What Is the Human Microbiome?

Each of us has an internal complex ecosystem of bacteria located within our bodies that we call the microbiome. The microbiome is defined as a “community of microbes.” The vast majority of the bacterial species that make up our microbiome live in our digestive system. And appreciate that you will also find these microbes occupying our respiratory system and our skin (integumentary) system. 

According to the Department of Chemistry & Biochemistry at the University of Colorado, “the human microbiota consists of the 10–100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut. The human ‘microbiome’ consists of the genes these cells harbor.”

Our individual microbiomes are sometimes called our “genetic footprints” since they help determine our unique DNA, hereditary factors, predisposition to diseases, body type or body “set point weight,” and much more. The bacteria that make up our microbiomes can be found everywhere, even outside our own bodies, on nearly every surface we touch and every part of the environment we come into contact with.

The microbiome can be confusing because it’s different than other organs in that it’s not just located in one location and is not very large in size, plus it has very far-reaching roles that are tied to so many different bodily functions. Even the word “microbiome” tells you a lot about how it works and the importance of its roles, since “micro” means small and “biome” means a habitat of living things.



It’s been said by some researchers that up to 90 percent of all diseases can be traced in some way back to the gut and health of the microbiome. Believe it or not, your microbiome is home to trillions of microbes, diverse organisms that help govern nearly every function of the human body in some way. The importance of our gut microbiome cannot be overstated: Poor gut health can contribute to leaky gut syndrome and autoimmune diseases and disorders like arthritis, dementia, heart disease, and cancer, while our health, fertility and longevity are also highly reliant on the balance of critters living within our guts.

Throughout our lives, we help shape our own microbiomes — plus they adapt to changes in our environment. For example, the foods you eat, how you sleep, the amount of bacteria you’re exposed to on a daily basis and the level of stress you live with all help establish the state of your microbiota.

The Microbiome Diet: Eating to Support Immunity and Lower Inflammation

Your diet plays a big part in establishing gut health and supporting your microbiome’s good bacteria. Research over the past several decades has revealed evidence that there’s an inextricable link between a person’s microbiota, digestion, body weight and metabolism. In an analysis of humans and 59 additional mammalian species, microbiome environments were shown to differ dramatically depending on the specie’s diet.

The flip side is also true: Your gut health can impact how your body extracts nutrients from your diet and stores fat. Gut microbiota seem to play an important role in obesity, and changes in bacterial strains in the gut have been shown to lead to significant changes in health and body weight after only a few days. For example, when lean germ-free mice receive a transplant of gut microbiota from conventional/fat mice, they acquire more body fat quickly without even increasing food intake, because their gut bugs influence hormone production (like insulin), nutrient extraction and fat (adipose tissue) storage.

Now that you can see why it’s critical to lower inflammation and support gut health, let’s take a look at how you can go about this.

Foods that promote inflammation include:

• Refined vegetable oils (like canola, corn and soybean oils, which are high in pro-inflammatory omega-6 fatty acids)
• Pasteurized dairy products (common allergens)
• Refined Carbohydrates and processed grain products
• Conventional meat, poultry and eggs (high in omega-6s due to feeding the animals corn and cheap ingredients that negatively affect their microbiomes)
• Added sugars (found in the majority of packaged snacks, breads, condiments, canned items, cereals, etc.)
• Trans fats/hydrogenated fats (used in packaged/processed products and often to fry foods)

On the other hand, many natural foods can lower inflammation and help increase good bacteria in the gut. High-antioxidant foods help reduce gut damage caused by oxidative stress and turn down an overactive immune system while safeguarding healthy cells. 

Anti-inflammatory foods that should be the base of your diet include:



• Fresh vegetables (all kinds): loaded with phytonutrients that are shown to lower cholesterol, triglycerides and symptoms of rheumatoid arthritis, Alzheimer’s disease, cancer, cardiovascular disease and diabetes. Aim for variety and a minimum of four to five servings per day. Some of the best include beets; carrots; cruciferous vegetables (broccoli, cabbage, cauliflower and kale); dark, leafy greens (collard greens, kale, spinach); onions; peas; salad greens; sea vegetables; and squashes.
• Whole pieces of fruit (not juice): Fruit contains various antioxidants like resveratrol and flavonoids, which are tied to cancer prevention and brain health. Three to four servings per day is a good amount for most people, especially apples, blackberries, blueberries, cherries, nectarines, oranges, pears, pink grapefruit, plums, pomegranates, red grapefruit or strawberries.
• Herbs, spices and teas: turmeric, ginger, basil, oregano, thyme, etc., plus green tea and organic coffee in moderation.
• Probiotics: Probiotic foods contain “good bacteria” that populate your gut and fight off bad bacterial strains. Try to include probiotic foods like yogurt, kombucha, kvass, kefir or cultured veggies in your diet daily.
• Wild-caught fish, cage-free eggs and grass-fed/pasture-raised meat: higher in omega-3 fatty acids than farm-raised foods and great sources of protein, healthy fats, and essential nutrients like zinc, selenium and B vitamins.
• Healthy fats: grass-fed butter, coconut oil, extra virgin olive oil, nuts/seeds.
• Ancient grains and legumes/beans: best when sprouted and 100 percent unrefined/whole. Two to three servings per day or less is best, especially Ansazi beans, adzuki beans, black beans, black-eyed peas, chickpeas, lentils, black rice, amaranth, buckwheat, quinoa.
• Red wine and dark chocolate/cocoa in moderation: several times per week or a small amount daily.

Dr. Huntoon has spent 30 plus years understanding the importance of all disease, what causes sickness to begin and what it takes to be and stay healthy. It is his passion and he can and will help you understand how to restore balance to your digestive system and your overall health. Please appreciate that any time you are exposed to antibiotics (70 percent of them are put into our food supply) you will disrupt your microbiome. Also of importance is understanding the stress, over-the-counter medicines, prescription medicines, alcohol, refines and processed sugar, additives, preservatives, plastics etc., will contribute to having problems with your microbiome. And finding a practitioner like Dr. Huntoon who can walk you through the different steps necessary to restore your microbiome becomes paramount. Below are 3 main things you should be aware of and practice if you choose to be healthy.

How Else Can You Establish a Strong Microbiome?

1. Avoid Antibiotics and the Digestive System Disruptors as Much as Possible

Antibiotics have been commonly prescribed for over 80 years now, but the problem is that they eliminate good bacteria in addition to cleaning the body of dangerous “germs,” which means they can lower immune function and raise the risk for infections, allergies and diseases. While antibiotics can save lives when they’re truly needed, they’re often over-prescribed and misunderstood.

Over time, dangerous bacteria can become resistant to antibiotics, making serious infections harder to fight. Before taking antibiotics or giving them to your children, talk to your doctor about alternative options and the unintended consequences to our microbiomes that can result from taking antibiotics too often and when they aren’t needed.

1. Lower Stress and Exercise More

Stress hinders immune function because your body diverts energy away from fighting off infections and places it on primary concerns that keep your alive — which is one reason why chronic stress can kill your quality of life. When your body thinks it’s facing an immediate danger, you become more susceptible to infections and experience more severe symptoms while also developing higher levels of inflammation.

Stress causes immune compounds known as cytokines to contribute to the inflammatory response that damages healthy cells. Exercise is a natural stress reliever that can help lower inflammation, balance hormones and strengthen the immune system.

1. Add Supplements



Begin with the source of good bacteria within your digestive system. This requires a high quality probiotic and should be kept in your refrigerator when being stored. If the bottle says it does not need to be refrigerated, you are probably wasting your money. Next, you will need some type of supplement to get rid of the excess amounts of Yeast/Candidia that create the leaky gut syndrome. This will help to restore balance to the microbiome and return the body back to health. Other supplements that may be helpful, especially if they are gotten from whole food sources are Co-enzyme Q10, carotenoids, omega-3 fish oil, selenium and antioxidants (vitamins C, D and E). These can help keep free radical damage from disturbing micrbiota gut health.

How the Gut Microbiome Works

Would you believe that within the human body there are about 10 times as many outside organisms as there are human cells? Microbes inhabit both the inside and outside of our bodies, especially residing in the gut, digestive tract, genitals, mouth and nose areas. What determines if someone’s microbiome is in good shape or not? It comes down to the balance of “bad bacteria” versus “good bacteria.”

Essentially, we need a higher ratio of gut-friendly “bugs” to outnumber those that are harmful in order to stay resilient and symptom-free. Unfortunately — due to factors like a poor diet, high amounts of stress and environmental toxin exposure — most people’s microbiomes are home to many billions of potentially dangerous bacteria, fungus, yeast and pathogens. When we carry around more pathogenic bacteria than we should, and also lack the diversity of protective bacteria we need, the microbiota suffers.

The human microbiome is home to more than just bacteria. It also houses various human cells, viral strains, yeasts and fungi — but bacteria seem to be the most important when it comes to controlling immune function and inflammation. To date, researchers have identified more than 10,000 different species of microbes living in the human body, and each one has its own set of DNA and specific functions. There’s still lots to learn about how each strain of bacteria affects various parts of the body and how each can either defend us from or contribute to conditions like obesity, autoimmune disorders, cognitive decline and inflammation.

Your Solution

Dr. Huntoon has spent 30 plus years understanding the importance of all disease, what causes sickness to begin and what it takes to be and stay healthy. It is his passion and he can and will help you understand how to restore balance to your digestive system and your overall health. Please appreciate that any time you are exposed to antibiotics (70 percent of them are put into our food supply) you will disrupt your digestive system. Also of importance is understanding the other Digestive System Disruptors of stress, over-the-counter medicines, prescription medicines, alcohol, refines and processed sugar, additives, preservatives, plastics etc., will contribute to having problems with your microbiome. And finding a practitioner like Dr. Huntoon who can walk you through the different steps necessary to restore your microbiome becomes paramount. 

Begin with the source of good bacteria within your digestive system. This requires a high quality probiotic and should be kept in your refrigerator when being stored. If the bottle says it does not need to be refrigerated, you are probably wasting your money. 

Next, you will need some type of supplement to get rid of the excess amounts of Yeast/Candidia that create the leaky gut syndrome. This will help to restore balance to the microbiome and return the body back to health. 



If you have any questions, feel free to contact Dr. Huntoon directly at 845-561-2225. He looks forward to serving you.