title: Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli.
abstract: Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g. between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for 'domesticated' E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and doubts are frequently raised on the status of E. coli as a defined species. The variability of important (eco-)physiological functions, such as carbon substrate uptake and breakdown capabilities, as well as stress defence mechanisms, in the genomes of commensal and pathogenic E. coli strains were therefore investigated. Furthermore, (eco-)physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high-affinity substrate uptake systems. The results obtained indicate that significant (eco-)physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation.
authors.affiliation: Empa, Swiss Federal Institute for Materials Testing and Technology, Lerchenfeldstrasse 5, CH-9014 St Gallen, Switzerland.|Swiss Federal Institute for Environmental Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Julian
authors.initials: J
authors.lastname: Ihssen
authors.affiliation: Department of Biology, University of Genova, Corso Europa 26 V piano, 16132 Genova, Italy.|Istituto Cantonale di Microbiologia, Via Mirasole 22A, CH-6500 Bellinzona, Switzerland.
authors.forename: Elena
authors.initials: E
authors.lastname: Grasselli
authors.affiliation: Swiss Federal Institute for Environmental Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Claudio
authors.initials: C
authors.lastname: Bassin
authors.affiliation: Genomic Research Laboratory, University Hospitals of Geneva, rue Micheli-du-Crest 24, CH-1211 Geneva 14, Switzerland.
authors.forename: Patrice
authors.initials: P
authors.lastname: François
authors.affiliation: Istituto Cantonale di Microbiologia, Via Mirasole 22A, CH-6500 Bellinzona, Switzerland.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Piffaretti
authors.affiliation: VIDO - Vaccine & Infectious Diseases Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada.|Swiss Federal Institute for Environmental Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Köster
authors.affiliation: Genomic Research Laboratory, University Hospitals of Geneva, rue Micheli-du-Crest 24, CH-1211 Geneva 14, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
authors.affiliation: Swiss Federal Institute for Environmental Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Egli
mesh_terms: D004783:Environmental Microbiology; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism*; D008969:Molecular Sequence Data
chemical_list: D029968:Escherichia coli Proteins; D005947:Glucose