{"doi":"10.1073/pnas.1018249108","title":"Evolutionary dynamics of bacteria in a human host environment","abstract":"<jats:p>\n                    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,\n                    <jats:italic>Pseudomonas aeruginosa</jats:italic>\n                    , 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.\n                  </jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2011,"id":682821,"datarank":0.8862124407253398,"base_score":5.908082938168931,"endowment":5.908082938168931,"self_citation_contribution":0.8862124407253398,"citation_network_contribution":0.0,"self_endowment_contribution":0.8862124407253398,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":367,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":209305,"name":"Lars Jelsbak","orcid":"0000-0002-5759-9769","position":1,"is_corresponding":false},{"id":1783762,"name":"Rasmus Lykke Marvig","orcid":null,"position":2,"is_corresponding":false},{"id":1783763,"name":"Søren Damkiær","orcid":null,"position":3,"is_corresponding":false},{"id":1783764,"name":"Christopher T. Workman","orcid":null,"position":4,"is_corresponding":false},{"id":1783765,"name":"Martin Holm Rau","orcid":null,"position":5,"is_corresponding":false},{"id":1783766,"name":"Susse Kirkelund Hansen","orcid":null,"position":6,"is_corresponding":false},{"id":1783767,"name":"Anders Folkesson","orcid":null,"position":7,"is_corresponding":false},{"id":812643,"name":"Helle Krogh Johansen","orcid":"0000-0003-0268-3717","position":8,"is_corresponding":false},{"id":1783768,"name":"Oana Ciofu","orcid":null,"position":9,"is_corresponding":false},{"id":1756118,"name":"Niels Høiby","orcid":null,"position":10,"is_corresponding":false},{"id":1783769,"name":"Morten O. A. Sommer","orcid":null,"position":11,"is_corresponding":false},{"id":812644,"name":"Søren Molin","orcid":"0000-0002-7973-2639","position":12,"is_corresponding":false},{"id":1022355,"name":"Lei Yang","orcid":"0000-0002-9767-9026","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Evolutionary dynamics of bacteria in a human host environment","abstract":"<jats:p>\n                    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,\n                    <jats:italic>Pseudomonas aeruginosa</jats:italic>\n                    , 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.\n                  </jats:p>","is_dataset_classified":null,"base_score":5.908082938168931,"endowment":5.908082938168931,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"21518885","pmcid":"PMC3088582","openalex_id":"https://openalex.org/W2015502647","authors":[],"funders":[],"total_grants":0,"fwci":18.3382,"citation_percentile":0.99487442,"influential_citations":0,"citation_trend":[{"year":2012,"count":32},{"year":2013,"count":31},{"year":2014,"count":26},{"year":2015,"count":33},{"year":2016,"count":26},{"year":2017,"count":22},{"year":2018,"count":28},{"year":2019,"count":25},{"year":2020,"count":25},{"year":2021,"count":30},{"year":2022,"count":16},{"year":2023,"count":11},{"year":2024,"count":40},{"year":2025,"count":4},{"year":2026,"count":7}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://pnas.org/doi/pdf/10.1073/pnas.1018249108","host_type":"publisher"},{"url":"https://doi.org/10.1073/pnas.1018249108","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/21518885","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3088582","host_type":"repository"},{"url":"https://curis.ku.dk/portal/da/publications/evolutionary-dynamics-of-bacteria-in-a-human-host-environment(b4715a3f-66aa-45e3-b443-b63dec68d87a).html","host_type":"repository"},{"url":"https://orbit.dtu.dk/en/publications/50db68b9-0f1e-4227-a2ef-9ad6ed502023","host_type":"repository"},{"url":"https://researchprofiles.ku.dk/da/publications/b4715a3f-66aa-45e3-b443-b63dec68d87a","host_type":"repository"}],"fields_of_study":["Evolution and Genetic Dynamics","Bacterial Genetics and Biotechnology","Bacteriophages and microbial interactions"],"mesh_terms":["Adaptation, Biological","Base Sequence","Cystic Fibrosis","Biological Evolution","Humans","Molecular Sequence Data","Phenotype","Phylogeny","Pseudomonas aeruginosa","Selection, Genetic","Genetic Variation","Genome, Bacterial","Sequence Analysis, DNA","DNA Primers","Oligonucleotide Array Sequence Analysis","Polymorphism, Single Nucleotide","Gene Expression Profiling","Genetic Drift","Genetic Pleiotropy"],"keywords":["Host (biology)","Dynamics (music)","Bacteria","Evolutionary biology","Biology","Evolutionary dynamics","Ecology","Genetics","Physics","Sociology","Demography"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-17T21:27:20.249105Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}