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Viewing Bacterial Dark Matter

A microfluidic chip lets researchers identify elusive human-dwelling microbes.

Vast and complex microbial communities teem on and inside our bodies. These bacteria, which outnumber our own cells by a factor of 10, play a vital role in human health and in various diseases. But microbiologists have very little idea what most of these organisms are or what they do. The reason is that 99 percent of bacteria can’t be grown in pure culture in the lab, and thus they have not been identified and studied: they are biology’s dark matter.

Spotting cells: This microfluidic chip can amplify the genome of single bacterial cells for sequencing–even those that are impossible to grow in the lab. In this photograph, the channels and control lines on the chip are filled with blue and red food coloring.

Stephen Quake, a Stanford bioengineer, has designed a microfluidic device that microbiologists can use to pick a single cell from a sample and prepare its genome for sequencing. A major hurdle to studying many bacteria that can’t be cultured has been the difficulty of creating a pure sample of a single bacterial cell’s genome that is large enough to sequence. Quake’s microfluidic device overcomes this problem.

The chip, which can handle eight samples at a time, holds a series of tiny pipes and valves that can shuttle and sort bacterial cells as well as add and remove chemicals to and from the solution. (See “Microfluidics.”) Looking through a microscope at a chamber in the chip, a researcher can pick out a single bacterial cell for further study, then send it into a chamber where chemicals burst it open, releasing its genetic material. The burst cell is pushed into another chamber where its DNA is copied many times over. After this last step–the amplification of a single cell’s DNA–the cell’s genetic material can be retrieved for sequencing.

Sequencing the whole genome of single bacterial cells is “really impressive,” says Norm Dovichi, a chemistry professor at the University of Washington, in Seattle.

Researchers in Quake’s group used the microfluidic device to isolate and copy DNA from an oral bacterium, which they then sequenced. This bacterium was previously uncharacterized: no other researcher had been able to sequence its genome or grow it in the lab. Quake’s group was able to isolate and study it even though the organism made up only a very small percentage of the bacteria in the initial sample.

Another approach to studying unculturable microbial communities, called metagenomics, is to create an inventory of a community’s genes. (See “Metagenomics Explained.”) These inventories are providing insight into complex bacterial communities, but they “lose the basic unit: the cell,” says Quake. “You can’t tell which gene is from which organism.”

Single-cell sequencing efforts will greatly expand microbiologists’ understanding of the complex bacterial communities living in our bodies, says Anthony Chow, emeritus professor of medicine at the University of British Columbia. (See “The Next Human Genome Project: Our Microbes.”) Before they can understand how these microbes might cause disease, researchers must learn what they are. “Our approach to investigating [possible] infectious causes of disease is still pretty rudimentary,” says Chow, who was not involved with Quake’s research.

Indeed, there is some evidence that still-unidentified bacteria that normally live in our bodies can cause miscarriages and heart disease. In mice, the composition of bacterial communities has been linked to body weight and health. (See “Our Microbial Menagerie.”) The causes of many health problems, including inflammatory diseases like rheumatoid arthritis and lupus, are poorly understood. Researchers suspect that many of them might be caused by “infections that are beyond our means to identify,” says Chow.

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