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Background   Streptococcus infantarius  subsp.  infantarius  ( Sii ) belongs to the  Streptococcus bovis/Streptococcus equinus  complex associated with several human and animal infections.  Sii  is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of  Sii  strain CJ18 was compared with that of other  Streptococcus  species to identify dairy adaptations including genome decay such as in  Streptococcus thermophilus , traits for its competitiveness in spontaneous milk fermentation and to assess potential health risks for consumers.    Results  The genome of  Sii  CJ18 harbors several unique regions in comparison to  Sii  ATCC BAA-102 T , among others an enlarged exo- and capsular polysaccharide operon;  Streptococcus thermophilus- associated genes; a region containing metabolic and hypothetical genes mostly unique to CJ18 and the dairy isolate  Streptococcus gallolyticus  subsp.  macedonicus ; and a second oligopeptide transport operon. Dairy adaptations in CJ18 are reflected by a high percentage of pseudogenes (4.9%) representing genome decay which includes the inactivation of the lactose phosphotransferase system ( lacIIABC ) by multiple transposases integration. The presence of  lacS  and  lacZ  genes is the major dairy adaptation affecting lactose metabolism pathways also due to the disruption of  lacIIABC .  We constructed mutant strains of  lacS, lacZ  and  lacIIABC  and analyzed the resulting strains of CJ18 to confirm the redirection of lactose metabolism via LacS and LacZ.  Natural competence genes are conserved in both  Sii  strains, but CJ18 contains a lower number of CRISPR spacers which indicates a reduced defense capability against alien DNA. No classical streptococcal virulence factors were detected in both  Sii  strains apart from those involved in adhesion which should be considered niche factors.  Sii -specific virulence factors are not described. Several  Sii -specific regions encoding uncharacterized proteins provide new leads for virulence analyses and investigation of the unclear association of dairy and clinical  Sii  with human diseases.    Conclusions  The genome of the African dairy isolate  Sii  CJ18 clearly differs from the human isolate ATCC BAA-102 T . CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. Metabolic adaptations to the dairy environment are evident and especially lactose uptake corresponds to  S. thermophilus.  Genome decay is not as advanced as in  S. thermophilus  (10-19%) possibly due to a shorter history in dairy fermentations.

bmc genomics

Comparative genome analysis of Streptococcus infantarius subsp. infantariusCJ18, an African fermented camel milk isolate with adaptations to dairy environment