Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis.
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.
Ward
Philip N
PN
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. Phil.Ward@ndcls.ox.ac.uk
Holden
Matthew T G
MT
Leigh
James A
JA
Lennard
Nicola
N
Bignell
Alexandra
A
Barron
Andy
A
Clark
Louise
L
Quail
Michael A
MA
Woodward
John
J
Barrell
Bart G
BG
Egan
Sharon A
SA
Field
Terence R
TR
Maskell
Duncan
D
Kehoe
Michael
M
Dowson
Christopher G
CG
Chanter
Neil
N
Whatmore
Adrian M
AM
Bentley
Stephen D
SD
Parkhill
Julian
J
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
D001426:Bacterial Proteins; D004269:DNA, Bacterial