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2011

Our Microbiomes, Ourselves
The New York Times (Sunday Review), December 4, 2011
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Imagine a scientist gently swabs your left nostril with a Q-tip and finds that your nose contains hundreds of species of bacteria. That in itself is no surprise; each of us is home to some 100 trillion microbes. But then she makes an interesting discovery: in your nose is a previously unknown species that produces a powerful new antibiotic. Her university licenses it to a pharmaceutical company; it hits the market and earns hundreds of millions of dollars. Do you deserve a cut of the profits?

It is a tricky question, because it defies our traditional notions of property and justice. You were not born with the germ in your nose; at some point in your life, it infected you. On the other hand, that microbe may be able to grow and reproduce only in a human nose. You provided it with an essential shelter. And its antibiotics may help keep you healthy, by killing disease-causing germs that attempt to invade your nose.

Welcome to the confusing new frontier of ethics: our inner ecosystem. In recent years, scientists have discovered remarkable complexity and power in the microbes that live inside us. We depend on this so-called microbiome for our well-being: it helps break down our food, synthesize vitamins and shield against disease-causing germs.

“We used to think of ourselves as separate from nature,” said Rosamond Rhodes, a bioethicist at Mount Sinai School of Medicine. “Now it’s not just us. It’s us and them.”

For bioethicists, one of the most important questions is what our microbes can reveal about ourselves. Studies have revealed, for example, that people who are sick with certain diseases tend to have distinctive collections of microbes. Someday we may get important clues to people’s health from a survey of their microbes. Professor Rhodes argues that this sort of information will deserve the same protection as information about our own genes. Your germs are your own business, in other words.

But that is only one side of the issue. As scientists get to know the microbiome better, they are also looking for new medical treatments: after all, most antibiotics were first discovered in bacteria and fungi. Michael Fischbach, a biologist at the University of California, San Francisco, and his colleagues have discovered a wealth of promising druglike molecules made by microbes in human bodies.

It may even be possible to use the bacteria themselves as living drugs. Doctors have treated hundreds of patients suffering from gut infections by giving them so-called fecal transplants: the bacteria from healthy people can create a stable ecosystem that drives disease-causing microbes to extinction. In their more speculative moments, scientists have proposed using microbes to treat obesity or autoimmune diseases. Some researchers are even genetically engineering microbes to make them more effective.

Manufacturers already add beneficial bacteria, called probiotics, to a range of foods. But regulating a microbe is trickier than regulating a molecule. Probiotics can multiply inside us, and can later escape to colonize new hosts. When a doctor prescribes engineered microbes for individual patients, the ethical questions will extend far beyond them, to their families and communities.

Microbes defy a simple notion of individuality. They are essential to our biology, and they travel with us from birth to death. Yet they also flow between us, and can be found in water, food and soil.

One important rule for microbiome ethics is to be transparent with the people involved in scientific studies. “The key is respectful interaction,” said Kieran O’Doherty of The University of Guelph outside Toronto. That’s particularly important when scientists travel to poor communities to collect microbes. They should not try to woo their subjects with false hope about the benefits of the research.

“We’re trying to develop a way to engage in those discussions without overselling the knowledge,” said Paul Spicer, an anthropologist at the University of Oklahoma. But if practical good does come from the research -- say, a new drug -- these communities should also have a way to share the benefits.

The microbiome poses another bioethical balancing act, between the interests of microbe hosts and the public at large. If scientists become too consumed with protecting the individuals they study, research on the microbiome could slow.

Monitoring the bacteria flushed into the sewer system of a town, for instance, might reveal a lot about the entire town’s health. But a regulation requiring permission from every resident of the town would stop the study dead in its tracks.

Indeed, one outcome of the microbiome revolution may be to reorient bioethics itself. “We’re not in this alone,” Professor Rhodes said. “We’re part of the environment and part of the world. Instead of just focusing on protection, we can ask, ‘How can we help people?’ ”

Copyright 2011 The New York Times Company. Reprinted with permission.
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