Journal article
Evolutionary dynamics of bacteria in a human host environment
Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark1
Department of Systems Biology, Technical University of Denmark2
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark3
Copenhagen University Hospital Herlev and Gentofte4
Massachusetts General Hospital/Harvard Medical School5
Laboratory evolution experiments have led to important findings relating organism adaptation and genomic evolution. However, continuous monitoring of long-term evolution has been lacking for natural systems, limiting our understanding of these processes in situ. Here we characterize the evolutionary dynamics of a lineage of a clinically important opportunistic bacterial pathogen, Pseudomonas aeruginosa, as it adapts to the airways of several individual cystic fibrosis patients over 200,000 bacterial generations, and provide estimates of mutation rates of bacteria in a natural environment.
In contrast to predictions based on in vitro evolution experiments, we document limited diversification of the evolving lineage despite a highly structured and complex host environment. Notably, the lineage went through an initial period of rapid adaptation caused by a small number of mutations with pleiotropic effects, followed by a period of genetic drift with limited phenotypic change and a genomic signature of negative selection, suggesting that the evolving lineage has reached a major adaptive peak in the fitness landscape.
This contrasts with previous findings of continued positive selection from long-term in vitro evolution experiments. The evolved phenotype of the infecting bacteria further suggests that the opportunistic pathogen has transitioned to become a primary pathogen for cystic fibrosis patients.
Language: | English |
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Publisher: | National Academy of Sciences |
Year: | 2011 |
Pages: | 7481-7486 |
ISSN: | 10916490 and 00278424 |
Types: | Journal article |
DOI: | 10.1073/pnas.1018249108 |
ORCIDs: | Yang, Lei , Jelsbak, Lars , Marvig, Rasmus Lykke , Workman, Christopher , Folkesson, Anders , Sommer, Morten , Molin, Søren , 0000-0001-5648-4858 and 0000-0002-1347-725X |
Adaptation, Biological Base Sequence Biological Evolution Cystic Fibrosis DNA Primers Gene Expression Profiling Genetic Drift Genetic Pleiotropy Genetic Variation Genome, Bacterial Humans Molecular Sequence Data Oligonucleotide Array Sequence Analysis Phenotype Phylogeny Polymorphism, Single Nucleotide Pseudomonas aeruginosa Selection, Genetic Sequence Analysis, DNA chronic infection genome sequences microbial evolution natural population transcriptomics