The human body is constantly evolving alongside our microbiota, the community of microbes that live inside every one of us.
Since the time of Darwin, we have been fascinated by our own evolutionary trajectories. Where did we come from? Who were our ancestors? How did we make the slow but enormous transition from single-celled organisms to complex multicellular beings? It’s a story that we've heard time and time again, but there’s a side to this tale that largely goes untold.
Our history is not that of a single organism evolving with increasing complexity. We are not individuals, but ecosystems – host to trillions of microscopic lives that have inhabited our bodies for millennia. Human evolution is not just the evolution of a single species, but of an entire community.
Over the past two decades, advances in gene sequencing technology have allowed us to take a closer look at our resident microbiota, their genes, and the environments they inhabit – collectively known as our microbiome. Incredibly, we’ve found an abundance and diversity of microbes beyond our imaginations. And these inhabitants aren’t just along for the ride; they contribute dramatically to our physiology.
Scientists are still working to understand the tangled web of host-microbiome interactions, but already we know that our microbiota help break down our food, produce key vitamins, calibrate our immune systems, and defend our bodies from invading pathogens. Using animal experiments, we’ve found that if you wipe a host clean of its microbiome it will become very ill. For better or for worse, we are as dependent on our microbiota as they are on us.
Increasingly, evolutionary biologists also agree that our genes cannot be separated from those of our microbiota: they are all bundled together as one “hologenome” on which the pressures of natural selection may act. And the microbial contribution to our hologenome cannot be underestimated – their genes outnumber our own and contribute vital functions to our body.
According to science journalist Ed Yong, author of the recent book I Contain Multitudes, it's unlikely that microbiota actually drove our speciation. “But they almost certainly do influence our evolution," he says. "For example, we know that the gut microbiomes of Japanese people (and some others) are better at digesting the complex carbohydrates in seaweed because they have acquired seaweed-busting genes from marine microbes.”
This evolutionary influence runs both ways. Just as our microbes have shaped our evolution, we have shaped theirs. “The gut, in particular, is a weird environment for microbes – dark, low in oxygen, but high in nutrients," says Yong. "Time and again, we've seen that many lineages of microbes have entered that niche and diversified rapidly, just like the Galapagos finches or Hawaiian honeycreepers.
"By concentrating microbes in a small space, the human body also makes it more likely that these organisms will exchange genes – again, accelerating the pace of their evolution.”
The interesting part of this is that our microbial inhabitants evolve on a far more rapid timescale than we do. Several generations of microbes may rise and fall in a single day, allowing the forces of evolution to act quickly. A number of factors interplay to shape the short-term evolution of our microbiomes, including diet, genetics, and environment. These factors can drastically remodel our microbial communities and, in turn, have significant effects on our health.
But our microbiome has also been evolving with us on a larger timescale. As we have adapted to changes in our diet and environment, so too have our microscopic companions. According to Yong, we can trace our shared history with our microbiota by examining those of our closest cousins, the great apes. “Andrew Moeller and Howard Ochman have shown that several gut microbes have diversified in parallel with the great apes, such that their family history mirrors ours,” he says.
During African ape diversification, changes to the microbiome occurred slowly and in a step-wise fashion, reflecting the evolution of their hosts. Human evolution has since veered off this slow and predictable course at an accelerated pace, largely because of rapid changes to our diet and environment. Modern humans have lost the diversity of microbes that we see in our ape cousins and have become highly specialised for animal-based diets.
Other research has found that the microbiota of modern Western humans differ greatly from those of traditional hunter-gatherer tribes, and are better at processing carbohydrates and foreign compounds. Such changes have allowed Western humans to take advantage of our sugar-rich diets and process non-food items such as therapeutic drugs.
When you look at human evolution through the perspective of the microbiome, some interesting questions arise, especially given the rapid timescale on which microbes can evolve. Could we perhaps harness this evolution and direct it to improve our health? At this stage, we’re still not certain of precisely how our microbes are affecting us and how we are affecting them. Microbiome research is still a fledgling area, and there’s far more we don’t know than what we do.
The story of human evolution is the story of a relationship that has existed since the beginning of our existence, and will doubtless be an influential force in the future of our species. The lives that play out inside us can govern important bodily functions, and so affect our evolution. In turn, our own actions, such as diet and lifestyle, can govern the evolution of our microbes. Deeper research on a genomic scale will help to elucidate our history with our microbes ‒ and our future, too.
Edited by Andrew Katsis and Ellie Michaelides