THE MOST VERSATILE CHEMISTS in the world live inside us. Trillions of microbes, of several hundred species, an aggregation containing 150 times as many unique genes as a human, make our bodies their home. More biological activity may take place between and among these helpful hitchhikers than in our own cells. Their astonishing abundance and genetic diversity are matched by a vast repertoire of products and functions—inputs, outputs, and biochemical interactions—that profoundly affect human health.

Many microbes are beneficial, breaking down foods, manufacturing vitamins, and offering protection against pathogens—including, scientists recently discovered, viruses. But some increase the risk of cancer, cardiovascular disease, and diabetes, while others have been linked to neurological diseases such as Parkinson’s. A few are even known to metabolize drugs, blunting the effects of therapies administered to help maintain our human health. But given the scale and complexity of this vast sea of microscopic life, discerning which microbe is responsible for any of these effects—separating the good guys from the bad—has proven extraordinarily challenging.

A human chemist, Emily Balskus, Ph.D. ’08, is starting to address that problem using inventive strategies inspired by her training in organic chemistry. She studies the microbiomes of the human gut and recently, the vagina, by characterizing the metabolic activities taking place in communities of microbes that are associated with health on the one hand, and with disease on the other.

Broadly speaking, she says, microbial diversity is a good thing in the gastrointestinal tract. There, lots of microbes interact with their hosts, the foods they ingest, and with each other, forming metabolic chains and networks: one microbe’s trash is another’s treasure. (The production of many foods, of course, depends on domesticated microbes: yogurt, cheese, bread, and wine are just a few.) In the vagina, by contrast, such diversity is disadvantageous. The healthy vaginal microbiome is dominated by a single genus of bacteria, Lactobacillus, that maintains a protective, slightly acidic environment. If certain other microbial species become established in that ecosystem, unhealthy outcomes may follow: increased risk of preterm birth, vaginosis, and HIV infection.

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