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What Is The Gut Microbiome?

Our gut microbiome is home to trillions of bacteria that influence our health and well-being.
What Is The Gut Microbiome?
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In this article:

  • The human microbiome
  • Why does our gut microbiome matter?
  • How the gut microbiome affects autoimmunity
  • How can I increase the good bacteria in my gut?

The human microbiome

The human digestive tract serves several purposes. Our guts play a critical role in our health from absorbing energy and nutrients from food to fighting pathogens and regulating electrolytes. Our gut is also home to a massive ecosystem of microorganisms, which is called our microbiome. Trillions of bacteria reside in our digestive tract. Each contains genetic material and releases chemicals that can impact our health. There are over 1,000 different species in the human microbiome. Some may benefit us and others may be detrimental to our health. Studies suggest we have more cells in our microbiome than in our bodies, and the weight of this bacteria is around 4.5 pounds.

Bacteria are not the only microorganisms living in our gut. We also have fungi, viruses, archaea, and single-cell eukaryotes like yeast. Together, these organisms create our gut microbiota. While there is a vast diversity in our microbiota, nearly all of our gut bacteria are from about 40 different species. 

Why does our gut microbiome matter?

The more diverse our microbiome, the better. A diverse microbiome can help digest our first food (milk) and fiber, which is challenging to digest without good bacteria. It is also crucial for preventing disease like obesity, type 2 diabetes, or heart disease. 

Along with digesting our food, our gut bacteria regulate the immune system and produce chemicals circulating in our bloodstream. These chemicals can impact all of our organs, including the brain. Much of our immune system concentrates in our gut. Therefore, when our gut bacteria are off-balance or have an overaccumulation of "bad" bacteria, we are at an increased risk of infection, inflammation, and autoimmune diseases. 

Gut bacteria can also affect your digestive health. When the microbiome is off-balance, people can suffer from irritable bowel syndrome, inflammatory bowel disease, bloating, abdominal cramping, and weight gain. 

How the gut microbiome affects autoimmunity

Intestinal permeability (also known as "leaky gut") is a condition that allows bacteria and toxins to "leak" through the intestinal wall into our circulatory system. Leaky gut can exacerbate when our microbiota is out of sync and can cause inflammation and infection in other body areas. In response, our immune system can become overactive and attack our healthy tissues. Such is the case for people with Hashimoto's, the leading cause of hypothyroidism in the United States. In Hashimoto's, your immune system mistakenly attacks healthy thyroid tissue, causing inflammation and the thyroid's possible failure.

How can I increase the good bacteria in my gut?

We have discussed why a healthy microbiome leads to a healthy human. Now, let's explore ways to restore balance to your microbiome and increase the number of good bacteria living in your system. 

Food is the cornerstone of improving your gut microbiome. A healthy microbiome has a lot of diverse species. Unfortunately, the Standard American Diet (SAD) does not promote diversity among microbiota. Our SAD foods are often highly processed and don't contain enough nutrition (such as fiber) for good bacteria to survive.   

Our food choices also affect our risk for chronic health conditions. Consider making these changes to your diet to improve the health of your microbiome:

Eat a variety of different foods

Remember, diversity is key to a healthy microbiome. Expose your gut bacteria to a wide array of foods that can increase healthy bacteria like Bifidobacteria. Try different vegetables, fruits, meats, dairy products, and whole grains.

Eat prebiotics

Prebiotics are foods that contain fibers that you cannot digest. Our gut bacteria need fiber to survive and thrive. Without bacteria, we cannot digest some fibrous foods because we lack enzymes to break these foods down into absorbable molecules. Eating a diet high in fiber ensures that our good gut bacteria are well-fed to digest other foods and fight off infection and chronic illness. Examples of prebiotics include:

  • Apples
  • Leeks
  • Bananas
  • Asparagus
  • Dandelion greens
  • Onion
  • Jicama

Limit artificial sweeteners

Some studies suggest that simple sugars fuel the growth of harmful bacteria.

Consider trying probiotics

Unlike prebiotics, probiotics are live bacteria found in fermented foods. Our gut bacteria thrive off of fermented foods, such as yogurt and sauerkraut. Specifically, fermented foods can increase Lactobacilli, which fight off infections in your gut, such as diarrhea-causing pathogens. You can also take probiotics in a capsule. 

Aside from diet, your gut can benefit from overall stress reduction. Cortisol, our stress hormone, can affect the balance of bacteria in our gut. Try to relieve stress by getting enough sleep, doing self-care practices such as meditation, and getting regular physical exercise.

Also, antibiotics can wipe out both the good and bad bacteria in our gut. Therefore, it is important only to take antibiotics when necessary. After taking antibiotics, re-colonate your gut with good bacteria by taking probiotics and eating foods that restore good bacteria.

A note from Paloma Health

Many nutritional factors play a role in optimizing thyroid function. Paloma Health offers you the opportunity to work with a nutritionist in collaboration with a physician to determine nutritional status for optimal thyroid health.

Join us in the Thyroid Care Club Facebook Group for more on these topics and many others regarding thyroid health and wellbeing.


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Julia Walker, RN, BSN

Clinical Nurse

Julia Walker, RN, BSN, is a clinical nurse specializing in helping patients with thyroid disorders. She holds a Bachelor of Science in Nursing from Regis University in Denver and a Bachelor of Arts in the History of Medicine from the University of Colorado-Boulder. She believes managing chronic illnesses requires a balance of medical interventions and lifestyle adjustments. Her background includes caring for patients in women’s health, critical care, pediatrics, allergy, and immunology.

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