You’re Not All Human: The Wonder of Gut Microbes

The finely tuned collection of bacteria, archaea and fungi collectively known as the microbiome hold an exquisite power that we are only beginning to recognize.

Perhaps one of the most wondrous things we have learned about the human body in the past quarter century is that it is not entirely human. Each of us is engaged in trillions of symbiotic relationships every minute of our lives. Our partners, the finely tuned collection of bacteria, archaea and fungi collectively known as the microbiome, are not just along for the ride. They also hold an exquisite power that we are only beginning to recognize.

Day after day, our native gut microbes quietly churn away, producing compounds that elegantly communicate with our immune cells, endocrine system and brain, occupying evolutionary niches that we have grown to depend on.

Despite these essential roles, however, our microbes are not immune to human hubris. If we fail to nourish them with adequate fiber, they can alter their gene expression to instead consume our gut lining. If we change the pH of our intestinal tract, their population types and sizes can shift dramatically. If we take a partial course of antibiotics, they can trade resistance genes and enable invaders to weather the pharmaceutical storm. Individual microbes might cycle through their intricate little lives in a half-hour or less. But their collective presence has a crucial impact on our lives from the moment of our birth. Without them, many of our own systems would not properly develop or function. We would not be fully human.

Our resident biochemical companions have lived in secret for so long simply because we did not have the methods to detect them. Only recently has genetic sequencing technology adequately advanced to alert us to our microbiome’s presence.

Now we are learning, slowly and from a distance, what creatures inhabit this unlikely landscape. These early tools have given us hints about this enchanting, unseen world. But it is still a distant continent glimpsed through a high-throughput spyglass. We know little about these organisms’ lifestyles, their interactions with one another, and how they truly impact their environment (which is us). Science is just beginning to uncover enticing links between the gut microbiome populations and autoimmune diseases, heart disease, mental health and even some cancers. “There is so much excitement that through the microbiome we can make huge progress in medicine,” says Richard Bonneau, group leader for systems biology at the Flatiron Institute. But the nuance of this system goes beyond documenting species and even strains — it extends down to the level of ever-shifting gene expression within organisms and rapid exchanges of genetic code among them. So as we still struggle to understand the 20,000-gene human code, the prospect of puzzling out the variable, 3-million-gene gut microbiome would appear rather discouraging.

Fortunately, hundreds of thousands of people all over the world are helping researchers to set virtual foot on this terra interior. Through the IBM World Community Grid’s Microbiome Immunity Project, more than 65,000 computing years have been donated since late 2017 to digest this immense amount of data — results of which are shared freely.

This diffuse approach, like the microbiome itself, is creating something much larger than the sum of its parts. “We’ve barely scratched the surface in our understanding of the gut microbiome,” says Douglas Renfrew, a Flatiron research scientist. Today, thanks to this group’s work and that of hundreds of other teams across the globe, we stand on a new promontory of knowledge to better appreciate — and utilize — the elegant power held by these minuscule collaborators.