The Microbiome Explained in Plain English

The Microbiome Explained in Plain English

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Illustration of Human microbiota in gastro-intestinal tract

Your body is much less human than you think it is.

In fact, outside organisms outnumber human cells in your body ten to one! (Let that one sink in a moment.)

There’s a vast, complex ecosystem of microbes living in your body. This collection of tiny creatures is known as the “microbiome,” and it consists of a whopping 10-100 trillion microbial cells.

Everyone has an internal microbiome, and everyone’s microbiome is different. Very different, actually. Two random people share a 99.9% similarity in their human genes. Comparing those same two people, their microbiomes would be 80-90% different!

Most of the microbes in your microbiome are bacteria, and most of them live in your digestive system (your gut).

Seamless pattern with cute, funny childish design. Festive cartoon germs

I’d understand if your first, gut reaction (har har) to that last statement is a cringe. After all, we’ve been trained to associate the word “bacteria” with illness and poor health. However, not all bacteria are harmful.

In fact, good health would be impossible without the help of certain strains of “good” bacteria.

The field of human microbiome research is still fairly young. What we’ve learned so far, however, indicates that our microbiome plays a surprisingly large role in the health and functioning of our bodies.

Research indicates that a healthy body is almost wholly dependent on our having a healthy microbiome, and especially a healthy gut.

Illustration of human intestine microflora

What Does the Microbiome Do?

To date, scientists have identified more than 10,000 different microbe species living in the human body, each with its own unique set of genes and bodily functions.

While there’s still much to learn about how each bacterial strain affects your body, one thing is clear—the microbiome does a lot.

The microbes that make up your microbiome play important roles in nearly every function of your body.

First and foremost, your microbiome helps break down and extract nutrients from the food you eat. Microbes in your gut help produce nutrients (such as fat-soluble vitamins and fatty acids), fight off harmful bacteria, and maintain a healthy barrier between your gut and bloodstream.

Artistic representation of DNA in blue color

Microbes influence your genes, regulate inflammation levels, protect you from free radical damage, help maintain healthy bone density, promote healthy joints and connective tissues, and affect your immune system and metabolism.

Good bacteria in your gut also help manage neurotransmitter activity.

There are many neurochemical and neurometabolic pathways between your brain and your microbiome, which means that your microbiome can significantly impact your mood, energy levels, alertness, thought patterns, memory, reasoning, and capacity to manage stress.

Why Should I Care About My Microbiome?

Once again, the microbes in your microbiome affect nearly every function of your body.

Right now, your microbiome is helping with digestion, nutrient production, detoxification, immune system functioning, and much, much more. A healthy microbiome ensures all these functions and systems in your body run well.

Image of the man suffering from obese on the beach

When the microbiome is unhealthy, things get ugly fast. This may be shocking to hear, but nearly every disease out there is tied in some way to an unhealthy gut!

Research shows that an imbalanced, unhealthy gut microbiome can contribute or lead to:

  • Obesity
  • Type 1 diabetes
  • Autoimmune diseases (e.g., leaky gut, Hashimoto’s, arthritis, inflammatory bowel disease)
  • Cancer
  • Heart disease
  • Brain disorders (e.g., Alzheimer’s and dementia)
  • Infertility
  • Pregnancy complications
  • Decreased longevity
  • Deterioration of joints and connective tissues
  • Mood disorders (e.g., depression and anxiety)
  • Learning disabilities (e.g., autism and ADHD)
  • Allergies and sensitivities
Image of small intestine wall, villi and crypts

A large connection between your microbiome and many of these health issues is inflammation. Inflammation is the root cause of most diseases, and gut health is a major determinant of inflammation levels in the body.

A healthy microbiome will keep inflammation levels in the body low, which will in turn reduce the risk and symptoms of most (if not all) of the above-listed health issues.

Plain and simple, if you care at all about living a healthy life, you should care deeply about the health of your microbiome.

How Can I Take Care of My Microbiome?

Hopefully by now you’re fully committed to ensuring your microbiome is as healthy as can be! Assuming that’s the case, here’s how to take care of your microbiome:

Image of cabbage

Diet plays a huge role in the health of your microbiome. You can support your gut microbiome through diet in two ways

Eating anti-inflammatory foods. Aim for 4-5 servings each day of fresh vegetables and 3-4 servings of whole fruit (not juice). Herbs and spices like turmeric, ginger, basil, oregano and thyme are great too, so add these to your cooking or drink them in teas.

Also, include probiotics like yogurt, kimchi, kombucha, kvass, kefir, sauerkraut, and fermented vegetables. These will populate your gut with healthy bacteria, which will crowd out harmful bacteria. Along with this is prebiotics, like garlic, onions, tomatoes, radishes, asparagus, Jerusalem artichokes, and leeks.

Be sure to include healthy fats found in wild-caught fish, cage-free eggs, grass-fed/pasture-raised meat and butter, coconut oil, extra-virgin olive oil, and nuts and seeds. In moderation, you can even have red wine, dark chocolate/cocoa, green tea, and organic coffee!

Image of donuts

Cutting out inflammatory foods. These include:

  • Refined vegetable oils, such as corn, canola, and soybean
  • Refined carbohydrates and processed grains
  • Pasteurized dairy products
  • Foods with added sugars (packaged breads, canned items, condiments, cereals, etc.)
  • Processed and “junk” foods
  • Trans fats and hydrogenated fats, often found in fried foods and processed/packaged foods
  • Conventionally raised or factory-farmed meat, poultry, and eggs
  • Foods with preservatives, artificial ingredients, and sweeteners
Image of TURMERIC, one of the healthiest foods on the planet

Dr. Axe recommends selenium, co-enzyme Q10, omega-3 fish oils, carotenoids, and vitamins C, D, and E as good options for preventing free radicals from harming the microbes in your gut. Magnesium and curcumin have also been shown to promote a healthy microbiome.

Finally, a daily probiotic supplement will ensure your gut is full of healthy bacteria.

The problem with antibiotics is that they act less like scalpels and more like grenades.

While they can be extremely effective at killing harmful bacteria in the body, they also kill just as many good bacteria. Because of this, antibiotics can lower immune function and put you at high risk of infections, allergies, and diseases.

Photo of opened bottle with digestive enzymes pills

Sometimes, antibiotics are necessary— and when they are, they can save lives. If you must take them, make sure to supplement with probiotics to replenish your gut with good bacteria.

For the most part, however, avoid antibiotics whenever possible. Try using anti-microbial herbs and essential oils instead, such as cinnamon, clove, thyme, oregano, and tea tree.

Research shows that acid-blocking drugs like Nexium, Prevacid, Prilosec, and Aciphex lower microbial diversity in the microbiome, increasing the risk of infections.

Photo of a kitchen tap water filter

The chlorine used in municipal tap water has been shown to kill microbes in soil. Chances are good that drinking tap water kills microbes in your body as well. Use a water filter to drink chemical-free water.

Chronic stress can negatively impact your gut health, and thus your overall health, in a big way.

Stress can cripple immune function, throw your hormone levels out of whack, and increase inflammation through the production of immune compounds called cytokines.

Less stress promotes a healthy gut, which in turn promotes healthy neurotransmitter function, which will help you handle stress better!

Regular exercise, movement, meditation, and adequate sleep are all great ways to reduce and remove stress from your life.

Group of funny colorful microbes cartoon characters vector illustrations


A healthy microbiome is essential to a healthy life.

The microbes living throughout your body— and especially those living in your gut— help keep nearly every function of your body running smoothly and correctly. On the flip side, 90% of all diseases can be traced in some way back to an unhealthy, imbalanced, malfunctioning microbiome.

So take care of your microbiome!

Feed the “good guys” by eating plenty of healthy, natural whole foods that reduce inflammation, like a variety of vegetables, whole fruits, grass-fed meat and dairy products, and fermented foods.

Starve out the “bad guys” by avoiding inflammatory foods like vegetable oils, additives, conventionally-raised meat and dairy products, gluten, and sugary, packaged, and processed foods.

Furthermore, reduce stress, avoid antibiotic medications whenever possible, and supplement healthily.

Doing all this will ensure your own microbiome is a thriving, vibrant ecosystem contributing to your overall health rather than disrupting it.