Microbial genomics and pathogen discovery

This chapter discusses the concepts of microbial genomics and pathogen discovery. The discussion begins with an overview of traditional efforts, followed by a brief description of the evolution of sequencing technologies. Finally, the chapter illustrates how the two fields began to intersect in the first few years of the 21st century. The discoveries of Hepatitis C virus (HCV) and Human herpesvirus 8 (HHV-8), also called Kaposi's sarcoma-associated herpesvirus (KSHV), represented two breakthroughs in the application of candidate-independent molecular methods for pathogen discovery. The onset of the 21st century has seen the convergence of the fields of pathogen discovery and microbial genomics. The PhyloChip, a high-density 16S rRNA microarray containing 300,000 probes, was used to examine the microbial diversity in three environmental samples, including urban aerosol, subsurface soil, and subsurface water. This study demonstrated that the array could reveal broader diversity than classical cloning and sequencing of the same sample. The challenge facing the scientific community for the remainder of this century is to develop commensurate approaches to defining the biological relevance of this multitude of novel microbes to human disease.