CS&E Alum’s Research Published in ‘Nature Biotechnology’

Gang Fang
December 18, 2017

Ph.D. alum Gang Fang (2012) led a research team that recently published a report detailing a new method for identifying individual microbial species and strains in a community. Their innovative technique has potential long-term applications for clinical care and important implications for microbiome analysis. The paper came out in Nature Biotechnology.

Microbiomes are communities of bacteria, viruses, and other microbes that can be found everywhere from the surfaces of keyboards and cell phones to environments on and within us, such as our mouths or intestines. Disruption of the natural microbiome has been implicated in health conditions including infectious diseases, cancers, and complex disorders such as Crohn’s disease, ulcerative colitis, and diabetes, among many others. Successful analysis of microbiomes depends on the ability to zoom in on these communities and identify the individual species and strains living within them.

To date, most techniques for identifying microbial members of these groups provide insufficient resolution. Additionally, existing methods are not effective in the characterization of an important class of genetic materials that can shuttle between different bacterial species. Fang and his collaborators use a more comprehensive approach that is more precise than industry-standard protocols. The method provides a new way to link mobile genetic elements to their bacterial hosts, which allows scientists to more accurately predict critical traits of individual bacterial species and strains.

“The biomedical community has long needed a microbiome analysis method capable of resolving individual species and strains with high resolution,” said Fang, senior author of the paper. “We found that DNA methylation patterns can be exploited as highly informative natural barcodes to help discriminate microbial species from each other, help associate mobile genetic elements to their host-genomes and achieve more precise microbiome analysis.”

Currently an assistant professor at the Icahn School of Medicine at Mount Sinai, Fang joined collaborators from Sema4, New York University, and the University of Florida in this research. Fang’s overall research focuses on the fundamental understanding of the epigenomes of pathogens, microbiome and human, a field of study that his group have pioneered.

As a Ph.D. student with the Department of Computer Science and Engineering, Fang was supervised by Professor Vipin Kumar. He accumulated a solid foundation in data mining, computational biology and general research methodologies, all of which, Fang said, have had a critical impact on his current and future research in biomedical science.

To dive deeper into Fang’s work, read the paper here.

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