The tissues and cells of eukaryotic hosts serve as the environment for vast numbers of bacterial species, with associations ranging from obligatory and beneficial to antagonistic. The complexity of such interactions derives from the fact that the host offers a protected and nutrient-rich environment, but also poses insult in the form of antimicrobial defenses and immune responses. The opposing forces presented by the host environment have resulted in varied types of genetic alterations in microbial genomes, ranging from single base substitutions conferring resistance to massive changes in mutation rates, gene contents, and genome architecture. Such changes, whose previous characterization was largely limited to the few human pathogens amenable to genetic manipulation, have become increasingly evident with the recent availability of whole genome mapping techniques and of complete genomic sequences for several host-associated bacteria.
Our research investigates how gene transfer and gene loss have shaped the genome and lifestyle of bacteria. The acquisition of genes through lateral gene transfer and the loss of genes by reductive evolution have played major roles in bacterial diversification and in promoting the interactions between bacteria and their hosts. Novel genes brought in through lateral transfer are responsible for numerous species-specific traits (such as new metabolic capabilities or virulence determinants), permitting rapid exploitation of new environments. Similarly, gene loss, as exemplified by the genomes of certain pathogens and symbionts, is also a significant factor in bacterial adaptation because it dictates reliance on specific environments or hosts. We combine experimental, comparative and bioinformatic approaches to examine such broad scale changes in bacterial genomes.
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Wirth, T., D. Falush, R. Lan, F. Colles, P. Mensa, L.H. Wieler, H. Karch, P. Reeves, M.C. Maiden, H. Ochman, and m. Achtman. 2006. Sex and virulence in Excherichia coli: an evolutionary perspctive. Molecular Microbiology 60: 1136-1151.
Ochman, H., and L.M. Davalos LM. 2006. The nature and dynamics of bacterial genomes. Science 311: 1730-1733.
Moran, N.A., P.H. Degnan, S.R. Santos, H.E. Dunbar, and H. Ochman. 2005. The players in a mutualistic symbiosis: insects, bacteria, viruses, and
virulence genes. Proceedings of the National Academy of Sciences U.S.A. 102: 16919-16926.
Ochman, H. 2005. Genomes on the shrink. Proceedings of the National Academy of Sciences U.S.A. 102: 11959-11960.
Lerat, E., and H. Ochman. 2005. Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Research 33: 3125-3132.
Ochman, H., E. Lerat, and V. Daubin. 2005. Examining bacterial species under the specter of gene transfer and exchange. Proceedings of the National Academy of Sciences U.S.A. 102 Suppl 1: 6595-6599.
Lerat, E., V. Daubin, H. Ochman, and N.A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biology 3: e130.
Ochman, H., V. Daubin, and E. Lerat. 2005. A bunch of fun-guys: the whole-genome view of yeast evolution. Trends in Genetics 21: 1-3.
Ochman, H., and S.R. Santos. 2005. Exploring microbial microevolution with microarrays. Infection, Genetics and Evolution 5: 103-108.
