title: Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. Phil.Ward@ndcls.ox.ac.uk
authors.forename: Philip N
authors.initials: PN
authors.lastname: Ward
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.forename: James A
authors.initials: JA
authors.lastname: Leigh
authors.forename: Nicola
authors.initials: N
authors.lastname: Lennard
authors.forename: Alexandra
authors.initials: A
authors.lastname: Bignell
authors.forename: Andy
authors.initials: A
authors.lastname: Barron
authors.forename: Louise
authors.initials: L
authors.lastname: Clark
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: John
authors.initials: J
authors.lastname: Woodward
authors.forename: Bart G
authors.initials: BG
authors.lastname: Barrell
authors.forename: Sharon A
authors.initials: SA
authors.lastname: Egan
authors.forename: Terence R
authors.initials: TR
authors.lastname: Field
authors.forename: Duncan
authors.initials: D
authors.lastname: Maskell
authors.forename: Michael
authors.initials: M
authors.lastname: Kehoe
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Dowson
authors.forename: Neil
authors.initials: N
authors.lastname: Chanter
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Whatmore
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002417:Cattle; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D044404:Genomic Islands; D008414:Mastitis, Bovine / Q000382:microbiology; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013291:Streptococcus / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D014774:Virulence
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial