Tuesday, August 01, 2017

UIS professor part of a research study that finds new biological sequencing method less effective

Michael Lemke, professor of biology at the University of Illinois Springfield, is part of an international research team led by the American Museum of Natural History that has found that a next-generation DNA sequencing method is less effective at microbial diversity description than originally thought.

Next-generation sequencing has given biological scientists the ability to sequence millions to billions of small fragments of DNA in parallel, revolutionizing the field.

In a study, published this week in the Nature research journal “Scientific Reports”, scientists compared two next-generation sequencing techniques – called amplicon and shotgun – on water samples from four of Brazil’s major river floodplain systems. Less than 50 percent of phyla—a category for a very broad group of related organisms—identified via amplicon sequencing were recovered from shotgun sequencing, challenging the belief that shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed about 27 percent more families.

“It is not a matter of setting back sequencing research,” said Lemke. “Sequencing is an amazingly effective tool for understanding what exists in the microbial world, but every tool does not fit the need for every job, and here, we really have a variation on the same tool. Many parts of microbial world remain unknown, and the unknown portions are even more mysterious when there are less studies, for there are less data that has been contributed to building a database.”

Lemke, through a collaboration with the Universidade Estadual de Maringá in Brazil, helped collect samples and extract DNA used for the data in the present study. He was on site to collect water samples from the Amazon and Paraguay Rivers during two trips in 2011 and 2012. These samples, along with those from the other river systems, were sequenced using both amplicon and shotgun methods.

“In the case with the Brazil large rivers study, the study that came out represents evidence for a ‘better’ way to use the sequencing tool in this case,” said Lemke. “You can think of the work led by Michael Tessler and Mercer Brugler as having two different (sequencing) flashlights used to look into the microbial black boxes we retrieved from Brazil. It turns out that the amplicon flashlight shed double the light into the box than the shotgun flashlight.”

Lemke’s work continues as a research associate for the American Museum of Natural History with the DeSalle Lab, part of the Sackler Institute for Comparative Genomics.

“I’m preparing the last samples from a nine-year study on The Nature Conservancy’s restoration project at Thompson Lake (located near the Emiquon Preserve in Fulton County) to take to the Museum for sequencing yet this summer,” he said. “Application of sequence technology is a big issue in our work.”

Other researcher partners included in the American Museum of Natural History study are the City University of New York (CUNY), Weill Cornell Medicine and Instituto Cesumar de Ciȇncia, Tecnologia e Inovação.

This study was supported in part by the Korein Foundation, the Gerstner Family Foundation, the Irma T. Hirschl and Minque Weill-Caulier Charitable Trusts, the Bert L. and N. Kuggie Vallee Foundation, the WorldQuant Foundation, the Bill and Melinda Gates Foundation (grant #OPP1151054), and the Brazilian National Council of Technological and Scientific Development.

For more information, contact Michael Lemke, UIS professor of biology, at 217/206-7339 or mlemk1@uis.edu.

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