title: A genomic polymorphism located downstream of the gcvP gene of Escherichia coli that correlates with ecological niche.
abstract: Current evolutionary theory proposes that niche-adapted microbial populations might evolve through selection for favoured genotypes followed by clonal expansion (Maynard-Smith, 1991). Possible correlations between genomic variation and ecological niche in Escherichia coli isolates derived from human and animal sources were investigated by randomly amplified polymorphic DNA (RAPD) analysis. A 1.6-kb polymorphic marker was identified which was present in 60% of isolates from human clinical specimens but was present in less than 5% of isolates derived from ovine and bovine faeces. The marker maps to a region of the chromosome located immediately downstream from the gene encoding the glycine decarboxylase P-protein (gcvP). DNA sequences from marker-positive and marker-negative isolates exhibit an abrupt loss of homology immediately downstream from the transcription termination point of the gene which extends for at least 130-base pairs beyond the gcvP transcription terminator. Sequences spanning this region in marker-negative isolates exhibit similarity to the cognate sequence from E. coli K-12, while the corresponding region in marker-positive isolates bears no similarity to any other published sequence. The utility of the marker for investigating the occurrence of human-derived E. coli in the environment was studied in a rural stream. Although the stream carried a high background of animal-derived E. coli, the marker could only be detected in isolates obtained downstream of the human faecal input. The polymorphism therefore shows promise for identification of human-derived E. coli within environments containing isolates from multiple and diverse sources. The methods described here could be used to generate further markers suitable for investigating microbial population ecology.
authors.affiliation: Microbiology and Molecular Genetics, School of Biological Sciences, Univeristy of Auckland, New Zealand. sturner@sbsnov2.auckland.ac.nz
authors.forename: S J
authors.initials: SJ
authors.lastname: Turner
authors.forename: G D
authors.initials: GD
authors.lastname: Lewis
authors.forename: A R
authors.initials: AR
authors.lastname: Bellamy
mesh_terms: D000594:Amino Acid Oxidoreductases; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D002417:Cattle; D004926:Escherichia coli / Q000502:physiology*; D029968:Escherichia coli Proteins; D005243:Feces / Q000382:microbiology; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D019105:Random Amplified Polymorphic DNA Technique
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D005819:Genetic Markers; D000594:Amino Acid Oxidoreductases; C087190:GcvP protein, E coli