Submitted to: Methods in Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 4, 2011
Publication Date: August 26, 2011
Citation: Bhagwat, M., Bhagwat, A.A. 2011. Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources. Methods in Molecular Biology. 765:297-307.
Interpretive Summary: Outbreaks of enteric human pathogens such as E. coli, Salmonella and Shigella spp. have been reported and the isolated outbreak stains have shown a wide range of genetic differences. Understanding the molecular basis of genetic diversity is important to analyze the risk associated with a particular pathogenic strain. We demonstrated the utility of several community resources to interpret the pairwise genome comparison information obtained from several genome sequence projects. Genetic analysis revealed new virulence proteins in E. coli O157:H7 strain associated with spinach outbreak in 2006. Whole genome sequence analysis tools will strengthen food-borne pathogen surveillance and subsequent risk assessment by various regulatory agencies to make the US food supply safer.
Fully annotated genome sequences of many microorganisms are publicly available as a resource. However, in-depth analysis of these genomes using specialized tools is required to derive meaningful information. We describe here the utility of three powerful publicly available genome databases and analysis tools. Protocols outlined here are particularly useful for performing pairwise genome comparisons between closely related microorganisms to identify similarities and unique features, for example, to identify genes specific to a pathogenic strain of Escherichia coli compared to a non-pathogenic strain.