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Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis

Philip N Ward1, Matthew TG Holden2*, James A Leigh3, Nicola Lennard2, Alexandra Bignell2, Andy Barron2, Louise Clark2, Michael A Quail2, John Woodward2, Bart G Barrell2, Sharon A Egan3, Terence R Field4, Duncan Maskell5, Michael Kehoe6, Christopher G Dowson7, Neil Chanter8, Adrian M Whatmore79, Stephen D Bentley2 and Julian Parkhill2

Author Affiliations

1 Nuffield Department of Clinical Laboratory Sciences, Oxford University, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK

2 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

3 The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK

4 Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berks, RG20 7NN, UK

5 Dept. of Veterinary Medicine, The University of Cambridge, Cambridge, CB3 0ES, UK

6 Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK

7 Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK

8 Centre for Preventative Medicine, Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK

9 Veterinary Laboratories Agency, Weybridge, UK

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BMC Genomics 2009, 10:54  doi:10.1186/1471-2164-10-54

Published: 28 January 2009



Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen.


The genome revealed 1,825 predicted coding sequences (CDSs) of which 62 were identified as pseudogenes or gene fragments. Comparisons with related pyogenic streptococci identified a conserved core (40%) of orthologous CDSs. Intriguingly, S. uberis 0140J displayed a lower number of mobile genetic elements when compared with other pyogenic streptococci, however bacteriophage-derived islands and a putative genomic island were identified. Comparative genomics analysis revealed most similarity to the genomes of Streptococcus agalactiae and Streptococcus equi subsp. zooepidemicus. In contrast, streptococcal orthologs were not identified for 11% of the CDSs, indicating either unique retention of ancestral sequence, or acquisition of sequence from alternative sources. Functions including transport, catabolism, regulation and CDSs encoding cell envelope proteins were over-represented in this unique gene set; a limited array of putative virulence CDSs were identified.


S. uberis utilises nutritional flexibility derived from a diversity of metabolic options to successfully occupy a discrete ecological niche. The features observed in S. uberis are strongly suggestive of an opportunistic pathogen adapted to challenging and changing environmental parameters.