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Series GSE6486

Query DataSets for GSE6486

Status

Public on Apr 01, 2007

Title

Comparative genomic hybridization and physiological characterization of environmental E.coli

Platform organism

Escherichia coli

Sample organisms

Escherichia coli; Escherichia coli K-12

Experiment type

Genome variation profiling by array

Summary

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 frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated 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. 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. Our results indicate that the major 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.
Keywords: CGH, E. coli, gDNA, environmental strains, eco-physiology

Overall design

gDNA from E.coli test strains was labeled with Cy-5 and hybridized against E.coli K12, reference strain, labeled with Cy-3. Hybridization, performed in Agilent proprietary buffer was performed for 17H at 60°C. Slides were then scanned in the Agilent scanner and extracted with Feature Extraction software. Background subtracted data were normalized for unequal incorporation or loading (LOWESS). Normalized data were then analyzed using GACK (Leonard et al, JID, 2003)

Contributor(s)

Ihssen J, Grasselli E, Bassin C, Francois P, Piffaretti J, Koster W, Schrenzel J, Egli T

Citation(s)

17600050

Submission date

Dec 08, 2006

Last update date

Mar 16, 2012

Contact name

FRANCOIS Patrice

E-mail(s)

patrice.francois@genomic.ch