Dr. Vaughn S. Cooper

Ph.D., Michigan State University, 2000
Microbial Evolution

Why are some bacteria so prone to causing human disease, while others are not?

Our ability to predict when and where new infectious diseases will emerge depends on a more complete understanding of the factors that favor the evolutionary transition from microorganisms that are non-paathogenic to a state capable of causing sustained infection in humans. Using a combination of approaches, I seek to determine what factors govern this ecological transition

Adaptation by E. coli during 20,000 generations of evolution
in a constant environment; each line is the mean for each of
12 replicate populations. I study this process in three different microbial systems:

Serially isolated clones from human Burkholderia cepacia infections. Cystic fibrosis patients are prone to long-term colonization by opportunistic soil microbes of the B. cepacia complex. In collaboration with John LiPuma (University of Michigan), I am studying evolutionary adaptation to the human lung by developing novel genomic screens and model host assays.
Long-term evolving populations of Escherichia coli founded by Richard Lenski (Michigan State University) more than 30,000 generations ago. In this system, I study the molecular and population genetics of evolutionary specialization and whether specialization is an evolutionary dead-end.
Laboratory model microcosms of Vibrio cholerae. In cultures that replicate elements of the natural estuarine environment of V. cholerae, I am quantifying the effect of genes important for human virulence on the bacterium and, in the future, selected putative hosts, such as copepods and algae.

Most recently, I have begun collaborating with faculty of the University of Michigan School of Public Health to develop novel genomic screens of populations of commensal Escherichia coli to describe the emergence and spread of antibiotic resistance genes in communities.

Publications:

Cooper, V. S., M. H. Reiskind, J. A. Miller, K. A. Shelton, B. A. Walther, J. S. Elkington, and P. W. Ewald. 2002. Timing of transmission and the evolution of virulence of an insect virus. Proc. Roy Soc. Lond. B, 269: 1161-1165.

Certain strains of B. cenocepacia are lethal to the
nematode C. elegans; their competition in liquid medium is illustrated here.

Cooper, V. S., D. Shneider, M. Blot, and R. E. Lenski. 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of E. coli B. J. Bacteriology 183: 2834-2841.
Cooper, V. S., A. F. Bennett and R. E. Lenski. 2001. Evolution of thermal performance of Escherichia coli populations during 20,000 generations in a constant environment. Evolution 55(5):889-896.
Riley, M. S., V. S. Cooper, R. E. Lenski, L. J. Forney and T. L. Marsh. 2001. Rapid phenotypic radiation of a soil bacterium maintained for 1000 generations in a laaboratory environment.
Cooper, V. S. and R. E. Lenski. 2000. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 407:736-739.
Turner, P. E., V. S. Cooper, and R. E. Lenski. 1998. Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution 52(2):315-329.
Elena, S. F., V. S. Cooper, R. E. Lenski. 1996. Punctuated evolution caused by selection of rare beneficial mutations. Science 272: 1802-1804.