Fine Reading: Microbial Genomics and Infectious Diseases
Would you like to read a concise and well-written review about how genomics has influenced our understanding of infectious diseases? Click here for a satisfying account by David Relman, one of the leading contributors to this field.
After summarizing the dizzying accelerating pace at which complete genome sequences are being acquiredeukaryotic, viral, bacterial, archaeal—Relman discusses how microbial genomic diversity impacts on health and disease, as illustrated by concepts such as the pangenome, genome reduction, genomic islands, CRISPR loci, and others. We read about the evolution of pathogens such as the plague bacillus, including its origin between 2600 and 28,000 years ago in China, and that the common ancestor of all the strains in the USA today probably arrived in San Francisco in 1899. We learn that comparing genomic sequences of Helicobacter pylori strains has been used to determine the timing and direction of human migrations, and that Vibrio cholerae traveled, with human help, from South Asia to Haiti.
Microbial Genomics and Tool Development. (Click on the image for a readable, full-size version.) A genome sequence facilitates the development of a variety of tools and approaches for understanding, manipulating, and mitigating the overall effect of a microbe. The sequence provides insight into the population structure and evolutionary history of a microbe for epidemiologic investigation, information with which to develop new diagnostic tests and cultivation methods, new targets of drug development, and antigens for vaccine development. Source.
Symbiosis and pathogenesis are smartly interwoven here. Relman highlights the importance of horizontal gene transfer and genomic islands. He points out that innocuous microbes often carry virulence factors, which suggests that these factors have other uses, such as aiding colonization or resistance to phagocytes. Some of them likely originated as protection against predation by protists and worms. As expected for a paper from a leading human microbiomicist, the microbiome receives ample coverage. Lastly, he discusses the productive use of genomic concepts and tools in the discovery of pathogens and in the development of diagnostic and therapeutic tools. Although this piece is intended primarily for physicians, I believe that Relman's lucid overview will benefit many others as well.