What Is the Microbiome: You Are What Your Bacteria Eat!

November 19, 2018
What is the Microbiome?

Rate this Post: 

Average: 4.9 (20 votes)

Trillions of bacteria live inside our body. There’s an entire ecosystem—or, microbiome—that we host! It turns out that these bacteria greatly influence our health—from obesity to allergies to our autoimmune system. What can we do to change our diet and lifestyle to improve our well-being?

What is a microbiome? What does it do? 

The microbiome is the genetic material of all our microbes—bacteria, fungi, protozoa and viruses - that live on and inside the human body. Microbes outnumber our human cells ten to one.

The majority of bacteria and microbes live in our gut, particularly in the large intestine. The health of these bacterial communities directly influences our own health. Yes, it’s all interconnected!


This image originally appeared in the Hartford Courant.

The microbiome is a hot topic.  Research, primarily since the 1990s, reveals the microbiome isn’t just to help our body digest food, but also to regulate our immune system and protect against disease. In addition:

  • Obesity has also been associated with a poor combination of microbes in the gut. 
  • Type I diabetes is an autoimmune disease associated with a less diverse gut.
  • Dust from homes with dogs may reduce the immune response to allergens and other asthma triggers by changing the composition of the gut microbiome. Infants who live in homes with dogs have been found to be less likely to develop childhood allergies.

Where do microbiomes come from?

Much of your microbiomes comes from your mother during birth and breastfeeding. However, throughout life, we add to our microbiome from the food we eat, from contact with siblings, close contacts with other people and animals, with soil, and pretty much anything else we contact in our environment.

Is everybody’s microbiome the same?

The species and distribution of microbes within the microbiome vary greatly among individuals. Your microbiome is unique to you and changes continuously throughout your life, depending on your life experiences, including use of antibiotics.

What do antibiotics have to do with the microbiome?

Most antibiotics kill beneficial bacteria in our microbiota, sometimes permanently. Researchers hypothesize that one dramatic “collateral harm” of their widespread use has been loss of intestinal microbes.

Many scientists have suggested that we, as a society, be slower to give children antibiotics. (Note: This is not a statement rejecting antibiotics.)

What else can harm microbiomes?

Antibacterials such as those we use to clean our homes, sterilize food-preparation surfaces, or wash our hands or even our food may also kill off the good bacteria we depend on. Antimicrobials are also found in food-packaging materials, athletic shoes, and clothing.

Many scientists suggest moving away from an over-reliance on these antibacterial products. Get kids exposure to the outdoors and dirt, thus building up the health of the microbiome.

What food and diet keeps my microbiome healthy?

Yes, you are what you eat, and so are the bacteria that live in your gut!

If you’re going to switch from a typical American diet which is high in processed foods and carbohydrates to a diet that is more plant-based or meat-based, your body may not react quickly. Think of your gut as an active community; it takes a long time to build a healthy community but it will happen.

  • Consume prebiotic foods. These are nondigestible carbohydrates that get fermented by microbes in the gut; they are found in foods that are high in fiber. Examples of prebiotic foods include dry beans and other legumes, fibrous vegetables such as asparagus, cabbage, root vegetables, onions, garlic, leeks, whole grains.
  • Also, consume probiotic foods, which include live micro-organisms. When they get fermented by the microbes in the gut, this nourishes the microbiome and health. Examples of probiotic foods include include yogurt, kefir, fermented vegetables such as sauerkraut and kimchi, miso, and (hooray!) dark chocolate.

A little fermentation goes a long way to activate and nourish your your microbiome!


Try fermenting some of your own food. See some of our fermentation recipes here: 

Should you take a probiotic supplement?

Many physicians have begun recommending probiotic supplements to increase the “good bacteria” that antibiotics and other aspects of modern life may have removed from the gut.

But should you take one?  If so, which one? Because these supplements aren’t regulated like pharmaceutical drugs, they pose many concerns related to labeling truth, quality, and dosing. From the health standpoint, how many strains of which bacteria do you need and how often? Will the live bacteria you swallow survive their passage through the acidic stomach contents? Can some of the live bacteria contained in a probiotic supplement harm some people?


Where can I learn more about microbiomes?

With new research papers and popular articles appearing on a daily basis, health consumers should remain open, but skeptical. I would recommend this wonderful unit on the human microbiome from the University of Utah genetics department as a quick and easy way to learn some of the critical functions of microbes in our bodies.

Exciting though microbiome research appears, many medical and ethical questions remain (page 2). Keep them in mind as you begin seeing advertisements for products or services promising to analyze, protect, or improve your microbiome. And keep  your critical eye open as you begin exploring news articles and research reports on this exciting new field of health research.

Learn more

The hoops, hopes, and hypes of human microbiome research

Structure, function and diversity of the healthy human microbiome

About This Blog

"Living Naturally" is all about living a naturally healthy lifestyle. Margaret Boyles covers health tips, ways to avoid illness, natural remedies, food that's good for body and soul, recipes for homemade beauty products, ideas to make your home a healthy and safe haven, and the latest news on health. Our goal is also to encourage self-sufficiency, whether it's relearning some age-old skills or getting informed on modern improvements that help us live better, healthier lives.