Whose microbiome is it? Take an educated guess

Carl Zimmer's articles in the New York Times are usually a treat.  Indeed, he's one of the best science journalists around.  But his op/ed piece on Sunday told only part of the story.

Called "Our Microbiomes, Ourselves", Zimmer describes the efforts to sequence entire populations of microbes -- the microbiome -- in various orifices of the human body, and he considers the ethical questions this is bringing to light.  Long considered to be separate from us, recent understanding has shown that many bacterial species are vital to our survival.  The bacteria in our gut are the classic and best example: we can't live without them in our intestines because our digestion depends on it.  So they may have their own species name, but in a very real way, and evolutionarily as well as today, their genome is really our genome, too (and to some extent vice versa).

Zimmer proposes a scenario whereby the microbiome of someone's nostril is sequenced, and a unique microbe is identified, and found to have pharmaceutical uses, and industry goes on to make millions from the new drug that results.  If it was found in your nose, he asks, do you deserve a share 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.

But, while the specific scenario might be new, the question of who profits from stuff going on in or coming out of other people's bodies certainly isn't.  As a recent book reminded us all, Henrietta Lacks' tumor cells have been used since the 1960's for various profit-making purposes, but she and her family got nothing from her unwitting donation of cells.  From best-selling books written about neurological case histories to clinical testing of new drugs to the reaping of cells for research, there's nothing new here.

Some bioethicists, Zimmer says, believe that people's private microbiomes should be kept private, just as people's genomes should be, because the microbiome may hold clues to future illness.  But, there's nothing new here, either.

And,

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.

Zimmer adds that microbiomes may be harvested from subjects in poor countries, because of their potential usefulness to pharmacology or to understanding disease risk.  But that's an old story, too -- pharmaceutical companies have been doing clinical trials in poor countries for decades because it's cheaper and there's less regulation.  And agribusiness has inflamed many countries for raiding them of commercially modifiable plants and then selling them at high cost to farmers, making them dependent on buying seeds annually, rather than beneficiaries of royalties.

Sequencing the microbiome of an entire town's sewage system might reveal a lot about the entire town's health, but, Zimmer asks, would permission be required from each person living in the town?

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.

So, Zimmer poses some interesting questions about the ethics of microbiome research, but there's nothing new here.  The same questions of who owns what and who should profit apply to all biomedical research. And, we're willing to bet that, as usual, the answers will favor the researchers.