, skin, airways, urogenital tract, blood and eye. The effort, called the Human Microbiome Project, takes advantage of new technology that can rapidly analyze samples of genetic material, making it possible to identify the organisms present in these tissues.
Depending on the body site, anywhere between 20 per cent and 60 per cent of the organisms that make up the microbiota cannot be cultured and identified with the older, traditional techniques used by microbiologists.
If the institute’s five year project succeeds in defining changes in the microbiome that are associated with disease, it has the potential to transform medicine, assuming ways can be found to correct microbial distortions in the affected tissues.
Here are some of the scientific projects already under way:
Dr. Martin Blaser, microbiologist and director of the human microbiome project at New York University School of Medicine, is directing examination of the organisms on the skin of 75 people with and without psoriasis, checking if agents used to treat it adversely alter the microbiome and possible make it worse.
Dr. Jaques Ravel at the University of Maryland School of Medicine and Dr.Larry Forney at the University of Idaho are studying 200 women to determine the microbial changes that may result in a common infection called bacterial vaginosis which affects more than 20 million U.S. women of child-bearing age.
At Washington University in St. Louis, Dr.Gregory Storch, a specialist in pediatric infectious disease and colleagues are examining the role of viruses and immune system in the blood and respiratory and gastrointestinal tracts of children who develop serious fevers that result in about 20 million visits a year to emergency rooms.
Dr. Claire Fraser-Liggett, a microbiologist, and Dr. Alan Shuldiner, a geneticist, both at the University of Maryland School of Medicine, are exploring how the microbiome affects the body’s use of energy and the development of obesity.
Previous studies have already found differences in the gut microbial of lean and obese adults. There is also evidence that the typical high-caloric North American diet rich in sugar, meats and processed foods may adversely affect the balance of microbes in the gut and foster the extraction and absorption of excess calories from food.
A diet more heavily based on plants may result in a microbiome containing a wider range of healthful organisms. In studies, mice that had a microbiota preconditioned by the typical North American diet did not respond as healthfully to a plant-based diet.
Compared with lean mice, obese mice have a 50 per cent reduction in organisms called Bacteroidetes and a proportional increase in Firmicutes, and lean mice get fat when given fecal transplants from obese mice. A similar shift has been observed in people, and the distorted ratio of organisms was shown to reverse in people who lose weight after bariatric surgery.
There is also evidence that microbes residing in the gut can affect distant sites through their influence on a person’s immune responses. This indirect action has been suggested as a possible mechanism behind rheumatoid arthritis. In mice, certain bacteria in the gut have been shown to foster antibodies that attack the joints, resulting in the joint destruction typical of rheumatoid arthritis.
Studies have suggested a role of the gut microbiota in the risk of developing neuropsychiatric illnesses such as schizophrenia and even chronic fatigue syndrome. Researchers have suggested that in genetically susceptible people, altered microbes in the gut may disrupt the blood-brain barrier, leading to the production of antibodies that impede normal brain development.
Among the challenges in discovering the microbiome’s role in health and disease is determining if changes found in the microorganisms inhabiting various organs are a cause or an effect. Most of what is known about the microbiota in people with various health problems is based on observation, making it difficult to say which came first: the disease or the disrupted microbial.
Animal studies are a clue but not proof of a similar effect in people. Until therapeutic studies now under way are completed, people with conditions thought to be influenced by the microbiome have no choice but to rely on possible treatments suggested by animal research and some preliminary human studies.
For example, people with irritable bowel syndrome and inflammatory bowel disease, allergic disorders and infections with drug-resistant organisms may benefit from taking high dose probiotics, not the very low does found in yogurt or the non-therapeutic bacteria in kefir. It may be necessary to tailor-make the remedy for each condition or even each patient.
People interested in fostering a health-promoting array of gut micro-organisms should consider shifting from a diet heavily based on meats, carbohydrates and processed foods to one that emphasizes plants.
Another thing to consider is the danger of a colon cleanse in which laxatives are used to empty the colon but also empty the colon of all its good gut bacteria. The health food store has a fine array of good high potency probiotics. Think more of adding to your gut health than subtracting from it.
Finally remember that the nutritional value of food is influenced in part by the microbial community that encounters that food. The healthier your microbial community, the more value you will get from the food that you eat.