Tools used for metagenomic research under scrutiny

Mathematical biologist David Koslicki

A recent critical assessment of software tools represents a key step toward taming the “Wild West” nature of the burgeoning field of metagenomics, said mathematical biologist David Koslicki, who took part in the research.

Metagenomics refers to the science of genetically studying whole communities of microorganisms, as opposed to sequencing single species grown in culture.

“Microbes are ridiculously important to life,” says Koslicki. “They not only can cause terrible things to happen, like blight and disease, but in general, overwhelmingly, microbes are our friends. Without them doing their jobs, crops couldn’t grow as well, it would be hard to digest our food, we might not get sleepy at appropriate times. Microbes are so fundamental to life, to health, we really need to know as much as we can about them.”

Koslicki, a leader in a university-wide research and education program known as OMBI – the OSU Microbiome Initiative – described the findings, published recently in Nature Methods, as “sobering.”

“There are not a lot of well-established, well-characterized computational techniques and tools that biologists can use,” he said. “And the assessment showed that a lot of the tools being used do not do nearly as well as had been initially thought, so there’s definitely room for improvement there.”

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