When you look in the mirror, you might think that the entire image reflected back to you represents a human being exclusively, but that is not the case. Only 10% of the cells in your body are human, the rest are made up of billions of microorganisms that colonize your body. We are literally walking ecosystems, miniature versions of the Amazon rainforest.

My son, Barrett, went through a short-lived phase of germ phobia around the time he turned four years old. He refused to wear second-hand clothing from other children, 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 me, “Did you wash your hands, Mom?”

Where did he get this phobia?

Counter to what one might assume, he did not get his phobia 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 to Barrett 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 that the bacteria posed no threat, and with time, he made peace with the microorganisms—the bugs—and the phobia disappeared.

Microscopic life forms, also 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 different species. Most of our microbes are beneficial and play a significant role in keeping us healthy and are essential to life on earth. Some microbes are neither beneficial nor harmful. They are called commensal organisms. Only a small percentage of the microbes are parasitic and can cause us harm.

All the microbes living in a community are referred to as a microbiome. This word has been appearing with growing frequency in the science literature. The word “biome” refers to 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% 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 already digesting plants in the wild found a new home in humans. The human intestines provided a nutrient-rich habitat for the microbes. 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 to babies. These molecules act as the perfect food for the breast-fed baby’s intestinal microbes. These microbes return the favor by training the baby’s developing immune system to react appropriately.

Bottle-fed babies, on the other hand, have fewer of these 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:

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

• 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 that line the intestine. 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 blood stream. These errant molecules are regarded as “foreign” and provoke attack by the immune system, leading to inflammatory conditions.

• Microbial genes code for proteins that keep harmful bacteria and fungi from overpowering us. In fact, some of these proteins have been harnessed by drug companies that synthesize them into powerful antibiotics. Our skin, for example, is populated by bacteria called Staph epidermis. These bacteria send signals to our cells, prompting them to produce microbe-fighting molecules that protect us from invasion.

• 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.

• 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 discovered a link between obesity and the state of one’s microbiome. When thin mice were given fecal transplants from obese mice, the thin mice became obese.

• The friendly microbes in the gut—the probiotics—stimulate the immune tissue found throughout the intestines to make antibiotics that fight the 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.

• Certain microbes produce compounds that block inflammation. The organisms make these compounds to protect our immune system from attacking them. We benefit from the anti-inflammatory compounds by experiencing less inflammation in our bodies. Our immune systems are less likely to overreact to our environment.

• 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 produce the same neurotransmitters as the brain. The neurotransmitters relay information along the vagus nerve up to the brain. The information can go in both directions, brain to gut and gut to brain. Intestinal microbes make some of the exact same neurotransmitters as found in the brain and in the gut, such as GABA, acetylcholine, and serotonin, each of which can affect one’s mood and cognitive abilities.

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

As you might have concluded from what you just read, 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 unable to resist infection 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 children raised on a farm for example.

Over the years I have had patients who were raised by physician parents who were germ phobic. 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 important it is for us to tend to our internal ecosystems if we want to maintain physical and mental health—not too different from what the environmentalists tell us about maintaining healthy ecosystems in our outer world.

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.

• 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. (Refer to the cancer blog post to find how to do the viability test. It’s very easy.)

• One of my patients got rid of her persistent yeast overgrowth by giving herself daily enema with homemade kefir whey. She simply put the kefir into a syringe, inserted it into her anus, and then squirted the whey up her rectum. The process is quick, easy, and without leaving a mess.

• 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 the beneficial bacteria.

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

• Include large portions of vegetable in your meals.

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

• Eat organic foods. The 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 US 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 blood stream.

• 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.

If you have a chronic medical condition in spite of taking many measures to get well, the state of your micro biome could be a missing piece of the puzzle in the path to wellness.

Next time you crave some ice cream or other sugar-laden foods, you might stop and ask yourself, “Who is it that wants this ice cream? Could the cravings be caused by the fungal colonies and other bad guys in my gut? Could they be sending signals to my brain, making me unable to resist indulging in the foods that help them thrive?” It’s certainly a possibility. The microbes, both the beneficial and harmful ones, will go to great lengths to get what they need 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 wellbeing 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 wellbeing for better or for worse.

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