Adaptive evolution of bacterial populations in a human airway environment

Speaker: Søren Molin, Department of Systems Biology, DTU
Host: Kenn Gerdes, Biomolecular Sciences

Many investigations of microbial evolution in laboratory experiments (ALE, Adaptive Laboratory Evolution) have been performed in the past. The probably most famous of these was started in the US in 1988 by Richard Lenski – he started 12 cultures of Escherichia coli, followed them by serial dilutions since that time, and froze samples from these cultures to create a fossil collection for future profiling. This experiment is still running now covering more than 50,000 bacterial generations!

Since 1973 a collection of isolates of Pseudomonas aeruginosa isolated from cystic fibrosis (CF) patients was established at Rigshospitalet in Copenhagen, and this collection of bacteria have been exploited by us in order to profile the evolutionary processes shaping the genomes and phenotypes of bacteria persisting in a natural environment characterized by structure, dynamic changes, and severe stress. The strain collection comprises isolates covering adaptive processes for more than 200,000 bacterial generations.

We have used this strain collection as a model system for our studies of evolutionary mechanisms operating on microbial populations invading a completely novel ecosystem. The bacteria migrate from the natural environment to the human airways creating persistent monoclonal colonization, which are ideal objects for our investigations of adaptive evolution. We now have detailed genomic and phenotypic information from a number of parallel studies (infected CF patients) from which we can describe the adaptation and evolution of bacterial populations migrating to an entirely new environment. I will present an overview of what we have learned about genome evolution and the relationship between the mutations accumulated in the genomes and the new (host) environment. Interestingly we see many similarities between the evolutionary processes going on in one bacterium grown in the laboratory under controlled conditions and in another species adapting to a complex, dynamic and hostile environment. On the other hand it is also clear that the actual mutational paths towards final adaptation can vary a lot – even if they finally may converge towards to a common phenotype.

Suggested reading
Marvig RL, Madsen LM, Molin S and Johansen HK. Convergent evolution and adaptation of Pseudomonas aeruginosa within cystic fibrosis patients. Nature Genet 47: 57-64 (2015)

Damkiær S, Yang L, Molin S, Jelsbak L.: Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts. Proc Natl Acad Sci USA. 110(19):7766-71 (2013)

Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O, Høiby N, Molin S.: Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Microbiol. 10(12):841-51 (2012)

Yang, L., Jelsbak, L., Marvig, R.L., Damkiær, S., Workman, C.T., Rau, M.H., Hansen, S.K., Folkesson, A., Johansen, H.K., Ciofu, O., Høiby, N., Sommer, M. and Molin, S.: Evolutionary dynamics of bacteria in a human host environment. Proc Natl Acad Sci USA 108: 7481-6 (2011)