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  • Writer's pictureAmy Loughman, PhD

So…this microbiome thing?

Updated: Jan 9, 2020

You’ve probably heard about it…everywhere. Masquerading under topics and terms like ‘gut health’, ‘gut flora’, ’gut bacteria’, ‘good bacteria’, ‘forgotten organ’, ‘probiotic’ and ‘gut-brain axis’. The microbiome is the DNA associated with the community of microorganisms that live in a number of niches around the human body, in largest number in the large intestine (or colon). These microorganisms comprise mostly of bacteria, but also viruses, archaea and fungi.

Light micrograph of a cross section of a coralloid root of a cycad, showing the layer that hosts symbiotic cyanobacteria. A cycad is plant matter, not human. But similarly attractive micro-art is visible in the human body! By Curtis Clark — Own work, CC BY-SA 3.0,

So what’s the big deal? We’ve known for a long time that there is bacteria in the gut, and there have been guesses throughout history about their relationship to health and disease. Many wrong by the way, such as the now defunct idea that removing parts of people’s bowel could be good for mental illness. Recently though, huge gains have been made in understanding this field. You might remember in April 2003, the human genome was sequenced. Well using that same technology, researchers are now able to sequence the DNA of all the bacteria that live in our gut (and other hosts of the microbiome such as the mouth, vagina, and even the belly button). So we don’t just know what’s there, we can know all of its DNA information too. More importantly, we’re now able to relate what DNA is there to various physiological processes in the body, and certain diseases too.

It turns out that the microbiota in the gut are essential for digesting food, making nutrients available to the body and turning nutrients into chemical messengers that go to other parts of the body (such as the neurotransmitter, serotonin). Wonky, out of balance microbiota (more officially known as dysbiosis) has been found to be at play in all sorts of medical conditions, from the gut related kind (e.g. irritable bowel syndrome and inflammatory bowel diseases), to cardiovascular disease, diabetes, cancer, obesity, asthma and autoimmune conditions.

The craziest, and in my opinion most interesting of the research about the microbiome, are the revelations of just how important this bacterial mass is for brain function.

A quick aside: we’re increasingly realising how important the brain is for all kinds of things, not just mental health. Behaviours of addiction and substance use are obviously extremely relevant to the brain, as is eating and the propensity for obesity.

The best evidence of gut-brain links so far comes from animal models. Mouse behaviour is known to be different if it’s germ-free (no bacteria), conventionally raised (‘standard’ bacteria) or from a particular species bred to have a behavioural phenotype. And to some extent, these behavioural tendencies can be ‘transplanted’ from one mouse to the other. For example, when you put anxious mouse poo into another mouse’s bowel (yes, they really do it. But then again, mice eat their own/each other’s poo so it’s not any grosser than that), the previously non-anxious mouse starts to behave like the anxious mouse. All because of what is in it’s gut. So at least in theory, if you feel like certain foods or diets make you feel like shit (or to be slightly more appropriate, a bit anxious or a bit down), you could be right. However the human evidence isn’t quite as clear as that of rodents, at least not so far.

So now you know the microbiome and all those tiny bugs living within you is a big deal in medical science. We’re starting to understand how they’re important for almost all basic bodily functions, as well as behaviour. Hang tight though, there’s a lot more of this to come.

A cute video from The Canadian Digestive Health Foundation to introduce the human microbiome.

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