February 2017

Your Microbiome: Making Friends with Your Colonies


Erica M. Elliott, M.D.


When you look in the mirror, you might think that the entire being reflected back to you is human, but that is not the case. Only 10 percent of your cells are human; the rest are made up of billions of microorganisms that colonize your body. We are truly walking ecosystems.


My son, Barrett, went through a short-lived phase of germ phobia around the time he turned 4 years old. He refused to wear secondhand clothing, washed his hands frequently and did not want to use public bathrooms. He said, “I don’t want to get any bugs on me.” He repeatedly asked, “Did you wash your hands, Mom?”


Where did he get this phobia? He did not get it from me, his Dr. Mom. Instinctively, I knew most microorganisms posed no threat and could actually be beneficial. I loved playing in the dirt as a child.


When I told Barrett that everyone is covered with bugs—his word for bacteria—he looked incredulous and said, “Not me, Mom. I don’t have any bugs on me.” I borrowed a high-powered microscope, took a moistened Q-tip and swabbed the skin on Barrett’s forearm, then smeared the swab on a glass slide, added a drop of water and put the slide under the microscope. Barrett looked in horror at the little bacteria squirming around at the other end of his eyepiece.


I explained that most of the bacteria caused no harm and that some of them kept the bad guys from taking over and could improve our health. Barrett eventually believed me, and with time, his phobia disappeared.


Microscopic life forms, referred to as microbes, inhabit every niche on Earth, including the air, soil and water—and all surfaces of our bodies, both inside and outside. Like any species of life on our planet, microbes find a niche in our bodies where they can thrive. These microbes include many thousands of species. Most are beneficial and play a significant role in keeping us healthy and are essential to life on Earth. Some are neither beneficial nor harmful. They are called commensal organisms. Only a small percentage are parasitic and can cause us harm.


Microbes in the body include many thousands of different species.

All the microbes living in an ecological community are referred to as a microbiome. This word has been appearing with growing frequency in science literature. The word “biome” refers to all the genes in a microbial community. The genes in our microbiome outnumber the genes in our human genome (gene pool) by about one hundred to one. Only 1 percent of the genes in our bodies are human!


Our symbiotic relationship with our microbiome requires that the microbes stay in balance with each other. These delicate relationships are the result of millions of years of co-evolution, beginning with the Earth’s first inhabitants—the bacteria. When our ancient ancestors appeared on the scene, they probably ate microbes along with their food. Those microbes that were digesting plants in the wild found a new home in humans. The human intestines provided a nutrient-rich habitat. In exchange, the microbes gave us some of their genes that got spliced into our human genes and sped up our evolution.


An example of our mutual dependence can be seen in breast-fed babies. Human breast milk contains short chains of sugar molecules called oligosaccharides that provide no nutritional advantage. These molecules act as the perfect food for the breast-fed baby’s intestinal microbes, which return the favor by helping the baby’s developing immune system, training the immune cells when to react and when not to react.


Bottle-fed babies, on the other hand, have fewer beneficial immune-boosting microbes and are more likely to suffer from allergies, asthma and eczema during the first few years of life.


In case you’re not giving your microbiome the attention and respect it deserves, let me tell you about just a few of the many benefits you receive from having healthy, balanced microbial colonies:

1.     Some microbial genes code for enzymes, help us digest our food and build proteins. Others help us utilize starches, fiber and sugars. Researchers estimate that up to 10 percent of the calories we absorb are made available by our microbes.

2.     When the microbes digest carbohydrates in our intestines, bacteria in the lower GI tract produce a chemical called n-butyrate, a source of energy for the cells that line the intestinal tract. N-butyrate also acts as a signal that strengthens the connections between the cells. When the cell connections are strong, there is less chance for developing leaky gut syndrome, a condition that can cause a whole constellation of symptoms related to the immune system’s reaction to molecules that have leaked into the bloodstream. These errant molecules are regarded as “foreign” and provoke attack by the immune system, leading to inflammatory conditions.

3.     Microbial genes code for proteins that keep harmful bacteria and fungi from overpowering us. In fact, drug companies have synthesized some of these proteins into powerful antibiotics. For example, bacteria called Staph epidermis populate our skin. These bacteria send signals to our cells, prompting them to produce microbe-fighting molecules that protect us from invasion.

4.     We benefit from the microbes’ vitamin-making genes. Microbes in our large intestine make vitamins that we are not able to make on our own, including B vitamins that are essential to our metabolic functioning, vitamin K for clotting blood and preventing calcium from being deposited in the wrong places, and vitamin B-12 for healthy blood and brain tissue.

5.     The microbes make small molecules that travel to all parts of the body and help regulate metabolism, influence appetite, insulin sensitivity and how sugar is utilized. Researchers have recently discovered a link between obesity and the state of one’s microbiome. In one experiment, thin rats were given fecal transplants obtained from the feces of obese rats. The thin rats became obese.

6.     Friendly microbes in the gut—the probiotics—stimulate immune tissue found throughout the intestines to make natural antibiotics that fight pathogenic bacteria. They also train the immune system not to attack friendly microbes. One of the major benefits of this training is that the immune system is less likely to attack itself and cause autoimmune disease.

7.     Certain microbes produce compounds that block inflammation. The organisms make these compounds to protect our immune system from attacking their colonies. We benefit from these compounds by experiencing less inflammation in our bodies. Our immune systems are less likely to overreact to our environment.

8.     Microbes in the gut have direct communication with our brains. The gut is loaded with nerve tissue and hence the nickname “the second brain.” The nerve tissue in the gut produces the same neurotransmitters as the brain. The neurotransmitters relay information along the vagus nerve. The information can go in both directions, brain to gut and gut to brain. Intestinal microbes make some of the exact same neurotransmitters, such as GABA, acetylcholine and serotonin, each of which can affect one’s mood and cognitive abilities.

9.     Some beneficial microbes even have the capacity to inactivate toxic molecules that we ingest along with our food. 


Living in a sterile, germ-free environment is not a good idea if you want to be healthy—unless of course you have an unusual immune system disorder that makes you vulnerable to infection from bacteria under any circumstances. Baby mice raised in a sterile environment don’t develop a complete immune system. They produce inadequate amounts of antibodies and are vulnerable to infections. Studies on humans show that children with asthma tended to have had less germ exposure than children with heavy germ exposure, such as those raised on farms, for example.


Over the years I have had germ-phobic patients who were raised by physician parents. They thought they were helping their children by instilling in them a fear of germs. These patients tend to get sick frequently.


The more researchers investigate our microbiome, the more it becomes apparent how vitally important it is to take care of our internal ecosystems—not just the external ones.


Here are some suggestions on ways to nurture the beneficial bacteria:

·        Use synthetic antibiotics sparingly and only when absolutely necessary. Practice prevention in order to decrease the need for antibiotics. Most antibiotics have a deeply disruptive impact on the delicate balance of the intestinal flora and make overgrowth of harmful bacteria and fungi more likely. Recent research has shown that after a single course of antibiotics, it can take up to a year to re-establish the beneficial colonies to their pre-antibiotic state of equilibrium.

After taking antibiotics, it can take up to a year to re-establish beneficial colonies.

·        Eat a primitive diet, free of processed foods. Do your food shopping mostly on the periphery of the grocery store where the fresh foods are located.

·        Eat raw sauerkraut and other cultured foods, like kimchi and kefir.

·        Take probiotics. Test each bottle for the viability of the organisms because they are fragile and die easily—no matter how expensive your brand is.

·        Use chicory root powder as a sweetener (brand name “Just Like Sugar”). The powder is made of finely ground fiber that acts as food for beneficial bacteria.

·        If you are a carnivore, eat animals that have been raised without antibiotics.

·        Include large portions of vegetables in your meals. They are good sources of prebiotics, the soluble and insoluble fibers that feed beneficial bacteria.

·        Introduce a wide variety of foods into your diet. Remember that you are host to a huge variety of organisms with different tastes in foods and nutritional needs.

·        Avoid farm-raised fish. They are fed a diet that includes antibiotics.

·        Eat organic foods. Pesticide-contaminated foods harm the beneficial colonies.

·        Avoid genetically modified foods. They are usually heavily contaminated with glyphosate, the active ingredient in herbicides such as Roundup, made by Monsanto and banned in a growing list of countries around the world. The most common genetically modified foods in the U.S. include wheat, corn, soy, sugar beets, Hawaiian papaya, squash and canola oil. Genetically modified wheat and corn derivatives are commonly found in processed foods. 

·        Eat a healthy diet high in fiber and low in sugar, optimal conditions for supporting bifidobacteria, which keep toxins produced by other bacteria from passing through the intestinal wall and into the bloodstream.


Eat lots of foods with high fiber and low sugar.

·        Avoid harsh skin sanitizers that obliterate all the bacteria on the hands. Wash with plain soap. The mechanical action of washing is enough to remove potentially harmful bacteria from the skin.

·        Avoid exposures to toxic chemicals. They can upset the delicate balance in the gut, not only through ingestion, but also through inhalation of the fumes.


Keep the well being of your bacterial colonies in mind during daily choices.

Next time you crave ice cream or other sugar-laden food, you might stop and ask yourself, “Who is it that wants this ice cream? Could it be the fungal colonies in my gut that are sending signals to my brain, making me unable to resist indulging in foods that help the bad guys thrive?” It’s certainly a possibility. Microbes, both beneficial and harmful, will go to great lengths to survive.


You might think you are the captain of your ship, but it’s not always clear who is in charge. So, be sure to say “Good morning” to your colonies when you wake up, and remember to keep their well-being in mind as you make choices throughout the day about what you do with your body, a vessel teaming with nonhuman life that can profoundly affect your well-being for better or for worse.


Let’s drink a toast of sparkling water to our microbial friends. May there be peace and harmony throughout our colonies!



Dr. Erica Elliott is board-certified in family practice and environmental medicine She has often been nicknamed “the medical detective.” She has given weeklong workshops, has been a public speaker and is co-author of Prescriptions for a Healthy House. She blogs regularly at www.musingsmemoirandmedicine.com. Her professional website is www.ericaelliottmd.com 




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