What is Your Gut Microbiome? Why Does It Matter?

What is Your Gut Microbiome? Why Does It Matter?

There are trillions of bacteria that inhabit our digestive system and, together, they make up the gut microbiome. 

So, what is the role of the gut microbiome? The microbiome is more than just a collection of bacteria, helping the body with many regular processes including the following:

  • Digesting food
  • Regulating how energy is used
  • Supporting the immune system
  • Synthesizing certain vitamins and amino acids (building blocks for proteins); here’s more info:
  1. key enzymes necessary for the formation of vitamin B12 are only found in bacteria, not plants and animals 
  2. they break down toxic food compounds 
  3. they send signals to the brain that impact our hunger and mood

At birth, the microbiome is determined by one’s genetics, but the following factors can all have an impact on what types of bacteria inhabit the gut throughout a lifetime:

  • Diet 
  • The environment we live and work in
  • Genetics
  • Medications
  • Level of physical activity
  • Stress levels

It’s normal for the microbiome to contain bacteria that are both beneficial and harmful, but they must exist in the correct proportion so that the amount of “bad” bacteria doesn’t get too high. A disturbance to the balance of good to bad microbiota can be caused by diseases, certain diets, antibiotics, and certain medications. 

This is known as “dysbiosis” and can cause issues in the entire body. Dysbiosis has many negative impacts on the body, but one that will be discussed in more detail is its impact on the immune system. Hippocrates said that “all disease begins in the gut,” and now science supports his long-ago claim. It is known that 70-80 percent of immune cells are actually found in the gut! How incredible is that? This means that the diversity and health of our gut microbiome is crucial to our immune system. 

There are two theories when it comes to immunology: the germ theory and the landscape theory. The germ theory states that pathogens enter the body and make an individual sick, and the landscape theory states that a healthy host can fight off a pathogen more effectively. It is important to consider both theories when looking at immunity and the gut microbiome. A pathogen can enter the body and cause illness; however, a healthy and diverse gut landscape can support the immune response and help the host to recover faster. 

Gut Microbiome and the Immune System

The GI tract is a hollow tube, and microbes on the outer lining of this tube send information to immune cells on the inner lining. The gut microbiome differentiates harmful from non-harmful particles and can signal immune cells to attack pathogens. 

Said a different way, gut microbes basically order specialized immune cells to eliminate viral infections by producing antiviral proteins. For example, when certain viruses enter the GI tract, microbes known as bacteroidetes in the gut lining trigger a message, which releases cytokines (inflammatory “fighter” cells) to destroy the virus.  

The microbiota present in the gut actually have the power to educate immune cells to fight off certain pathogens and protect the body against foreign substances. Microbiota can compete with invading organisms for resources, which prevents the invader from surviving and spreading. Bacteria can sense what is present in the environment and subsequently produce protective compounds against the invader, and this sensing system can be negatively impacted by an unhealthy microbiome and lead to inflammation and increased infection rates.

It has been found that antibiotics eradicate gut bacteria that help the immune system, which illustrates the importance of gut diversity. When this happens, this causes lower amounts of white blood cells, a weaker antibody response (antibodies recognize pathogens), and poor production of a protein that fights viruses.

The development of the microbiome in the first few years of life is actually crucial to the development of the immune system, illustrating the interplay between the two. At birth, a lot of the child’s microbiome is determined by the mother's microbiota and her breastmilk. Being exposed to certain environmental factors that are harmful to the immune system can negatively impact the microbiome—even at later life stages.

Individuals with chronic inflammatory diseases have an overactive immune system, which cannot distinguish a harmless stimulus and may react as if it were pathogenic. This is linked to the person having a less diverse microbiome.

Maintaining a Healthy Gut Microbiome

Having a healthy microbiome is crucial to fighting off pathogens. The good news is that you do have some control over the microbiota in your gut, and a good place to start is the diet because you can include certain foods to help beneficial bacteria flourish. 


There are two types of fiber: soluble and insoluble. Soluble fiber is not digested in the gut, so it slows sugar and fat absorption. It’s fermented by good bacteria, which produces something called short-chain fatty acids; these support the gut lining and protect against the growth harmful microorganisms. Sources of soluble fiber include garlic, onions, leeks, asparagus, bananas, and seaweed.

Insoluble fiber acts as a prebiotic, which are specific types of fibers that are fermented by bacteria in the gut to increase “good” bacteria. Sources include Jerusalem artichokes, dandelion greens, garlic, onions, leeks, asparagus, oats, and bananas.


These plant compounds are not digested in the stomach and, instead, go to the large intestine to be digested by microbes. Polyphenols have antioxidant capabilities, reducing chronic disease risk; reduce inflammation in the body; and may improve mood and brain function. Some also have antimicrobial properties. Sources include apples, blueberries, broccoli, cauliflower, tomatoes, green tea, coffee, soy, and peanuts.

Omega-3 Fatty Acids

This type of polyunsaturated fatty acid is known to reduce inflammation and can help to balance microbiota, decrease inflammatory microbes, and strengthen the gut lining. Sources include salmon, mackerel, sardines, tuna, walnuts, laxseeds, and chia seeds.


Probiotics are live, beneficial microorganisms that can be consumed. They help to increase proportion of beneficial bacteria and support immune response. Sources include yogurt with live active cultures, kefir, sauerkraut, sourdough, kimchi, and miso. 

As always, in addition to these specific nutrients, consuming a diet full of colorful fruits and vegetables and food from the Earth will support the microbiome and your immune health. 

Limiting Foods to Support Gut Microbiome

There are also foods that should be limited to support a diverse and healthy microbiome. Too much of any of the following can disrupt the balance of bacteria in the gut. These are foods associated with a typical western diet, which is high in:

  • Processed foods
  • Refined sugar
  • Saturated fat
  • Factory-farmed meat
  • Artificial sweeteners
  • Alcohol 

In addition to food, other lifestyle-related ways to support the microbiome and the immune system include the following: 

  • Limit antibiotic use to when it is absolutely necessary; frequent use of antibiotics can kill off too much good bacteria in the gut.
  • Avoid anti-inflammatory drugs and/or opioids when possible. Overuse of these drugs can negatively impact gut diversity; NSAIDS (like ibuprofen) can create tiny holes in the gut lining and lead to impaired immunity.
  • When sick, consider holding off from taking anti-fever medication right away. Fever tightens up the lining of the gut wall, which prevents pathogens from entering the body.
  • Consider the benefits versus risks:
    • when using hormonal therapy; evidence shows that hormonal birth control may lead to gut dysbiosis
    • if taking a proton pump inhibitor; taking PPIs for long periods of time reduces stomach acid and lessens host defenses since stomach acid can kill pathogens. 
  • Get. adequate sleep:
    • Erratic sleep patterns can disrupt the microbiome and lead to inflammation.
    • The neurotransmitter serotonin is made in the gut and is a precursor to melatonin (sleep hormone). An unhealthy microbiome can disrupt serotonin production and impact sleep quality.
    •  Less than four hours of sleep in one night leads to a 70 percent drop in critical immune cells the next day.
  • Get enough physical exercise. Individuals who are more active have more diverse microbiomes.
  • Find ways to manage stress because it negatively impacts the microbiome via the gut-brain axis.
  • Find ways to get your hands in the soil, which is actually beneficial to the microbiome!

The interplay between the gut microbiome and the immune system is quite powerful, and supporting one means supporting both. Here’s more direction about what specific vegetables to eat for immune health.

Consider building your own “farmacy” box with these farm-fresh vegetables, which have many immune supporting phytonutrients.  

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