Next-Generation High-Throughput Functional Annotation of Microbial Genomes

Abstract

Host infection by microbial pathogens cues global changes in microbial and host cell biology that facilitate microbial replication and disease. The complete maps of thousands of bacterial and viral genomes have recently been defined; however, the rate at which physiological or biochemical functions have been assigned to genes has greatly lagged. The National Institute of Allergy and Infectious Diseases (NIAID) addressed this gap by creating functional genomics centers dedicated to developing high-throughput approaches to assign gene function. These centers require broad-based and collaborative research programs to generate and integrate diverse data to achieve a comprehensive understanding of microbial pathogenesis. High-throughput functional genomics can lead to new therapeutics and better understanding of the next generation of emerging pathogens by rapidly defining new general mechanisms by which organisms cause disease and replicate in host tissues and by facilitating the rate at which functional data reach the scientific community.

FIG 1

The current release of the protein sequence family database, Pfam (version 30, July 2016; http://pfam.xfam.org/), contains 16,306 sequence family entries, 3,751 of which are families/domains of unknown function (DUFs). The release years for Pfam version 4.0 and version 30.0 are marked with arrows.