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10 Tips for a Healthy Microbiome

by Sarah Cimperman, ND

Our bodies contain 10 times more microbial cells than human cells and 100 to 150 times more microbial genes than human genes. The collective community of microorganisms and their genes is called our microbiome and we wouldn’t live long without it. Studies of germ-free environments have shown that a diverse and balanced microbiome is essential for the normal development and function of important body systems. Friendly bacteria protect us from disease-causing bacteria and they help digest our food.They break down environmental toxins and manufacture essential nutrients like vitamins and short chain fatty acids. They also modulate the immune system,help regulate inflammation, influence the production of neurotransmitters like serotonin, and play an important role in appetite, satiety, fat accumulation,and energy usage.

            When the delicate balance of the microbiome is disrupted, illness often follows.Alterations in intestinal microflora are now recognized as contributing factors to many chronic and degenerative diseases including digestive problems, immune system dysfunction, mood disorders, vaginal infections, and allergic and metabolic diseases.

            The health of our microbiome is greatly influenced by our environment. The foods we eat, the products we use, the medications we take, and the way we live our lives all affect the livelihood of protective and pathogenic microbes inside our bodies. According to Dr. Raphael Kellman, MD, author of The Microbiome Diet, the composition of microbes inhabiting our bodies can change within twenty-four hours in response to stress, antibiotics, and illness, and it can change within days or weeks in response to diet, supplements, and exercise. Support your inner ecosystem with these ten tips.

 #1  Eat more fermented foods.

Fermented foods contain the protective bacteria our bodies need and we should be eating them every day. Good choices include sauerkraut, kimchi, pickled vegetables, vinegar, soy sauce, tamari, tempeh,miso, cacao nibs, vanilla beans, yogurt, kefir, and aged cheeses. Look for labels listing "live cultures" and products that have not been pasteurized after fermentation.

 #2  Eat foods that contain prebiotics.

Prebiotics are compounds found in plant foods that nourish protective bacteria. They include inulin, oligosaccharides,and arabinogalactans. Find them in onions, garlic, leeks, artichokes, Jerusalem artichokes, beans,asparagus, carrots, radishes, tomatoes, bananas, ground raw flax seeds, and bittergreen leafy vegetables like dandelion, chicory, endive, and radicchio.

 #3  Avoid processed foods.

Chemical preservatives in manufactured and pre-packaged foods can harm protective bacteria, while refined and over-processed ingredients promote the growth of harmful ones. Avoid foods made from like flour, whether they contain gluten or not. This includes pasta,cereal, granola bars, and baked goods like bread, crackers, and pastries. Also avoid foods made with additives like preservatives and sweeteners, both natural and artificial. In a 2008 study, researchers in North Carolina found that Splenda changed the pH of the gastrointestinal tract and reduced populations of protective intestinal bacteria.

 #4  Avoid genetically modified foods. 

When we eat genetically modified (GM) foods,the modified genes they contain become incorporated into bacterial cells inside our digestive tract, causing intestinal bacteria to produce genetically modified proteins long after the original food has left our bodies.In the United States, GM crops account for about 90% of corn, soy, canola oil, and sugar from sugar beets. Other foods that may be genetically modified include cottonseed oil, meat from grain-fed animals, dairy products from cows treated with rBGH, Hawaiian papaya, and some varieties of zucchini and yellow squash. Buy the organic varieties of these foods(and any products that contain them as ingredients) or avoid them all together.

 #5  Eat organic.

Pesticides also alter our microbiome and,like GM foods, the only way to avoid them is to eat organic. If you can, grow your own organic produce, even it's is just a pot of tomatoes on your patio oran herb garden in your window. If you shop at a farmers’ market, keep in mind that some small farmers sell unsprayed produce but lack the official certification required to call it organic. Don’t be afraid to ask questions.

 #6  Avoid unnecessary antibiotics. 

Antibiotics are indiscriminate when it comes to killing bacteria. They wipe out protective species along with ones that cause disease. In the United States, rates of antibiotic prescribing are among the highest in the world and most kids receive between ten and twenty courses before they turn eighteen. Each course of antibiotics affects the microbiome and it can take months or even years to correct these imbalances, so they should only be used when absolutely necessary.

 #7  Filter your water.

An analysis of almost 20 million records obtained from state water officials found that tap water in the United States contains more than 300 pollutants including several kinds of antibiotics,so even if you aren't actively taking them, you could be ingesting them anyway.Find a filter using the Environmental Working Group's Water FilterBuying Guide.

 #8  Avoid unnecessary stomach acid-reducing medications.  

Stomach acid helps us digest our food and discourages the growth of harmful microbes. When we don't have enough, we’re atrisk for developing intestinal infections and bacterial overgrowth in the stomach and small intestine. In some cases, like the treatment of ulcers,medications that reduce the production of stomach acid are necessary. But in other cases, like the treatment of gastroesophageal reflux disease, they are often unnecessary. (GERD is caused by incomplete closure of the valve that separates the stomach from the esophagus. It is not caused by too much stomach acid.) Like antibiotics, acid-suppressing medications must be used wisely because they can have harmful effects on our microbiome.

 #9  Avoid hand sanitizers andanti-bacterial soaps.

Like antibiotics, hand sanitizers and anti-bacterial soaps kill good and bad bacteria alike. They have negative effects on the delicate balance of microbes as well as the diversity essential for a healthy microbiome. Researchers who compared children living in an urban slum in Bangladesh to kids of the same age from the United States living in upper-middle class suburban communities found that the Bangladeshi kids harbored a much greater diversity of microbes, likely due to the"frequent" and "intensive" exposure to unhygienic conditions. Keeping clean isn’t always a bad thing, but sterilizing our hands,bodies, and environment is unnecessary and it can have harmful effects on our microbiome.

 #10  Consider supplementation.

Probiotics are a supplement form of the protective bacteria our bodies need. They don't supply all of the species we depend on fora healthy microbiome but they can supply several. An even stronger form of supplementation is fecal microbiota transplant (FMT) which delivers a more potent and diverse dose of bacteria, reflective of the thousand different species found inside our intestines, all in the exact right proportions. FMT is already being used to treat irritable bowel syndrome, Crohn’s disease, ulcerative colitis, and antibiotic-resistant C. difficile infection,with good success. There’s also interest in using FMT to treat diabetes,obesity, allergies, autoimmune diseases, and even cancer. It’s a good indication that our microbiome is an important factor in the maintenance of health and the development of disease.


References are available upon request. Dr.Sarah Cimperman, ND is a naturopathic doctor in private practice in New York City and author of the new book, The Prediabetes Detox: A Whole-Body Program to Balance Your Blood Sugar, Increase Energy, and Reduce Sugar Cravings (www.prediabetesdetox.com). Follow Dr. Cimperman on Facebook, Twitter and her blogs, A Different Kind of Doctor and The Naturopathic Gourmet. Find her at www.drsarahcimperman.com.

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