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Deep in your gut, 40 trillion chemists are hard at work helping you digest your lunch, making essential vitamins and nutrients you can’t produce on your own, protecting you from disease, and more. These talented creatures are bacteria, fungi, and other single-celled organisms.

These organisms live together in complex communities called microbiomes. They reside all over your body — and far beyond it. Microbiomes have been found anywhere scientists choose to look for them, from the hottest deserts to lakes hidden deep beneath Antarctic ice.


The chemistry that microbiomes perform in us and on us varies between individuals and populations. For example, most people can’t digest seaweed. But some residents of Japan are able to do this because their gut microbiomes contain seaweed-eating bacteria.

Given how closely our lives are intertwined with these microbes, it’s surprising how little we know about them. Your gut microbiome, for example, possesses at least 100 times more genes than your cells do, and we don’t understand what the vast majority of these microbial genes are for. Nor do we fully appreciate how our actions alter these microbiomes and, in turn, ourselves and our planet.

The new National Microbiome Initiative aims to change this. Announced this spring by the White House, this coordinated effort will support scientists in academia, government, and industry in their quests to understand Earth’s uncountable microbial inhabitants.


I am excited about this effort even though I’m a chemist, not a biologist. As a graduate student, I spent my days combining chemicals in flasks and vials, hoping to find new methods for building molecules. Discovering the right chemical reaction can help chemists make lifesaving medicines or convert harmful greenhouse gases into useful products.

Today I want to find out how other chemists, namely microbes, manipulate molecules. Like astronomers charting the night sky, my students and I scan DNA sequences from microbes, seeking signs of as-yet-unknown chemical capabilities. We’ve already unearthed a few chemical reactions I couldn’t have even imagined developing as a graduate student.

We do this partly for the fun of scientific discovery. But there are practical applications as well. Gut microbes carry out chemical transformations that interfere with medications we take and processes that potentially increase the risk of cancer and heart disease. Finding how they do this can potentially improve human health.

There are more microbes on Earth than stars in the visible universe. That means they can carry out chemical reactions on a scale that can alter the planet. Life on Earth looks the way it does today thanks to a breakthrough in microbial chemistry — whose byproduct was oxygen — that occurred 3 billion years ago.

That’s why many microbiome investigators are looking beyond the human body. Some seek new ways of using microbes to consume chemical pollutants and help clean up contaminated environments. Others are exploring how the chemistry of ocean and soil microbiomes is being altered by Earth’s changing climate, how the activities of plant microbiomes can protect crops from devastating diseases and avert food shortages, and more.

There’s plenty of work to be done. Scientists have studied in the lab fewer than 1 percent of all microbes. Shedding light on the hidden chemical talents of these creatures will be one of the most important contributions of the National Microbiome Initiative and is absolutely critical if we hope to understand, preserve, and ultimately harness these microbial ecosystems.

Finally, the National Microbiome Initiative plans to include the general public in helping to access and explore microbial habitats across the globe. The American Gut Project has already given thousands of citizen scientists a glimpse of their own microbiomes. As part of the national initiative, this project will form new partnerships to obtain even more information about the gut microbiome’s connections to diet and disease. Another participant, the Small World Initiative, will expand its efforts to engage high school and college students in searching soil microbiomes for new antibiotics. These efforts may help foster a greater appreciation for these amazing creatures and inspire a generation of young scientists.

The National Microbiome Initiative represents the start of an exciting new chapter in our relationship with our microbial companions. It will change not only how we view ourselves but how we view our world as well. Although we’ve always lived with these organisms, we are only now beginning to realize that they may hold solutions to some of our most important global challenges. We can now dream of better living — through microbial chemistry.

Emily P. Balskus, PhD, is an associate professor of chemistry and chemical biology at Harvard University.

  • Though you suggest,
    “Gut microbes carry out chemical transformations that interfere with medications we take and processes that potentially increase the risk of cancer and heart disease. Finding how they do this can potentially improve human health….”,
    I believe it is of far greater importance to recognize that damage to this microbiome, itself, and to its own genetic integrity (when potentially altered by prescribed medication, OTC supplements, GMOs, pollutants in our air and water as well as related and unrelated climate change) has far greater implications for our lives.

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