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Worlds Within Us

Pulled from an unlikely source, ancient microbial DNA represents a new frontier in the study of the past—and modern health

By SAMIR S. PATEL

Monday, September 26, 2016

The largest ancient DNA laboratory in the United States sits behind a heavy steel door in a plain service hallway at the University of Oklahoma. Inside, researchers find, extract, isolate, and amplify DNA molecules and proteins, producing voluminous mounds of data that can address grand, complex questions about migration, diet, and human health—in the deep past and today. They’re probing the limits of new methodologies. They’re encountering the advantages and pitfalls of interdisciplinary science. And they’re writing the first drafts of a new chapter in archaeological research. But before they can do any of this, they have to ensure that the lab is scrupulously clean.

 

Next to the door, a red button, when pressed, produces a satisfying thump and turns off powerful UV lights inside. A series of pressure gauges climbs next to it. The lab’s six rooms are kept under positive pressure, double-sealed, and have their own air supply, filtered free of anything larger than 1,000 daltons—the mass of just 1,000 hydrogen atoms. People who enter must take off their shoes, change into scrubs, and, by the time they reach the two innermost rooms, don Tyvek suits, surgical masks, hairnets, and face shields. Those chambers are free of anything extraneous: Only sample vials and scientific equipment are visible. The DNA and proteins that the researchers work with there come from ancient microbes, and keeping the lab free of contamination is a tall order in a world that is positively swimming with their modern counterparts.

 

Microbiome DNA Calculus

 

“Usually, ancient DNA work is performed in dungeon-like labs located in windowless basements,” says Christina Warinner, anthropologist and codirector of the Laboratories of Molecular Anthropology and Microbiome Research (LMAMR). This lab, however, is fitted with picture windows that face the atrium of the university’s Stephenson Research and Technology Center, so visitors can watch the scientists and students inside process microscopic genetic samples that can be centuries or even millennia old.

 

The microbes that are the focus of the LMAMR—from both ancient and modern sources, with separate lab facilities for each—come from what is known as the human microbiome, the myriad communities of bacteria (as well as eukaryotes, viruses, and archaea) that reside in and on our bodies. In only the last few years researchers have begun to understand that studying how the microbiome has shifted over thousands of years, particularly at moments of great change in human history, has the potential to reveal some of the ways in which how we eat, live, and move around the world have affected human biology. Any number of questions—medical, archaeological, demographic, evolutionary—that were unframeable just five years ago can now be asked and ultimately answered on scales ranging from molecular to continental.