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Microbiome and What You’re Eating

Over the last decade or so, microbes and our microbiome have been the subject of great interest and research. Every day it seems like there is a new colon cleanse, a gut health reboot diet, or a fancy new probiotic sure to solve all your woes. 

But unlike other health and diet fads, the focus on a healthy gut is here to stay, and it can have a great impact on your overall health and well-being. So let’s break down what it all means, why it matters, and the steps you can take to promote a healthy gut. 

What Are Microbes?

mi·crobe /ˈmīˌkrōb/
Learn to pronounce

plural noun: microbes

  1. a microorganism, especially a bacterium causing disease or fermentation.

Basically, microbes are the extremely small living organisms inside our bodies. These can be broken down into 5 types:

  • Bacteria
  • Fungi
  • Algae
  • Protozoa
  • Viruses*

*While a virus is not a living organism on its own, it attaches to a host cell (a microbe). 

What is the Microbiome?

The Microbiome is the collection of individual microbes. If we think of each microbe as a tiny person, the microbiome would be the city they all live in. It’s estimated that nearly 30 trillion bacterial cells are living in or on each of us that make up our individual microbiome.

The microbiome is so significant to our health and body function that it is considered a supporting organ

Why It Matters

Recent studies have suggested that our intestinal microbiome plays an important role in tempering the risk of some chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. 

It’s All About The Gut

How large a role does a healthy microbiome play in our overall health? A large one. 

A 2013 study showed that dietary changes could rapidly affect the abundance of specific species of bacteria in people’s digestive tracts

“All disease begins in the gut.

– Hippocrates

The microbiome consists of microbes that are both helpful and potentially harmful. Most are symbiotic, meaning they get along and help each other out. Some are pathogenic, meaning they promote disease. In a healthy body, pathogenic and symbiotic microbiota coexist to create balance in the body.

But when there is a disruption in that balance – whether due to illness, medications, poor diet, pregnancy, or other changes in the body – we become more susceptible to disease. This disruption is called dysbiosis. 

Recently, this has even come into the discussion surrounding COVID. There have been studies conducted that look at the possible impact that dysbiosis has on a COVID infection, and how the diversity and abundance of key microbes may play a role in vaccine research and efficacy. 

How What You Eat Affects Your Gut

Diet plays a huge role in determining what kinds of microbes make up your microbiome. 

A diet that is both high in fiber and rich in probiotics and prebiotics will help maintain a healthy gut balance. 

Probiotics – Probiotics are live microorganisms promoted with claims that they provide health benefits when consumed, generally by improving or restoring the gut flora.

Prebiotics – Prebiotics are compounds in food that induce the growth or activity of beneficial microorganisms such as bacteria and fungi. 

Foods with natural probiotics

  • Preboticfermented vegetables
  • kefir
  • kimchi
  • kombucha
  • miso
  • sauerkraut
  • tempeh

Foods with natural prebiotics

  • garlic
  • onions
  • leeks
  • whole grains
  • bananas
  • asparagus
  • apples
  • cocoa
  • flax seed
  • seaweed

Be aware though that a high intake of prebiotic foods introduced suddenly can increase gas production (flatulence) and bloating. Individuals with gastrointestinal sensitivities such as irritable bowel syndrome should introduce these foods in small amounts to first assess tolerance. 

Plant-Based Foods

A review in 2019 found that a plant-based diet may promote a healthy diversity of gut flora.

Dr. Raphael Kellman created a specific diet, called the Microbiome Diet, based on eating and avoiding certain foods to restore and maintain gut health. The diet claims other benefits, such as a faster metabolism and weight loss.

Foods to Avoid

Just as there are foods that can improve the health of our microbiome and ultimately our gut, there are certain foods that can trigger and an overabundance of unhealthy microbes. 

Some foods to avoid are:

  • Processed and fried foods
  • Sugar and high-fructose corn syrup
  • Artificial sweeteners
  • Trans and hydrogenated fats
  • Starchy fruits and vegetables like potatoes, corn, and peas
  • Deli meats that are high in salt and fats
  • Peanuts, soy, and other legumes, except for chickpeas and lentils.
  • High-mercury fish
  • Dried fruit and fruit juices
  • All grains containing gluten
  • Eggs and dairy, except for butter and ghee
  • Yeast and foods containing it

Other Ways to Improve Gut Health

Diet is only one factor in improving our gut health. There are other things you can do to promote a healthy microbiome. 

  • Eat less sugar & artificial sweeteners
  • Reduce stress
  • Get enough sleep
  • Exercise regularly
  • Don’t smoke
  • Avoid unnecessary antibiotics


The health of your gut is fundamental to your overall health. Probiotic and prebiotic supplements can help you maintain a better balance of microbes, but they’re only part of the equation. A healthy diet rich in fiber is key, as is taking care of your body. Exercising, sleeping right, and reducing your stress can all have a positive impact on your microbiome. A healthy gut is one key to a healthy you! Now go drink your kombucha tea! 


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