What affects the composition of our microbiome

What affects the composition of our microbiome

  • Gut Health

  • By Mathieu Millette, Ph. D., Mcb. A.

    There’s a lot of discussions these days around our intestinal flora, and more specifically the bacteria, both good and bad, that populate (or should be populating) it. But believe it or not, our microbiome is a diverse ecosystem that contains much more than just bacteria. In fact, the human gut microbiome is comprised of ten different types of microorganisms, including bacteria, viruses, fungi, and protozoa. While we are just starting to unravel specific information on each, we do know that they all play a role in the health, the gut ecosystem and ultimately, you.

    We're still exploring answers to questions about the optimal balance of organisms in the gut, how to best influence specific populations, and what affects the presence of particular communities. However, one thing we do have clarity on is that various lifestyle factors can directly alter the composition of our microbiota.


    How Our Lifestyle Shapes Our Gut Microbiome

    You might not think of it this way, but our intestinal flora is an organ in its own right. And just as we give attention to other parts of our body, it’s critical that we take care of our intestinal flora too, as it plays a crucial role in both our daily bodily functions (like bowel movements) and long-term health.

    Each day, many lifestyle factors can, and do, disrupt the makeup of our intestinal flora potentially altering its composition.1,2 Unfortunately, some of these factors, like heredity, are out of our control. But others are influenced strongly by our lifestyle, including diet, environmental exposures to toxins (like alcohol and smoking), and medications (like the over-use of antibiotics). Armed with the knowledge that we can, and should, support our microbiome, gone is the thinking that bacteria is bad. Instead, people are now learning to limit their medication use (when possible), washing their hands (versus using antibacterial hand sanitizer) and increasing their exposure to natural environments, such as dirt, all in the name of microbiome diversity.

    Why? Because when our intestinal flora is unbalanced, and an influx of bad bacteria take over, it can (and typically does) lead to a host of complications including digestive ailments, illness, infections, fatigue, depression and more. Long-term studies have been conducted in attempts to understand this further and define what a ‘normal’ gut microbiome is, as well as what factors affect the microbial species living there.3 And while there are many influences on the average person's digestive tract, there is growing recognition of the role of diet and environmental factors regulating both the composition and metabolic activity of the microbiome.4


    Your Diet and Your Microbiome

    It should come as no surprise that diet plays a significant role in shaping the composition of the microbiome. Macronutrients (carbohydrates, protein and fat), have been examined the most when it comes to diet and gut health with the majority of research exploring the action of carbohydrates on the entire gut ecosystem; though more and more research is emerging around the role of both proteins and fats, too.

    Carbohydrates serve as the principal energy source for microbes. But it is essential to recognize that not all carbohydrates are created equal. While many carbohydrate-rich foods including sprouted grains, fruits, vegetables and fermented foods are beneficial to our gut bacteria, highly processed and refined carbohydrates, are not. Specifically, your gut bacteria takes organic acids from healthy carbs and breaks them down into fermentable substrates that they then use as fuel.4 Among all the different types of carbohydrates that you consume, fibre is most readily fermented in the colon and has been shown to be one of the best ways to maintain and support a healthy gut microbiota population.

    But it’s not all about carbohydrates. A balanced diet is critical for both overall wellness and gut health. Dietary protein is an essential source of nitrogen for microbial growth in the colon, and it is also a necessary factor in bacteria’s ability to absorb and use ingested carbohydrates. However, unlike carbohydrates, the microbiota's fermentation of protein sources produces a much higher diversity of gases and metabolites, which can result in negative substrates for the bacteria.4 To protect against this, consider a plant-centric diet (smaller portions of animal protein and lots more fruits and veggies), or swapping out animal protein for some veg options like tempeh or legumes.

    Finally, when it comes to fat, little is still understood around its ability to influence metabolic activity and disease in the gut as well as inflammation, although, like carbs, consuming healthy fats in your diet, contributes positively to overall health and certain fats do play a role in combating inflammation.

    While the above speaks to specifics on nutrients in the gut, the important takeaway is how it relates to your day to day diet. As mentioned, when discussing carbohydrates, a diet such as the common Western style of eating (the over-consumption of highly-refined carbohydrates, saturated fats and added sugars but low in vegetables, fruits, and grains), all negatively affect the diversity of intestinal flora including growth of microbial species such as E.coli bacteria and Candida yeast.4 Current research suggests that we should be eating plenty of colourful, high fibre plant foods to feed beneficial bacteria and help to control inflammation in the gut.


    Medication and The Microbiome

    Even more than food, medication has a massive impact on our gut. It is widely understood that antibiotics disrupt our gut bacteria, wiping out all both good and bad intestinal flora. This obliteration of bacteria does positively help to treat the initial disease but can set us up for long-term consequences if the good bacteria is not properly restored. 

    Beyond antibiotics, proton-pump inhibitors, metformin (a drug often prescribed for diabetes), anti-cancer drugs are all linked to reduced microbiome diversity. While these drugs are designed to act on human cells (versus bacteria, like antibiotics), we’re now understanding how they interfere with bacteria, hindering their growth, contributing to a lack of microbial diversity, and promoting persistent gut disorders and chronic inflammation.


    Sleep, Stress & The Environment

    Other lifestyle factors, such as sleep, stress, and exposure to toxins from our environment can affect our microbiome too.

    Evidence suggests that poor sleep patterns and disruptions to our natural circadian rhythm result in microbial dysbiosis, which can have health consequences including obesity, metabolic syndrome and inflammatory bowel disease.5 

    Chronic stress, common in our modern lifestyle, not only causes persistent inflammation in the body but also negatively impacts gut health. Research suggests that the release of stress-related hormones change the intestinal surface, relocating bacteria, viruses and more from where they should be.6

    Finally, toxins including pesticides, artificial sweeteners, alcohol and smoking, all have adverse effects on intestinal ecosystem showing persistent dysbiosis.7


    How You Can Support Your Intestinal Flora

    Our gut microbiome has a profound influence on our overall health and the state of our gut very much depends on the lifestyle decisions we each make. Macronutrients, prebiotics, food - derived probiotics, and polyphenols (from colourful fruits and veggies), and medications all induce shifts (positively and negatively) in the microbiome.

    While dietary intervention, reduced use of medication, and mindfulness of environmental conditions, can support gut diversity, it is possible that the level of impact from these factors may not always be sufficient enough to maintain or elicit changes in the microbial population of the gut. To proactively promote microbial diversity, the use a daily probiotic is recommended.

    Bio-K+ is a clinically proven probiotic, containing three unique strains that have been proven to compete with pathogenic bacteria (like C. diff). Beyond that, the strains of probiotic bacteria found in Bio-K+ help to create a favourable environment for good bacteria to grow, helping to support microbial diversity.

    Throughout our life we will be faced with factors that will shift our microbiome. At some point we may have to take medication, like antibiotics, our diet may be less than optimal, or we may experience bouts of stress or poor sleep. Knowing that these factors can impact your microbiome health and understanding the role that has in your overall health and well-being, provides you with more tools to take charge of your health and support your body the right way.


    If you have any other questions about the health of your microbiome, ask us in comments below. If you are looking to stock up on Bio-K+, head to our store locator. For more information on Bio-K+, probiotics and digestive health, contact us, find us on Facebook and Instagram or join our community.



    1. Dethlefsen and Relman. 2010. Incomplete recovery and individualized responses of the human distal gut... PNAS. 108(suppl1) : 4554- 4561.

    2. Connolly et al, 2010.In vitro evaluation of the microbiota modulation abilities of different sized whole oat... Anaerobe 16 : 483- 488.

    3. https://www.ncbi.nlm.nih.gov/pubmed/27126039

    4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303825/

    5. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097500

    6. https://www.ncbi.nlm.nih.gov/pubmed/20941511

    7. https://www.nature.com/articles/npjbiofilms20163


    Best Sellers


    Drinkable Vegan Probiotic

    Gluten-free, organic and non-GMO probiotics with a minimum of 50 billion live & active beneficial bacteria per bottle.

    Peach & Turmeric

    Extra Drinkable Probiotic

    80 billion live & active bacteria per bottle, with additional functional benefits

    Daily Care+ 50 Billion

    Vegan Probiotic Capsules

    Certified gluten-free and vegan probiotics. A great option for those who need daily support or a need a stronger alternative for better benefits.

    Mathieu Millette Mcb. A.
    About the author
    Graduated with honors from INRS-Armand-Frappier Institute, Dr Mathieu Millette is an authority on probiotics for the last 20 years.
    View all articles by Mathieu Millette
    Back to blog