Are We Less “Gutsy” Than we Used to Be? New Clues about the Evolution of the Human Microbiome from Research in Apes


By Sharon Greenblum, PhD

Humans have come a long way in the last few millennia. Physically and culturally, we’ve grown up.  Over millions of years, humans evolved from apes – through tiny blips that snuck into the genome. We have been able to stand up straight, switch from leaf-chomping to steak-scarfing, and eventually ascend to become the self-proclaimed kings of the biological world.

Throughout our billion year evolutionary journey, each of us has had “passengers” – tiny, one-celled living creatures called microbes – that have ridden along with us every step of the way, adjusting to our new body and surroundings as we evolved. Each human is home to over a trillion microbes – a collection referred to as the human microbiome. To these microbes, we are a living, breathing mother Earth, a vast expanse of natural resources upon which they are entirely dependent.  Our gut is the rainforest of this world – a habitat teeming with thousands of different types of microbes.  In exchange for a home, microbes lend us a few of their “super-powers” that we may take entirely for granted – like the ability to digest certain nutrients from our food and the ability to keep our immune system in check.  

However, some have suggested that our new and improved lifestyle has actually cast a shadow on our inner rainforest.  A number of recent studies have suggested that not only is the way we live our lives today (e.g. consuming less varied diets, use of antibiotics, etc.) depleting our microbiome’s diversity, but may be linked to certain health conditions, such as asthma and digestive disorders.

There is much more research needed to understand the relationship between the human microbiome and health, but in terms of humans’ evolutionary journey, Howard Ochman and his research team wanted to know what microbes’ evolutionary journey has looked like

In their recent paper in the Proceedings of the National Academies of Science, they set out to fill in some of the missing pieces.

Why study apes when you can study humans?

Since we don’t even know what the microbiome of our human ancestors looked like, it is difficult to pinpoint how exactly the human microbiome has changed over time. But we can compare the microbiomes of modern humans to the microbiomes of our closest living ape relatives.  The researchers could assume that whatever microbes we have in common probably got passed down from our common ape-like ancestor, with any differences occurring when humans became a separate species. 

Until recently, though, only a few ape microbiomes had ever been studied, not nearly enough to draw any firm conclusions. Ochman and his team of collaborators set out to change that.  They not only took samples from more than 400 ape microbiomes (from chimps, bonobos, and gorillas), they also came up with a way to reconstruct the series of changes that must have taken place in each species’ microbiome over time. 

What they found was that a certain number of the apes’ microbe types went up or down in abundance for each tick of the evolutionary clock.  But when they looked at changes to the human microbiome, it was a different story.  The researchers noticed three important things: 

1. Human microbiomes were dramatically different from all of the apes that they studied. Actually, human microbiomes looked like they’d been changing at hyper speed, with many more microbe shifts per clock tick than expected.

2.  Human microbiomes were also dramatically different from each other.  There wasn’t a clear ‘standard’ human microbiome – instead, microbiomes of people from different geographic regions and lifestyles looked very different. 

3. Just as other studies have suggested, it appeared that the human microbiome has been shrinking.  On average, human microbiomes contain only half as many microbe types as their gorilla counterparts, and significantly fewer than both chimps and bonobos.

These results indicate that humans have experienced a depletion of gut flora since diverging from our ape ancestors. Which aspects of human lifestyle might be having the most impact?  Without having measured this directly, it is impossible to infer from this study. More research is needed to understand why the human microbiome appears to have decreased in size, and what impact, if any, it has on our health.

This study is one of the first of its kind, and while there are still more questions than answers, we now know a little more about the epic saga of microbe and man.     

Sharon Greenblum, PhD is a Science Communications Fellow at Pacific Science Center in Seattle, Washington.