Are Probiotics, Prebiotics, and Fermented Foods Good for Your Gut Health?

Dr. Emma Allen-Vercoe of the University of Guelph explains why our microbiome is more important than we might think.

Link to 2017 Nutrition Forum Presentation

On a sunny, crisp May Wednesday morning in downtown Vancouver, 175 health professionals gathered at the Vancouver Convention Centre to learn about the trillions of microbes that make up our microbiome.

Over the past decade, we have seen growing interest by both researchers and the public in understanding this emerging field of science.  At the same time, questions bloom about the microbiome’s impact on one’s health.  To address this topic, the 17th annual BC Dairy Association Nutrition Conference was honoured to present Dr. Emma Allen-Vercoe, one of the world’s leading experts in the human microbiome.  As an internationally recognized microbial ecologist, and a self-proclaimed “speaker for the bugs”, Dr. Allen-Vercoe gave attendees a peek into the lives of our microbial friends.  Along the way, she smashed a few myths.

Part I: Overview

Dr. Allen-Vercoe’s opening session addressed three main questions:

  • what is the microbiome
  • how is it shaped
  • why is it important

According to Dr. Allen-Vercoe, every person has a unique microbiota, like a fingerprint, or “pooprint”.  Surprisingly, “we are more microbial than human in terms of the number of human cells vs microbial cells.”  By cell number alone, we are in fact not technically 100% human.

What is it?  In contrast to previous estimates, modern tools have identified 200-500 bacterial species amounting to an approximate 39 trillion bacterial organisms in the microbiome.  In addition to bacteria, the microbiome includes methane-producing, archaea, yeast, various microscopic single-celled eukaryotes, and viruses, all of which work in symbiosis in our gut.

How is it shaped?  Current research favours the sterile womb paradigm. The nascent gut is colonized at birth, and develops over the first 3 years of life.  Depending on the method of delivery, a vaginal birth will colonize a different microbiome compared to a cesarean birth for the first 6 weeks of life.  After 6 weeks, an infant’s gut will normalize, leading to indistinguishable differences in microbiota between the two groups.  According to Allen-Vercoe, what favors a more diverse and beneficial microbiome from this point forward is the practice of breastfeeding throughout infancy, the foods we eat, and environmental exposures.  After 36 months, the microbiome is essentially established, and remains relatively constant throughout the lifespan.  As Allen-Vercoe commented, the “window for proper gut microbiota development is narrow.”

Why is it important?  There exists a delicate equilibrium between our microbiome and our health.  A highly diverse microbial gene-count is desirable because if certain microbes are damaged, similar species can step in to ensure the gut remains healthy. This balance is known as “functional redundancy”. In contrast, a low bacterial gene-count, known as “functional disability” is problematic for both microbiota and human health because it creates a situation where potentially harmful bacteria monopolize the gut’s environment.

To understand the function of the microbiome, one approach is to think of it as a vital organ, like the liver.  The trillions of cells in the human gut process food from our diet we can’t digest, like fibre, for example.  They also regulate the immune system, provide energy, generate vitamins, and remove toxins and harmful pathogens.  Unfortunately, the unintentional damage from dietary and environmental conditions has decreased our bacterial diversity and its protective health effects.

Part II: Implications and practical applications

Studying the microbiome:  To Dr. Allen-Vercoe, the traditional petri-dish method of studying microorganism is ineffective.  Because bacteria are “social creatures”, they exist in symbiosis with each other and with their host.  That’s us!  In fact, Dr. Allen-Vercoe believes we should study gut bacteria in situ, or as close to the natural human digestive environment as possible.  To accomplish this, her lab at the University of Guelph created the first mechanical model representing the human digestive tract, in particular the colon, appropriately named ‘Robogut’.  Robogut is essentially a life support system for the gut microbiota. It serves as a model for the gut under various stressful conditions and enables her lab to study the gut in an ethical manner.

Microbial diversity: The importance of microbial diversity for managing bacterial infections, obesity, and disordered digestion from Crohn’s disease and ulcerative colitis was also discussed. While the cause of both Crohn’s disease and ulcerative colitis is unknown, the microbiota is thought to be pivotal. There is a decrease in the diversity of microbes in both conditions, but it is still unknown whether this causes the conditions or is an effect of the conditions.

Clinical dietitians frequently encounter patients with a bacterial infection caused by Clostridioides difficile.  Administration of broad-spectrum antibiotics dramatically reduces gut microbial diversity.  C. difficile, often resistant to antibiotics, is able to flourish in the absence of a diverse microbiome.  An emerging treatment to C. difficile infections is a fecal transplant.  Dr. Allen-Vercoe notes cases of rapid resolution of the disease after administration, but notes we do not yet fully understand the long-term negative health implications of doing fecal transplants and suggests Health Canada is justified in being cautious about approving this procedure.

Can diet fix a dysfunctional microbiota?  Prebiotics, probiotics, and fermented foods are increasingly popular in our diets, but what are they and how do they impact our microbiome?  Allen-Vercoe explained the difference between the three groups, and gave her top tips for incorporating more into our diet.

Key Points


  • Probiotics found in food are not the same as those found in a supplement.
  • Probiotics cannot colonize your gut.
  • Taking a probiotic does not cancel out antibiotic use.  At the same time, lack of regulation and overinflated claims of probiotic efficacy are important to consider.
  • When buying a probiotic, look for strain and species on the label.


  • Food for gut microbes.
  • Not a “one size fits all” situation.  Each person has a different microbiota to feed. Best form of prebiotics is from food, such as fibre-containing food!
  • Avoid fibre supplements, unless prescribed by a physician.

Fermented Foods:

  • Benefit of fermented foods may not be the foods themselves, but more the chemical products of fermentation.

Overall, Allen-Vercoe’s takeaway messages are:

  • Listen to your gut.
  • Eat a wide selection of fruits, vegetables, and fibre-rich foods.
  • Avoid fibre pills.
  • Avoid supplements that have no clinically proven claims.
  • Exercise.

Physical fitness is a surprising contributor to gut microbiome health. Moderate exercise seems to have positive effects on the microbiota composition and diversity.

Thank you Emma for an amazing presentation!

Still wanting to learn more about probiotics and health?  Connect with BCDA’s nutrition education team and book your workshop today

For more information on prebiotics, probiotics, fermented foods and fibre, read our articles:

Probiotics: What You Need to Know

Prebiotics: Feeding Your Healthy Gut Bacteria One Meal at a Time

FoodTrack Check on Fibre: Revised and updated with all the latest values

About BC Dairy

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