Pathway and genomic analyses among select Gammaproteobacteria

The following studies concentrate on the class Gammaproteobacteria, which includes many of the most pathogenic and commonly found organisms in clinical pathology. We utilize available genomic information from sequenced organisms to make comparisons among subgroups within the families Enterobacteriaceae, Vibrionaceae, and Francisellaceae. By combining predicted metabolic maps from multiple organisms with evolutionary information extracted from their genomes, we are attempting to catalog the types of pressures and genetic processes which give rise to certain phenotypic transformations including pathogenicity, host-association, and adaptation to new environmental niches. Our approach is bipartite: first, we have employed comparative genomics to examine the inter-specific changes among Gammaproteobacteria gene families; second, we have constructed and compared system-wide metabolic models using genomic data and clinical characterization tests from the American Type Culture Collection (ATCC^TM).

Here we include the published results of studies among Escherichia coli and Francisella tularnesis strains, Yersinia species, and Vibrionaceae genera. The comparative genomics studies herein provide predictions for important gene families which may prove useful for future determination of likely drug targets for prophylaxis or treatment of infection. The collection of metabolic pathway genome databases discussed within this dissertation will also become a publicly available knowledge pool on the MetaCyc website (www.MetaCyc.com).