Internet-Based Tool Simplifies Infectious Disease Diagnosis

Metagenomics, the genomic analysis of a population of microorganisms, makes possible the profiling of microbial communities in the environment and the human body at unprecedented depth and breadth. Its rapidly expanding use is revolutionizing the understanding of microbial diversity in natural and man-made environments and is linking microbial community profiles with health and disease.

The Taxonomer program is an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. The DNA sequence data for a clinical sample is uploaded via the Internet to Taxonomer. In less than one minute, the tool displays a thumbnail inventory of all pathogens in the sample, including viruses, bacteria, and fungi. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling.

Using real-world case studies, the developers showed that Taxonomer detected previously unrecognized infections and revealed antiviral host mRNA expression profiles.

“Our benchmark analyses show Taxonomer being ten to a hundred times faster than similar tools,” said senior author Dr. Robert Schlaberg, assistant professor of clinical pathology at the University of Utah. “Taxonomer provides a critical step forward, as it is extremely fast, accurate, and easy enough to use for implementation in diagnostic laboratories.”

To facilitate datasharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface at the address http://taxonomer.com.

Results of the Taxonomer study were published in the May 26, 2016, online edition of the journal Genome Biology.

Related Links:
University of Utah
Taxonomer