Technically, the human microbiome refers to the genetics of all of the various microbes (bacteria, viruses, fungi etc.) that live on or in the human body – there are literally hundreds of thousands of different species. These microbes are at least  neutral if not helpful (taking up space and producing by-products so that ‘bad’ microbes can’t grow). But when the balance of these microbes gets thrown off, or their environment changes, these friendly co-habitants turn out to be less than helpful (some play a role in acne and eczema) or downright dangerous (C. difficile, for example).

Here are some basics:

You have more microbes on/in your body than you do human body cells – they are absolutely necessary for our existence as we know it, and the rest of the animal kingdom is similarly microbially infested (for many of the same reasons).

Your microbiome is like your fingerprint – humans, in general, have a lot of the same types of microbes in their microbiome, but the exact composition is unique to you. There is an argument that, if the criminology lab power was sufficient, human microbial ‘fingerprint’ would be more effective at identifying criminals than relying on actual fingerprints.

Life events (before and after your birth) and habits play a huge role in determining the composition of your microbiome – your mom’s stress levels while she was pregnant, how you were born (vaginally or C-section), your stress levels, your physical environment, and your diet all contribute to the microbes you are exposed to and, therefore, which ones can colonize your skin and gut.

So, keeping those three things in mind (1- lots of microbes, 2- microbial fingerprint is unique, 3- life events shape your microbiome), what do these microbes actually do and why has this been such a hot topic?

Note: for the sake of not rambling on about bacteria for ages, I’m just going to focus on the gut microbiome because it’s more intricately linked with your brain. Skin microbes are equally fascinating, but that’s a story for another time.

“…the weight of the microbes in your gut is about the same weight as the average human brain.”

Your digestive tract hosts approximately 80% of the body’s immune system, produces about 90% of the serotonin produced in your body. A lot of this has to do with the 10,000-35,000 different species of microbes (about 3-4 pounds worth) to which the gut plays host. For context, the weight of the microbes in your gut is about the same weight as the average human brain.

From an evolutionary perspective, this is super cool. We (and the entire animal kingdom really) have evolved in such a way that allows microbes to take up residency in our digestive tract and help break down food that we wouldn’t otherwise be able to use. This means that we don’t have to develop or evolve a gene or enzyme or pathway to break down a new nutrient source, we just need to host a microbe that will do it for us. The perfect symbiotic relationship – microbes get a safe(ish) haven and free food, humans get access to new nutrient sources.

So great – we have this living culture of bacteria in our digestive tract that helps us with what we eat. Which is pretty cool all on its own, but it doesn’t stop there. As it turns out, the microbiome isn’t just important for your digestion. Remember all those things I listed earlier that the gut is responsible for? Turns out your microbiome affect those systems too.

Studies on rodents raised without microbes in a ‘germ free’ environment don’t turn out well – they have very bizzare patterns of anxiety responses, have all sorts of health problems, lose their fur, and don’t live very long (we really owe a lot to rodents in the research world).

The microbiome contributes to telling your body what kind of immune system it needs to develop and even influences how your central nervous system gets wired – if your microbiome gets thrown out of whack, that can have severe impacts on your immune and central nervous systems. So even when these ‘germ free’ rodents are given a ‘normal’ microbiome, the anxiety responses and other changes stick around.

Deficiencies in the microbiome impact your behaviour; but, it’s important to emphasize that this is a two-way street. Social stressors around you – picture a scenario where you’re always fighting for a social position, or trying to avoid being picked on by bigger, stronger members of your group– affect your microbiome. As with other forms of stress, there are significant changes in the proportions of the types of bacteria in response. Some strains decrease significantly, allowing other strains to occupy much more space than they would otherwise. If this happens early enough in life and the stress persists long enough, this can lead to a permanent change in the microbiome composition.  

Maternal stress is another good example. High stress during pregnancy has been shown to affect mum’s gut microbiome and overall levels of inflammatory cytokines (proteins and peptides created by the immune system) – this is not great for mum; but, eventually, she’ll go back to normal. However, this is really not great for baby. Rats (again, thank you to rodents) born to mothers who had high stress during pregnancy have different microbiomes, more inflammation, and more anxiety- and depression-like behaviour than those born to less-stressed controls.

So being stressed changes your microbiome (mostly in the ratio of different types of bacteria), but changes in your microbiome can also make you stressed.

So being stressed changes your microbiome (mostly in the ratio of different types of bacteria), but changes in your microbiome can also make you stressed*. Transplanting the microbiome of depressed human patients into rats without their own microbiomes results in the rats showing an increase in depression- and anxiety-like behaviours.

And this happens with all kinds of behaviours – mice that get fecal transplants (one way of inserting one individual’s microbiome into someone else) have developed behaviours from the transplant host ranging from activity levels to curiosity displays to anxious behaviours.

Further testing on stressed baby rats has shown that, although the composition of their microbiome changes in response to stress, some of this can be counteracted by pre and probiotics. The changes in the microbiome result in differences in the types and quantities of neurotransmitters that are produced (including a reduction of the stress response, which means less cortisol and less ‘leaky gut’), resulting in different behaviour.

There is a lot of research on microbiome changes in rodents, but what does this mean for humans?

Depression, anxiety, schizophrenia, autism, and bipolar disorder have been associated with changes in the microbiome. The progression of traumatic brain injury and post-traumatic stress disorder is impacted by the microbiome as well. Though there has been work in humans showing that the diversity of the microbiome is different in people with these conditions than those without, there have been very mixed results in terms of turning this knowledge into an actual treatment.

So will drinking kombucha or eating probiotic yoghurt cure your social anxiety? Unfortunately not (although both are delicious). Neither will the probiotic pills you buy off the shelf. That’s because 1) the bacteria in these things aren’t necessarily ones that live in the human digestive tract, and 2) your microbiota is kind of like the Toronto housing market – there is very little vacancy and real estate is expensive. Quirks and Quarks, a CBC radio program, did a great interview in November about over-the-counter probiotics (check it out here). The gist? The microbial needs of different people with different health concerns are … shocker… very different – there isn’t a one-stop-shop to fix your microbiome, and until healthcare has reached a point where they can tell you “you have problem A, which is a deficiency in micobe X, here’s a prescription for a microbe X probiotic”, over the counter probiotics are of limited use.

But all is not lost! There is plenty you can do to help your microbiome be its healthiest self: drink lots of water, eat a wide variety of nutrient-dense foods, make sure you get enough dietary fiber (also known as ‘prebiotics’) because this is what feeds the multitudes, minimize sugar, and avoid taking antibiotics if they’re not necessary.  

There is a huge conversation about the microbiome. Here are some sources for more reading!

* I want to clarify that I understand stress, anxiety, and depression are separated and distinct in the way humans experience them, but, in animals, they display in many of the same ways – that’s why I’m generalizing here.


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