New approach may improve study of hard-to-grow, disease-related microorganisms
Researchers for the first time have used a combination of microfluidics and genomics to fish out a specific gut bacterium from the sea of trillions of microbes in the human microbiome. The new method has broad applications for isolating and studying many now impossible or hard-to-grow microorganisms implicated in health and disease, according to a study published online the week of June 23, 2014, in the Proceedings of the National Academy of Sciences. The technique, described in an accompanying report in Integrative Biology, is funded by the Technology Development program of the Human Microbiome Project (HMP). The HMP is supported by the NIH Common Fund and coordinated by the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.
Researchers have characterized the genomes of many of the microorganisms that live inside or on humans, but growing them in the laboratory has proved difficult because of the growth conditions that many require. HMP investigators created a "Most Wanted" list for those important microbes that scientists have not been able to culture.
To find such microbes and their needed growth conditions, Rustem Ismagilov, Ph.D., Liang Ma, Ph.D., both at the California Institute of Technology, Pasadena, and their colleagues, turned to microfluidics, which is used to capture small amounts of liquid in flow cells of hair-thin channels and wells. The flow cells consist of two credit card size glass plates stacked on top of one another that allow individual cells to flow in small channels to receiving wells. The scientists introduce a mixture of microbial cells into the flow cells, where they are sorted into each well. Each microbe is grown under different combinations of growth conditions. Then, assuming that those microbes that grew under similar growth conditions were likely to be similar kinds of microbes, the scientists combined those cells that grew under the same growth conditions, and looked for the target microorganism by analyzing DNA from the pooled wells of microorganisms. This approach allowed the scientists to identify both the microorganisms they wanted to study and their required growth conditions. The researchers could then isolate and grow the specific microorganism from a specific well. The investigators tested the technique on a sample from a human colon, targeting, isolating and growing a microbe - the first member of a previously unidentified genus of the Ruminococcaceae family grown in culture, and on the HMP "Most Wanted" list.
Ma, et al. Genetically targeted microfluidic cultivation validated by isolation of a "Most Wanted" microbe from the human gut. Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1404753111. 2014. [Full Text]
Lita Proctor, Ph.D., program director, NHGRI, coordinator, Human Microbiome Project
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