Be Nice to Your Gut

Aloha friends!

I went to an interesting talk a couple of weeks ago about the human gut microbiota by Dr. Emma Allen-Vercoe, an associate professor of molecular and cellular biology studies at the University of Guelph. What exactly is the gut microbiota you ask? The gut microbiota houses a community of tiny microbes (e.g., bacteria) that have set up shop inside our intestines. But bacteria are bad you say? Not necessarily. If you are not convinced I hope you will be by the end of this post, as I will share with you some interesting tidbits I learned from that evening.

We all have a unique community of microorganisms living in our intestines (they out number our own cells ~3:1), and this community is establishing itself from the time we spend in our mom's belly up until the age of five, after which it is thought that this community stays relatively the same. However, if we harm this community or make these microbes angry, this can lead to a weakened community of microbes, or microbes that behave badly. The result? Research is showing a connection between our gut microbiota and health outcomes, such as obesity, colon cancer, depression and allergies (just to name a few). We need these microbes to contribute nutrients and other products to have a positive influence on our digestion and overall health (Flint, 2012).

There are a few ways we are affecting that community, including:

  • Being too clean (aka hygiene theory) (Willyard, 2011)
    • Getting exposure to different types of microbes during those first few years of life is important to help that microbe community build itself in our intestines. This is fundamental for our immune system, and can affect our body's defenses needed to prevent the development of asthma and allergies. Dr. Allen-Vercoe's advice for kids under 5? Get a pet that goes outside!
  • Taking antibiotics (Blaser, 2011)
    • Antibiotics saves lives. There is no denying that we need antibiotics, particularly to battle the 'bad' microbes that can make us sick. However, antibiotics damage the microbe community, and as a result, it can take some time for that community to rebuild, or in some cases, that community cannot rebuild itself back to it's original population (e.g., hospitalized individuals who get frequent infections). For some microbes, having the room to grow provides them with an opportunity to cause an infection (e.g., C. difficile).


  • Diet (Conlon & Bird, 2015; Emma Allen-Vercoe, 2014)
    • What we eat can affect how the microbes behave and/or impact the growth of good microbes in our intestines. The Western diet plays a large role in this, in addition to decreased physical activity, as researchers are learning that low intakes of fiber/fruits and veggies and high intakes of fat/processed foods or too much protein can change microbe behaviour. For example, the microbes may react by causing inflammation in the intestines, attacking our own body protein, or changing body processes (such as the way we lay down fat).
    • One interesting comment from talk is that researchers are finding that artificial sweeteners and food colouring added to foods have been found to influence the behaviour of gut microbes, and not in a good way!  

Naturally researchers are trying to explore these three aspects, as well as others, to determine what we can do to promote an environment for good microbes to flourish in the gut. For example, researchers are trying to work on developing antibiotics that won't harm the gut. As well, research studies on the use of fecal transplants (transplanting fecal bacteria from a healthy donor to a recipient) are proving to be effective to decrease recurrent infections in hospitalized patients (Gupta, 2016).

What can we do from a nutrition standpoint? It is suggested that we should consume a healthy diet, rich in a variety of fruits and vegetables, high in fibre, adequate in protein intake, as well as eliminating processed and high fat foods from our diets. Probiotics may also be helpful to help support a diverse community of gut microbes, particularly while taking antibiotics.

But buyer beware! 

Many probiotics on the market make false claims and are ineffective. The microorganisms you get from taking probiotics can have beneficial effects as they transition through your gut, but the microbes won't stick around in your gut once you stop taking the probiotic. If you want to make sure you are choosing the right product for your needs, there is a website available that identifies probiotic products available in Canada which have scientific evidence to support their use:

What was really cool was to hear about where researchers think the future of all this research will take us. Perhaps at our regular checkups with our family doctors we will be adding gut check ups and be provided with recommendations on how we should eat based on our individual gut microbe community? Perhaps we can take antibiotics without the worry about the side effects for our gut health? Perhaps medication and food product testing will take into consideration the effect the product has on gut microbes? Perhaps textbooks will include sections dedicated to gut microbes, considering the community as a 'virtual organ'? Time and research will tell!

I was so glad I was able to attend this talk, and I hope that by sharing with you what I have learned, that you may re-think about how nicely you treat the community of microbes living inside you! 

xo Michelle

PS- If you would like to hear Emma talk about this topic check out Speaker for the Microbes: Emma Allen-Vercoe at TEDxWaterloo 2013


Blaser, M. Antibiotic overuse: Stop killing the beneficial bacterial. 2011. Nature, 476, 393–494.

Conlon, M & Bird, A. The impact of diet and lifestyle on gut microbiota and human health. 2015. Nutrients, 7(1), 17-44.

Allen-Vercoe, E. Microbe-managing: Manipulating the Human Gut Microbial Ecosystem to Enhance Health. 2014 AMMI Canada – CACMID Annual Conference:

Flint, H et al. The role of gut microbiota in nutrition and health. 2012; Nature Reviews, 9, 577-89.

Gupta et al. Fecal microbiota transplantation: In perspective. 2016; Therap Adv Gastroenterol, 9(2), 229-39.

Willyard, C. Microbiome: Gut reaction. 2011. Nature, 479, S5-S7.