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What is our Gut Microbiome?

What is our Gut Microbiome?

Gut health. One of the top trends of this year as new and exciting research has come out citing how closely our guts are linked with many aspects of our health. You may have heard the terms “gut health” “microbiome”, and “probiotics” before, but what do they really mean? Let us break it down for you into simplified terms.

What is our Gut Microbiome?

Our gut is comprised of hundreds of TRILLIONS of living bacteria, fungi, protozoa, and viruses, mainly located in the large intestine. Our gut contains more than 10 times the amount of cells in our ENTIRE body and research has found that these critical cells play important roles in metabolism, immune health, digestion, development, and even human behavior and mental health. In fact, the gut flora comprises 75% of the immune system! The composition and variety of strains of bacteria in the gut microbiome varies from person to person, and as we age. Environmental factors and lifestyle factors affect them. So certainly, diet and exercise are important when it comes to supporting a healthy gut microbiome.


What does the research say, and why is it important to have a flourishing, varied gut microbiota?
If you take a look at the figure above (3), you can see all the various processes the gut microbiome is involved in. Research overall shows a link between a healthy immune system, a healthy BMI, prevention of disease, decreased inflammation, mental health etc. with a healthy, varied gut microbiome.
Here’s a breakdown of some of the findings of the latest research:

  • Helpful bacteria can lower serum cholesterol levels along with cardiovascular disease risk by preventing the activity of an enzyme involved in the synthesis of cholesterol, showing one reason why a healthy gut flora is helpful in disease prevention.
  • The gut communicates with bacteria that support digestion by their enzymatic capacity
  • The gut regulates major epithelial and immune functions of importance for gut health and health in general
  • The gut reports to the brain via the N. vagus and hormones about energy uptake and other conditions that might affect mood and general well-being
  • Research shows the GI barrier may play a central role in the pathogenesis of: Inflammatory Bowel Disease, IBS, Celiac Disease, Autoimmune diseases, Obesity, Fatty Liver Disease, NASH, Allergic diseases, and more.
  • Probiotics and ‘good’ bacteria are involved in many brain chemistry pathways that affect our emotions and moods, also known as the Gut-Brain Axis. Have you ever felt stressed and anxious, and then you noticed a stomachache, cramps, or bloating? This is because our guts and brains are uniquely and closely linked, therefore a healthy gut microbiome can support balanced mental health.
  • Intestinal microbiota, especially certain strands, may be linked with helping us maintain a healthy weight or BMI.
  • Those with a healthy, balanced gut microbiota may have a reduced risk of developing Type 2 Diabetes

“By influencing the composition and activity of the human gut microbiota, diet has an indirect effect on the gastrointestinal function of the host and thereby on health.”

Which foods support a healthy gut?

-   PREBIOTICS - prebiotics can be thought of as the 'food' for our good bacteria. Prebiotics are nondigestible fiber compounds that pass through the GI tract undigested by the body. They pass through, and then upon reaching the colon, they are fermented or "used" by the gut flora. Prebiotics work together with probiotics (see below) to help with important activities and composition of the GI tract.

Keep in mind though, although all food sources of prebiotics contain fiber, just because a food contains fiber does not make it a prebiotic. According to “Fiber and prebiotics: mechanisms and health benefits”, “Classification of a food ingredient as a prebiotic requires scientific demonstration that the ingredient: Resists gastric acidity, hydrolysis by mammalian enzymes, and absorption in the upper gastrointestinal tract; Is fermented by the intestinal microflora; and Selectively stimulates the growth and/or activity of intestinal bacteria potentially associated with health and well-being.


  • ​Artichoke
  • Banana
  • Leek
  • Onions
  • Raw jicama
  • Raw dandelion greens
  • Raw chicory root
  • Raw garlic
  • Raw asparagus

PROBIOTICS – probiotics are the living, beneficial good bacteria, so reintroducing this bacteria into our GI tract helps to flourish the gut microbiome. These are often found in fermented food sources, and can also be taken in pill form as a supplement (be sure to take only reputable brands, such as Thorne probiotics)


  • ​Yogurt
  • Kefir
  • Sauerkraut
  • Kimchi
  • Miso
  • Buttermilk
  • Sourdough bread
  • Fermented tofu (tempeh)
  • Kombucha

What other lifestyle factors are important to support a healthy gut microbiome?

Exercise: studies show that athletes have more diverse gut microbiota than those who do not exercise.

Limit antibiotics to only when absolutely necessary. Antibiotics do a great job of killing the unwanted bacteria, but they also take the good bacteria with it. Limit your use of antibiotics to only when necessary, and always supplement with probiotic- and prebiotic-rich foods or supplements when taking antibiotics.

-If you are a mother, breastfeeding your infant can help your baby have a more diverse gut flora, according to research.

Stress reduction. Practice yoga, meditate, laugh, journal, whatever helps you unwind!

Lastly, how do we know if we have a healthy gut?

Here are Five Criteria for a Healthy GI Tract, according to ‘Today’s Dietitian’:

Specific Signs of Gastrointestinal (GI) Health

• Normal nutritional status and effective absorption of food, water, and minerals
• Regular bowel movement, normal transit time, and no abdominal pain
• Normal stool consistency and rare nausea, vomiting, diarrhea, constipation, and bloating

Absence of GI Illness

• No acid peptic disease, gastroesophageal reflux disease, or other gastric inflammatory disease
• No enzyme deficiencies or carbohydrate intolerances
• No inflammatory bowel disease, celiac disease, or other inflammatory state
• No colorectal or other GI cancer

Normal and Stable Intestinal Microbiota

• No bacterial overgrowth
• Normal composition and vitality of the gut microbiome
• No GI infections or antibiotic-associated diarrhea

Effective Immune Status

• Effective GI barrier function, normal mucus production, and no enhanced bacterial translocation
• Normal levels of immunoglobulin A, normal numbers and normal activity of immune cells
• Immune tolerance and no allergy or mucosal hypersensitivity

Status of Well-Being

• Normal quality of life
• Qi (ch’i), or positive gut feeling
• Balanced serotonin production and normal function of the enteric nervous system

More research is still being conducted regarding the complex processes our gut microbiota is involved in, and the benefits on our health. With stress reduction, exercise, and a healthy diet, you can help to balance out your gut flora for optimal health. Contact one of our Registered Nutritional Dietitians today to come up with a personalized plan!

(1) https://www.ncbi.nlm.nih.gov/pubmed/23609775
(2) https://www.todaysdietitian.com/newarchives/060112p58.shtml
(3) https://bmcmedicine.biomedcentral.com/articles/10.1186/1741-7015-9-24
(4) https://academic.oup.com/jn/article/137/3/751S/4664737
(5) https://www.ncbi.nlm.nih.gov/pubmed/26459447
(6) https://www.ncbi.nlm.nih.gov/pubmed/24997043?refcode=perfecthealth&
(7) https://www.ncbi.nlm.nih.gov/pubmed/27633134