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Highway of Dreams for Microbiologists

Bac­teria are a per­va­sive and elu­sive bunch. Sci­en­tists esti­mate that between 10 mil­lion and 1 bil­lion dif­ferent micro­bial species pop­u­late the world, yet only a handful of them have so far been iden­ti­fied. Why? Because the over­whelming majority of microbes refuse to grow in the lab­o­ra­tory. This is despite decades of sci­en­tists’ best efforts at coaxing the micro­scopic organ­isms into action. 

by Northeastern University
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Slava Epstein, a biology pro­fessor at North­eastern Uni­ver­sity, has ded­i­cated his career to coming up with alter­na­tive methods for cul­ti­vating bac­teria. His favorite strategy, so to speak, is to take the lab bench into the wild. In nature, bac­teria are exposed to a host of nutri­ents and sup­portive chem­i­cals that help them grow. But sci­en­tists don’t know what they all are. This way, he explained, nature can work its secrets without him having to know what they are. So far, the devices he’s used incor­po­rate per­me­able mem­branes that allow sequestered bac­teria to be exposed to the nutri­ents and mol­e­cules of their native environment.

But a problem has remained: Nat­ural com­pe­ti­tion between species, even in the wild, has lim­ited the number of species Epstein can suc­cess­fully iso­late this way. A few years ago he and his col­lab­o­rator Yoshiteru Aoi at Hiroshima Uni­ver­sity in Japan began to fan­ta­size about a device that would permit just a single bac­te­rial cell to enter. Once inside, this cell would pro­lif­erate as in his other devices, but here it would be free of com­pe­ti­tion from other species. It would pro­vide a pure sample—just one species.

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But cre­ating that fan­tas­tical device pre­sented a chal­lenge to the team of biol­o­gists. Enter Edgar Goluch, DiP­i­etro assis­tant pro­fessor in the Depart­ment of Chem­ical Engi­neering at North­eastern. “Without Ed,” Epstein said, “we wouldn’t have been able to do anything.”

Goluch’s lab is focused on cre­ating microflu­idic devices for detecting var­ious bio­log­ical enti­ties, be it a bac­te­rial cell or an enzy­matic mol­e­cule. In 2012, he and Epstein teamed up to make the fan­tasy device a reality. With funding from a Tier 1 Inter­dis­ci­pli­nary Research Grant form Northeastern’s Office of the Provost, the duo man­aged to make a series of pro­to­type devices.

Think of a five lane highway going down to one lane,” Goluch explained. “That’s essen­tially what this does only for bac­teria.” The tiny device con­sists of an inner chamber con­taining a food source, to which the only access is a micro­scopic pas­sageway just slightly nar­rower than a single cell.

The device devel­oped by Goluch’s team con­sists of an inner food chamber and a micro­scopic con­stric­tion through which only a single bac­te­rial cell can pass.Image cour­tesy of Edgar GoluchThe pas­sageway is so small that the first cell to enter it gets stuck, blocking entry by any other cell or species. The trapped cell is still able to pro­lif­erate, how­ever, and when it does it fills up the inner chamber with a pure, single-species sample. “Who­ever gets there first wins and gets all the stuff inside,” Goluch said.

In a paper released Monday in the journal PLOS ONE, the team demon­strates the device’s ability to sep­a­rate mix­tures of cell types. In one exper­i­ment, the researchers sep­a­rated two dif­ferent bac­te­rial species whose cells are slightly dif­ferent sizes—E. coli and P. auerug­i­nosa. In a second exper­i­ment, they iso­lated a com­bi­na­tion of sim­i­larly sized but dif­fer­ently shaped species that com­monly show up together in the marine envi­ron­ment—Roseobacter sp. And Pscy­hoser­pens sp. Finally, they used the device to sep­a­rate cells of the same species that had been dif­fer­en­tially tagged to glow either red or green. This exper­i­ment val­i­dates the hypoth­esis that the cells grown inside the food chamber are daugh­ters of the single cell caught in the entryway.

Next week, Epstein will take the pro­to­types to Green­land for their first taste of real-world experimentation.

In the mean­time, funding from an Instru­ment Devel­op­ment Bio­log­ical Research Grant from the National Sci­ence Foun­da­tion will enable Goluch and his team of engi­neers to begin opti­mizing the device and its man­u­fac­ture. Cur­rently, they use a tem­plate to lay down the ini­tial archi­tec­ture and must then drill each indi­vidual micrometer-wide hole. But in order for the approach to really work, Epstein and Aoi would need many, many samples.

We’d like to throw these into any envi­ron­ment on the planet,” Epstein said. “The deep ocean, under the soil, into a pond.” In order to reach that kind of range, Goluch is working with a number of industry part­ners to stream­line and scale the fab­ri­ca­tion process.

The ben­efit will be the same: “It sim­pli­fies cul­ti­va­tion to the max­imum extent pos­sible,” Epstein said. “We don’t have to do any­thing, just build the devices and throw them into the envi­ron­ment. Nature does the rest.”