Microbiome Series 1/3: Introduction to the Microbiome

We know it’s all the rage; we know it’s important. But what exactly is the microbiome, and why is everyone so excited about it?

This is the first in a series of three posts where I dive into what the microbiome is, why it matters, and applications of microbiome research in both therapeutics and consumer goods.

What is the microbiome?

The microbiome is the name for the collective community of the trillions of bacteria, viruses, and eukaryotes that inhabit the human body. The gut is the primary residence of the microbiome, but your mouth and skin (and for women, your vagina) also support diverse microbial communities. These communities are critical to the healthy functioning of our bodies: they stimulate the human immune system, digest food, produce vitamins, and even help protect you from invasion from potentially harmful bacteria. A healthy microbiome is so essential, in fact, that it’s often referred to as another organ like the lungs or heart.

Infants receive their first microbial communities from their mothers

But unlike organs, which develop in utero, your microbiome has to be acquired. For those who are born via the vaginal canal (as compared to C-section), their first microbial communities are transfered from their mother’s vaginal microbiome. For all people, however, our microbiomes evolve as we age under the influence of our genetics, diets, and environments. This evolution results in a carefully balanced, symbiotic relationship between us and the trillions of microbes that help our bodies function.

This balance does not occur spontaneously. Humans and our microbial friends have actually been co-evolving for hundreds of millions of years. This co-evolution results in an interdependence between species, meaning we actually require the presence of our microbiome for critical functions, like processing certain nutrients or creating vitamins. The microbes in turn require the specific environments provided by our body to survive. This interdependence suggests why disruptions to microbiome health--or dysbiosis--can have such severe consequences.

Why is the microbiome important?

As I’ve previously stated, a healthy microbiome provides critical functionality such as in stimulating our immune system. But if a microbiome becomes dysbiotic, systemic effects can be serious. A balanced gut microbiome protects from inflammatory conditions, such as Crohn’s. But a dysbiotic microbiome is linked to obesity risk, as well as Type 1 diabetes. Disruptions in the vaginal microbiome can result in infections, and an unhealthy skin microbiome can lead to acne. An unhealthy gut also opens you up the risk of infection from harmful bacteria such as C. difficile.

But even something as simple as deriving nutrients would be a lot trickier without our gut microbial environment. The microbes in your large intestine help break down nutrients like complex starches, which we wouldn’t be able to process without help. When infants are born, their microbiome helps break down the nutrients in breast milk. Critical vitamins like folate are also produced by gut bacteria. What is most fascinating about the microbiome’s role in our diets, however, is that because microbial communities can differ between people, what constitutes an ideal diet based on your microbial profile can differ, too.

The more we learn about the microbiome, the more we realize how interconnected the microbiome is to all aspects of health and wellness. One key area of future research involves the gut-brain axis: how the health of our gut can affect our brain, including our behavior, personality, and mood.

The microbiome has a critical role to play, from the oiliness of our skin to our emotional wellbeing to our risk of disease. Now that we know it’s important, how do we know what affects it?

What can influence your microbiome

Compared to human DNA, which is about 99.9% identical between humans, microbiome communities can vary by 80-90% between people. This diversity is part of what makes it so fascinating to study. But what is enabling all that diversity?

A primary influencer of your gut composition is your genes. Your DNA codes the structure of your gut, and that in turn influences the communities of microbes you are predisposed to support. Just like how genes determine if you can digest lactose or not, your genes influence your microbial environment. But as we’ve just seen, our genes are mostly identical, so they can’t be the full story.

The most well-known influencer of the microbiome is diet. A diet high in fiber, for example, causes microbes to release short-chain fatty acids, which subsequently lower the pH of your colon. This lower pH influences the kind of microbes that can survive. In the case of digested fiber and reduced pH, this has the benefit of reducing your risk of C. difficile infection by making the gut environment less hospitable to bad bacteria. In this way, the byproducts of the food we eat influence the environment of our gut, subsequently influencing the microbes that inhabit it.

One of the most common destroyers of your microbiome are antibiotics. Antibiotics don’t discriminate against good and bad bacteria, and they can have the unfortunate side effect of destroying microbial communities in your gut. Recovery can take years, and it’s suggested that your microbiome never fully goes back to its pre-antibiotic state. Of course, sometimes antibiotics are critical, and the side effects of taking them are easily outweighed by the risks if you don’t. But it’s a gentle reminder about the risks of over-prescription and to avoid antibiotics unless you truly need them.

How do we study the microbiome?

Historically, testing a microbiome would require taking a sample and growing a culture to see what microbes were present. Now, scientists and doctors primarily rely on ‘culture-independent techniques’ that enable faster and more precise analyses of these diverse communities.

Metagenomics refers to sequencing the collection of microbial genomes within the total environment. The benefit of metagenomics is that it provides the genetic breakdown of species, giving scientists a highly detailed perspective on the current makeup. Instead of testing the entire genome, researchers can also rely on shorter snippets of DNA (such as 16s rRNA), as well as proteins and chemical metabolites.

As microbiome research continues, a greater number of resources are being developed to support effective investigation. Pipelines for microbiome data analyses are becoming more robust, with pipelines such as mothur, w.A.T.E.R.S, and QIIME providing platforms for high-throughput sequencing data to be measured.

The amount of data on the microbiome has been steadily increasing over the last few decades as public interest increases and the cost of sequencing DNA decreases. The Human Microbiome Project by the NIH, for example, provides a database of microbiome data that has been utilized in hundreds of studies.  But there remains significant work to be done, and the sheer diversity and complexity of the microbiome ensures that research will continue revealing new insights for decades to come.

Go with your gut!

Hopefully this article has provided an introduction to the microbiome and why we should care about it. In the next article, we’ll discuss the microbiome’s role in human health and the different therapeutic areas to which microbiome drugs are being applied.

Cover Photo: “Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,” The Microbe Discovery Project, 03-Jul- 2016.

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Sonja K. Eliason

August 21, 2020