top of page

Your Microbiome is the Key to Overall Health

It’s really unbelievable that the tiny, little microorganisms living in our gastrointestinal tract can influence health outcomes like allergic tendencies, body weight, joint pain, energy, mood, etc. The microbiome and its implication on human health is one of the fastest growing areas in scientific research.

This blog will start with the basics and define the microbiome and the various factors that influence it. Future posts in this series will look at specific topics like: Gut Health and Depression; Gut Health and Obesity; and Gut Health and Pain. Of course, additional topics can always be requested!

What is the “Microbiome”?

=Collective term for the diverse ecosystem of bacteria, yeast, and fungi living in our GI tract.

“Microbiota” = bacteria

“Dysbiosis” = Unfavourable microbiome. There is either low growth of good, health-promoting bacteria, and/or increased growth of neutral, or even harmful bacteria.

Fast Facts:

1. We each have a unique microbiome varying in the type and number of bacterial species. This is largely influenced by genetics, early life factors, and lifestyle. (More on this in next blog.)

2. We have ~100 trillion bacteria in our GI tract. Based on cell number, we technically can be considered more bacteria than human.

3. Half the weight of a bowel movement is bacteria.

4. Most of the microbiota resides within the large intestine, with fewer residing in the stomach and small intestine.

5. Microbiota produce metabolites which can have a positive or negative effect on host (us!)

6. A diverse microbiome with lots of different species is associated with positive health outcomes.

7. Comprehensive stool analyses are available via stool cultures that provide a "report card" on your microbiome - growth of good bacteria, presence of inflammatory markers, markers of digestion, etc.

8. A microbiome is transgenerational ie. it gets passed on to your child in utero. By supporting your gut health now (as a woman), you can impact the health of your future children and grandchildren!

What Do They Actually Do For Us?

The interactions and specific role of each bacterial species is complex. Certain species are considered ‘good’ in that they benefit our health, whereas others are either neutral, unknown, or have negative effects. The understanding is far from complete, but this much is known:

1. Immune System Regulation

The majority of our immune system can be found within the mucosa of our GI tract. You can think of our GI lining as a barrier keeping things out of our body that shouldn’t be there (like harmful bacteria), and allowing things we need (like nutrients from food) to pass through.

Our microbiota also resides in this lining, so they communicate directly with our immune system through the release of metabolites and even just their presence (via structural components) can influence immune response. They can drive hyper-responsive immune responses seen in allergies, food sensitivities, etc. and microbiome has even been linked to driving autoimmunity.

2. Hormone Regulation

Sex hormones like estrogen, progesterone, and testosterone are eventually broken down by liver and dumped into the gut for removal. Certain bacteria are capable of acting on these hormones to promote their re-absorption back into the body.

3. Maintain Overall Gut Health

‘Good’ bacteria feed on fibre we consume in our diet, and metabolize it into short chain fatty acids (SCFA.) There are several different types of SCFA with their own individual role, but in general, they collectively have the following benefits:

a.) Lowers pH of colon – This prevents growth of ‘bad’ bacteria and also helps with nutrient absorption.

b.) GI Barrier Integrity- SCFA is fuel for enterocytes, the cells that line our GI tract, which then produce mucin - a wet, substance that protects the mucosa. Mucin helps maintain tight cell junctions of the GI tract. If these tight junctions loosen, it can cause systemic inflammation and be a risk factor for a variety of chronic diseases and immunological conditions.

c.) Produce gut hormones- SCFA initiate signals to the brain telling us when we’re ‘full’ and to stop eating, which helps with weight control and cravings

d.) Anti-tumour/Anti-inflammatory- One SCFA in particular has been found to reduce tumours and be protective in patients with colon cancer. Low SCFA has been associated with colon cancer.

e.) Gut motility- SCFA aid in the contraction of smooth muscle in the walls of the colon. Contractions is how we eliminate waste – aka maintain regular bowel movements.

4. Nutrient Assimilation

Microbiota have enzymes that help us break down food – notably, complex carbohydrates and proteins.

Vitamin Synthesis- Our gut microbiota can make B Vitamins (like folate, biotin, cobalamin, etc.) and Vitamin K.

Metabolism of polyphenols – these are the antioxidant constituents found in a variety of foods (like grapes and green tea) that are very beneficial for human health.

5. Brain Health

The gastrointestinal tract is more than just digestion and bowel movements! There’s a whole nervous system, called the enteric nervous system within the GI tract that communicates with our brain through nervous activity– commonly referred to as Brain-Gut Axis. This communication is bi-directional, meaning brain-> gut and gut->brain. I’ll dive more into this later on a blog dedicated to microbiome and depression/anxiety.

Disruption of the ‘good’ microbiota and consequently, loss of the functions listed above is thought to underlie many human disease processes. When the “good” become lost, generally they’re replaced by the not-so-good ones. Dysbiosis is thought to contribute to many chronic diseases from Parkinson’s Disease to Type 2 Diabetes to Inflammatory Bowel Disease.

Next blog will cover what factors affect the health of our microbiome - stay tuned!


Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. Bmj. 2017 Mar 15;356:j831.

Hadrich D. Microbiome research is becoming the key to better understanding health and nutrition. Frontiers in genetics. 2018;9.

Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Science of the total environment. 2018 Jun 15;627:1018-38.

Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de los Reyes-Gavilán CG, Salazar N. Intestinal short chain fatty acids and their link with diet and human health. Frontiers in microbiology. 2016 Feb 17;7:185.

Thomas S, Izard J, Walsh E, Batich K, Chongsathidkiet P, Clarke G, Sela DA, Muller AJ, Mullin JM, Albert K, Gilligan JP. The host microbiome regulates and maintains human health: a primer and perspective for non-microbiologists. Cancer research. 2017 Apr 15;77(8):1783-812.

Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. European journal of nutrition. 2017 Apr 9:1-24.

Single post: Blog_Single_Post_Widget
bottom of page