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Analysis of Lake Washington microbes shows the power of metagenomic approaches
Date:8/17/2008

assemblies to rely on high-quality reads," said Alla Lapidus, microbial geneticist at the DOE JGI and co-author on the paper. If some of the sequence is of low quality, she said, it can lead to errors in assembly and gene annotation.

Because of the need for higher quality control, Lapidus said, the DOE JGI developed a new quality control approach that involves a computer tool called LUCY to trim out low-quality sequence in combination with the Paracel Genome Assembler, which appeared to be more appropriate for metagenomic assemblies. This approach was pioneered on the Lake Washington project, Lapidus said, and due to its superior results it is now the standard metagenomic assembly method at the DOE JGI.

"The DOE JGI's unique Integrated Microbial Genomics with Microbiome Samples (IMG/M) [http://img.jgi.doe.gov/m] data management system was used for detailed annotation, and was instrumental for efficient comparative analysis and metabolic reconstruction of the samples," Lapidus said.

Michael Galperin, a microbial geneticist at the National Center for Biotechnology Information at the National Institutes of Health, who was not involved in the study, said in an email that the paper describes "an interesting novel approach" and the results "constitute a significant advance in the emerging discipline of metagenomics."

"I think other people can use the same approach in different environments, as long as they have an enrichment technique," Chistoserdova said. "For us this work is just the beginning, because now we will be using this metagenomic sequence as a scaffold for downstream experiments in our lake."


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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert

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