Cooper Laboratory

We seek to understand how bacterial populations evolve and adapt to colonize hosts and cause disease.

By studying evolution-in-action, in experimental populations and in ongoing infections, using the latest methods in genomic sequencing, we are identifying mechanisms of bacterial adaptation in vitro and in vivo.


We are focused on how bacteria form complex communities within biofilms and how individual cells perceive cues to attach or disperse.

Check out our MicroSeminar video here on YouTube!

We have learned that adaptation involves a sequence of mutations in predictable targets that leads to diversification into ecologically differentiated subpopulations. Often, these subpopulations interact synergistically, with certain types affecting host response and others enhancing resistance. In addition, we now routinely sequence the genomes of hundreds of bacterial isolates from longitudinal samples to define evolutionary forces affecting the courses of infection and the driver mutations, whose functions we work to experimentally identify.


  1. Poltak S, Cooper V. Ecological succession in long-term experimentally evolved biofilms produces synergistic communities. The ISME journal. 2011;5:369-78. doi: 10.1038/ismej.2010.136. PubMed PMID: 20811470. PubMed
  2. Traverse CC, Mayo-Smith LM, Poltak SR, Cooper VS. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. PNAS. 2013;110(3):E250–E9. doi: 10.1073/pnas.1207025110; PMID:23271804 PubMed
  3. Cooper VS, Staples RK, Traverse CC, Ellis CN. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms. Genomics. 2014. doi: 10.1016/j.ygeno.2014.09.007. PubMed PMID: 25263109. PubMed

Origins of multicellularity

How different bacterial strains or species coexist and interact when bound together on a surface allows us to explore the origins of multicellular life. We are proud to be part of a NASA Astrobiology Institute that uses experimental evolution to pursue the goal:

.notice To discover the laws that create Darwin’s ‘tangled bank’ remains one of biology’s grand challenges, one that requires understanding how differences among forms are selected for and how interdependence among forms is enforced.


  1. Ellis CN, Traverse CC, Mayo‐Smith L, Buskirk SW, Cooper VS. Character displacement and the evolution of niche complementarity in a model biofilm community. Evolution. 2014; PMCID:25494960. PubMed

Why genome regions evolve at different rates

In bacterial genomes with multiple chromosomes, smaller, secondary chromosomes evolve more rapidly. We are exploring the root causes of this variation as it may bear on variation in genome stability in all organisms.


  1. Cooper, V.S., S. Vohr, S. Wrocklage, and P.J. Hatcher. Why Genes Evolve Faster on Secondary Chromosomes in Bacteria. PLoS Computational Biology, 2010.
  2. Flynn, K.M., S.H. Vohr, P.J. Hatcher, and V.S. Cooper. Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus. Genome Biology and Evolution, 2010.
  3. Morrow, J.D. and Cooper, V.S. Evolutionary Effects of Translocations in Bacterial Genomes. Genome Biology and Evolution, 2012.

How do mutation rates and spectra vary among genome regions?

Intra-genome variation in the rates and spectra of mutations could provide a mechanism by which selection acts on genome organization to influence both the origin of genetic variation as well as its fate. We use mutation-accumulation experiments (MA) paired with whole-genome-sequencing (WGS) to capture the mutational process of various bacterial species with unprecedented resolution.

  1. Dillon MM, Sung W, Lynch M, Cooper VS. The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia. Genetics. 2015;200(3):935-46. doi: 10.1534/genetics.115.176834; PMID:25971664. PubMed

EvolvingSTEM: evolution-in-action leads to inspired learning.

The real-time evolution of microbes into conspicuous new forms has inspired a high-school curriculum for learning evolutionary biology, ecology, and biotechnology by simple experimentation. Not only do students learn better, they become more engaged in science. We are working to share this curriculum nationwide.