Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche

BMC Genomics

Research Article

Nils Chr Stenseth¹  Pål Trosvik¹  Karin Lagesen¹  Eric J de Muinck²  Knut Rudi³  Xavier Didelot⁴  Jan Egil Afset⁵  Kjersti S Rønningen⁶ 

[1] Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box, 0316, 1066, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box, 0316, 1066, Oslo, Norway;Division of Epidemiology, Norwegian Institute of Public Health, PO Box, 0456, 4404, Oslo, Norway;NOFIMA - The Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box, 1430, 210, Ås, Norway;Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, PO Box, 1432, 5003, Ås, Norway;Department of Infectious Disease Epidemiology, Imperial College London, St Mary’s Campus, Norfolk Place, W2 1PG, London, UK;Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine, Norwegian University of Science and Technology, PO Box, 7491, 8905, Trondheim, Norway;Department of Medical Microbiology, St Olavs Hospital, PO Box, 7006, 3250, Trondheim, Norway;Department of Pediatric Research, Oslo University Hospital, PO Box, 0424, Rikshospitalet, 4905, Oslo, Norway;

关键词: Escherichia coli;    Comparative genomics;    Infant gut;    Commensal;    Pathogen;    Generation time;    Codon usage bias;   

DOI  :  10.1186/1471-2164-14-81

 received in 2012-11-02, accepted in 2013-01-30,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundDespite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche.ResultsHere, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles.ConclusionsOur results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.

【 授权许可】

Unknown   
© De Muinck et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.