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Why I’m obsessed with the microbiome – and you should be, too!

The microbiome is community of microbes, including bacteria, viruses, protozoa, algae, yeast and fungi that live on and in us with the majority living in our gut.
Mar 22, 2019 | Joy McCarthy

Like many of you, throughout my childhood and into my twenties, I thought microbes were something bad – something you had to eradicate with antibacterial soap, mouthwash and household cleaners. Wherever germs lurked, we would seek to eliminate them. But in reality, our microbiome, made up of trillions of microbes, is keeping us and our planet healthy. Nowadays, there are hundreds of scientists all around the world investigating how these microbes impact our gut health, oral health, immune system (especially allergies and asthma), cardiovascular system and mental health.

role of gut microbiome and bacteria illustration

This is a topic I feel deeply passionate about, which is why I’m so excited to share this post with you today! When I was a little girl my mom worked in the Microbiology department at Toronto Western Hospital where she would watch bacteria grow on Petri dishes and identify them so that patients would know what bacteria was causing their sore throat. (I even remember her bringing home some Petri dishes for me to grow my own bacteria for one of my science experiments.) It was pretty cool then but fast-forward 30 years later and what science has uncovered (and what we still have yet to learn) as it relates to the microbiome is simply mind-blowing.

I’m going to stick with the basics in this post, and in the coming weeks and months, I’ll share more of the latest research on the microbiome as it relates to our gut, skin, mouth, lungs and brain.

What is the microbiome?

It’s the community of microbes, including bacteria, viruses, protozoa, algae, yeast and fungi that live on and in us with the majority living in our gut. These microbes are our constant companions through life because they’re always with us – in sickness and in health.

We have microbes in every nook and cranny of our body, especially our armpits (blame microbes for your stink!).

gut microbiome illustration

Here are some cool facts about your microbiome:

  • Our large intestine is a popular place for microbes to hang out as it is home to 10 trillion microbes and 500 to 1,000 different species.

  • There are 100 billion microbes in a single gram of poop!

  • Our gut microbiome collectively weighs as much as our brain, which is why many scientists consider the gut microbiome an organ with its own distinct metabolic and immune activity and have dubbed it the “Second Brain”!

  • Our hand houses more microbes than there are people on earth.

  • In one square centimetre of skin, there are one billion microbes! 

  • Our microbes make up about 43% of our body’s total cell count.

  • We obtain a massive amount of bacteria that help to form our gut during a vaginal birth when we literally swallow and get covered in our mother’s vaginal microflora.

  • We have far more microbial genes (possibly up to 20 million) whereas we have only 20,000 human genes.


Microbiologist and professor Sarkis Mazamanian says what makes us human is the combination of our own DNA plus the DNA of our microbes.

I would say that we are more microbial than we are human, not that I’m going to argue with a scientist, of course!

So who’s really in charge here? Something we can’t even see with the human eye, something that’s so small millions of them can fit on the tip of a needle – our microbes? Before I get into the benefits of these microbes, I want to dive into where it all began.

How did these bugs get in us and on us?

If you’ve watched One Strange Rock on Netflix (you’ve gotta watch it!!) you already know that the breathable air we enjoy today was formed 2.8 billion years ago by none other than microbes! So that’s where life began.

small globe in hands being passed to child

As for us humans, scientists were in disagreement for many years (and they still are) as to whether a baby is "germ-free" before it travels through the birth canal or has it’s very own fetal microbiome in the womb. That being said, this study found that species typically found in the oral microbiome were also found in the placenta. What we do know for sure is the following:

  • When a baby is born via vaginal birth and travels through the birth canal, they swallow loads of beneficial vaginal and fecal microbes from mama, such as Bifidobacterium and Lactobacillus. Now that’s a birthday present!

This begs the question, should C-section-birthed babies get wiped with vaginal fluid in a “bacteria baptism” of sorts? Not all scientists are in agreement with this.

  • Every time a baby breastfeeds their microbiome is nourished from breast milk and mama’s skin. More accurately, a breastfed baby receives food for their gut microbes in the form of over 200 different oligosaccharides found in mama’s milk. These oligosaccharides are food for the bacteria especially B. longum infantis. They also coat the lining of the gut and bind to pathogenic bacteria, making it more difficult for bad bacteria to invade and cause disease. In simple terms, these bacteria help prevent sickness in infants. Here’s a great article from the NY Times you should check out if you want to learn more about the infant microbiome.


  • More microbes are adopted when that baby is licked by a dog (I always encourage this with my daughter even though we don’t have a dog!) or when a baby is exposed other people like when Grandma and Grandpa visit us as they have their own unique microbiome.

A very scary realization is that bacteria called B. infantis that’s been the dominant bacteria in babies for all of human history is disappearing from babies in the Western World. Could antibiotics and antibacterial products that people use on a daily basis be to blame? Or the rise in C-sections and infant formula? I will save that for another post.

What are the benefits of these microbial communities?

I’m going to keep this section brief because I want to dive deeper into the benefits with a blog post for each area the microbes impact, from gut health to mental health. So although this list is short, the benefits go far beyond what I’ve listed here.

  • They educate the immune system. A diverse gut flora established in early life with many types of bacteria, fungi and other microorganisms, is crucial for teaching the cells of the immune system what’s good and what’s bad. The mucosal lining of the gut is protected by the microbes that hang out there. This protects the inside of the body (note: the entire GI tract is actually considered the outside of the body) so that foreign invaders or bad bacteria (salmonella, for example) do not get absorbed into the bloodstream from the gut. These microbes reduce intestinal permeability.

  • Produce 13 essential vitamins. These nutrients are essential for us to thrive and for our immune system to function. They include the water-soluble vitamins thiamine (B1), riboflavin (B2), niacin (B3), pyridoxine (B6), pantothenic acid (B5), biotin (B7 or H), folate (B11–B9 or M) and cobalamin (B12) and C and the fat-soluble vitamins A, D, E and K. These are absorbed in the colon whereas dietary nutrients (these same vitamins we get from food) are absorbed in the small intestine. Thank you microbes!

  • Aid digestion. Certain microbes break-down the food we eat, such as the polysaccharides found in fruits and veggies, legumes and grains and other plant foods. These are broken down into something called Short Chain Fatty Acids (SCFA), which have an abundant number of benefits from reducing inflammation in the gut, decreasing obesity and insulin resistance and serving as food for other microbes.

  • Protect the gut from food poisoning. Research has shown that certain microbes prevent intestinal infections caused by salmonella and pathogenic E. coli. This is why two people can eat the same food and ingest the same pathogenic bacteria but only one gets sick – the difference is the microbes that live in the gut. 


This is the tip of the iceberg in terms of what the microbiome does for us, and the science is absolutely exploding. Not all that long ago, we thought all microbes were "germs" and this notion that all bugs should be eradicated still persists today but I think it's slowly changing. 

Now that we know the importance of the microbiome, it only makes sense for me to follow up with a post on how to keep your microbiome healthy.

In the meantime, if you want to read more about overall gut health and recipes and tips for supporting your microbiome here are some of my favourite posts:

Have a joyous week!

Joy xo

Heloise Breton   •   March 23, 2019

Thank you for a nice post on the microbiome. This is my field of work and I feel it's so important for people to understand more about it as the medical research that will dominate our lives for probably the next few decades will be microbiome driven. Keep up the great work! Heloise B. PhD

Joy McCarthy   •   March 24, 2019

Ashley   •   March 24, 2019

This was an eye opening post... I never knew that the microbiome could hold such a huge impact, not only individually, but globally as well. When I had my first baby I tested positive for strep-B, I wasn’t impressed when I went into labour and they informed me I had to have intravenous antibiotics during delivery. I was actually concerned that it would deplete my vaginal microbiome or reduce it’s effectiveness. This post pretty drove those assumptions home. My second baby I made sure I was consuming all the right probiotic foods and beverages, in hopes to circumvent that situation. Fortunately, I went into labour before the results of my test came back, so they didnt administer the drugs. I also made sure, through all the stress and initial annoyance of breastfeeding, that I would stick to it until they or I couldn’t physically do it anymore. I got a good 15 months out of both of my girls, so I’m happy with that. Thanks again for the post... putting on that Netflix doc right now! Cheers. -Ashley

Joy McCarthy   •   March 24, 2019

Heloise Breton   •   March 25, 2019

The fetal microbiome is such an interesting field of work! The biggest challenges I think for researchers is just getting the right samples to do the research they want and truly understand where the microbes are coming from.. When do they appear, how do they stick around, what makes them happy, when do they disappear??? There's been some interesting research on the state of health of children born via the birth canal vs c-section.. mostly pointing to "you have a better immune system if you are born vaginally". There was a great conference in Hamilton, ON just this past month called Women and their Microbes. I'd check out all the different speakers and see some of the research they've been putting out to get a feel for what people are thinking at this time..

Joy McCarthy   •   March 26, 2019

Marisol Medina   •   March 27, 2019

Great post! This topic is fascinating... I had my gallbladder removed almost 20 years ago, I wonder if that had an affect on my microbes?

Joy McCarthy   •   March 27, 2019

Heloise Breton   •   March 29, 2019

This popped up in my feed and thought it would be of interest... Sorry I am obsessed with the microbiome too, haha.

Joy McCarthy   •   March 30, 2019

Natalia   •   March 29, 2019

Incredible information. I am waiting for more :) I've read a little about how good a bacterial flora is in our intestines, but how important microbes are at the moment of birth is surprising. I born my daughter through the birth canal and I was breastfeeding for 6 month and I did't have any huge problem with her health. I know 2 mum who born their babies via c-section and their children had some healthy problems. I will certainly increase my knowledge about microbes. Thank You JOY ! :)

Natalia   •   March 31, 2019

Mats Lönne   •   April 5, 2019

...another one obsessed with the microbes. Thanks for a magnificent article! In Sweden I had the opportunity to launch one of the First pioneering probiotic Food brands in the 90s (ProViva - in US Good Belly). 20 ys later the research field explodes.. our contribution is The First unsweetened pre/probiotic Baby Yoghurt, LoveBugs, based on the same bacteria - and oats. We hope to launch it outside Sweden too; US to come if we find the right partner. Thanks again


sam jas   •   July 4, 2020 Thank you for sharing


sam jas   •   July 4, 2020 Thank you for sharing!


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