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Open Access Research article

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

Eric J de Muinck123, Karin Lagesen1, Jan Egil Afset45, Xavier Didelot6, Kjersti S Rønningen7, Knut Rudi8, Nils Chr Stenseth1 and Pål Trosvik1*

Author affiliations

1 Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box, 0316 Oslo, 1066, Norway

2 Division of Epidemiology, Norwegian Institute of Public Health, PO Box, 0456 Oslo, 4404, Norway

3 NOFIMA - The Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box, 1430 Ås, 210, Norway

4 Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine, Norwegian University of Science and Technology, PO Box, 7491 Trondheim, 8905, Norway

5 Department of Medical Microbiology, St Olavs Hospital, PO Box, 7006 Trondheim, 3250, Norway

6 Department of Infectious Disease Epidemiology, Imperial College London, St Mary’s Campus, Norfolk Place, London, W2 1PG, UK

7 Department of Pediatric Research, Oslo University Hospital, Rikshospitalet, PO Box, 0424 Oslo, 4905, Norway

8 Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, PO Box, 1432 Ås, 5003, Norway

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Citation and License

BMC Genomics 2013, 14:81  doi:10.1186/1471-2164-14-81

Published: 5 February 2013

Abstract

Background

Despite 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.

Results

Here, 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.

Conclusions

Our 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.

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