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Dr. Howard Ochman, Professor

Positions and Education

Professor, Dept. of Biochemistry & Molecular Biophysics, and Dept. of Ecology & Evolutionary Biology, University of Arizona, 1998-present
Assistant to Full Professor, Dept. of Biology, University of Rochester, 1992-1998
Research Asst. Professor, Dept. of Genetics, Washington University School of Medicine, 1988-1991
Staff Scientist, Lawrence Berkeley Laboratory, University of California, Berkeley, 1987-1988
""Postdoctoral Appointment in Biochemistry, U.C. Berkeley, 1984-1987
""Ph.D., Biology, University of Rochester, 1983
""M.S., Biology, University of Rochester, 1979
""B.A., Biology, Vassar College, 1975

Honors and Awards
National Institutes of Health, Research Career Development Award, 1997-2002
Lucille P. Markey Charitable Trust, Center Award for New Faculty, 1991-1992
National Research Service Award, National Institutes of Health, 1985-1987

Research Interests

My research program applies experimental, comparative and computational approaches to examine the evolution and adaptation of microbial genomes. Due to their complex and varied interactions as pathogens and commensal constituents of mammalian hosts, our work focuses on genome evolution within enteric bacteria, including E. coli, Shigella and Salmonella. These studies fall into four general areas, and some of the current projects in my laboratory include:

  1. Dynamics of bacterial genomes. Numerous opposing forces contribute to large-scale differences the size, contents and organization of the bacterial genomes. Such alterations, whose characterization was limited previously 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. Our research investigates the accumulated differences promoted by gene transfer and gene loss, and how the genome restructuring caused by these processes affect bacterial lifestyle.

  2. Origins and roles of novel bacterial traits. Within most bacterial genomes, the majority of genes is of unknown function and these genes are likely responsible for vast diversity in bacterial lifestyles and metabolic functions observed in the microbial world. Using a combination of experimental and bioinformatic methods, our research addresses two questions: What are the origins and roles of sequences that have been acquired through horizontal transfer, and what is function of genes for which no role can be assigned by conventional homology-based and genetic approaches?

  3. Phylogenetic classification and the history of bacterial genomes. The use of universally distributed molecular characters to resolve the relationships among organisms has been particularly informative in micro-organisms, in which the lack of morphological characteristics and lack of a robust fossil record have hinder previous attempts to determine their evolutionary history. In addition, recent studies provide clear evidence that lateral gene transfer is common among bacteria with the result that different portions of the genome have very different histories. Our research in this area generates and examines nucleotide sequences for a large set of genes that are universally distributed among Bacteria to determine: (i) how well the phylogenetic trees based on small different genes represent the relationships of organisms; (ii) whether organisms contain a core set of genes that are never subject to transfer; (iii) which genes are transferred among lineages, and what are the phylogenetic limits to lateral gene transfer; (iv) whether the genes subject to lateral transfer functionally related or genetically linked; and (v) what factors determine the amount of acquired DNA in a genome.

  4. Genomic analysis of diversity within bacterial communities. 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 and parasitic. We are exploring the assemblages of bacteria inhabiting the human GI tract to determine what properties determine the species composition, genetic characteristics and persistence and of bacteria within the intestinal flora. In a related project, we are developing methods to isolate individual constituents of bacterial assemblages for genomic characterization.

Visit Howard Ochman's lab here

PubMed list of publications for Howard Ochman
Selected Publications (last two years)
  1. Lerat, E. and H. Ochman (2005) Recognizing pseudogenes in bacterial genomes. Nucleic Acids Research 33: 3125-3132.

  2. Lerat, E., V. Daubin, H. Ochman and N.A. Moran (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biology 3: 807-814.

  3. Moran, N.A., Degnan, P.H., Santos, S.R., Dunbar, H.E. and H. Ochman (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses and virulence genes. Proc. Natl. Acad. Sci. USA 102: 16919-16926.

  4. Ochman, H. (2005) Genomes on the shrink. Proc. Natl. Acad. Sci. USA 102: 11959-11960.

  5. Ochman, H., V. Daubin and E. Lerat (2005) A bunch of fun-guys: the whole-genome view of yeast evolution. Trends Genet. 21: 1-3.

  6. Ochman, H. and L. Davalos (2005) The nature and dynamics of bacterial genomes. Science, in press

  7. Ochman, H., E. Lerat, E. and V. Daubin (2005) Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl. Acad. Sci. USA 102: 6595-6569.

  8. Ochman, H. and S.R. Santos (2005) Exploring microbial microevolution with microarrays. Infect. Genet. Evol. 5: 103-108.

  9. Wirth, T., Falush, D., Lan, R., Colles, F., Mensa, P., Wieler, L.H., Karch, H.,, Reeves, P., Maiden, M.C.J., Ochman, H. and M. Achtman (2005) Sex and virulence in Escherichia coli: an evolutionary perspective. Cell, submitted

  10. Daubin, V. and H. Ochman (2004) Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Research 14: 1036-1042.

  11. Daubin, V. and H. Ochman (2004) Recognizing lateral gene transfer by quartet mapping. Molec. Biol. Evol. 21: 48-51.

  12. Daubin, V. and H. Ochman (2004) Start-up entities in the evolution of new genes. Curr. Opin. Genet. Devel. 14: 616-619.

  13. Dale, C., Dunbar, H., Moran, N.A. and H. Ochman (2004) Extracting single genomes from heterogenous DNA samples: A test case with Carsonella ruddii, the bacterial symbiont of psyllids (Insecta). J. Insect Sci. 3: 5-15.

  14. Lerat, E. and H. Ochman (2004) Y—F: Exploring the outer limits of bacterial pseudogenes. Genome Research 14: 2273-2278.

  15. Santos, S.R. and H. Ochman (2004) Identification and phylogenetic sorting of bacterial lineages using universally conserved genes and proteins. Environ. Microbiol. 6: 754-759.

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