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Background  The genus  Lactobacillus  is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the  L. salivarius  clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the  L. salivarius  clade.    Results  The 2.06 Mb genome of the bovine isolate  Lactobacillus ruminis  ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%.  In silico  analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed  in vitro . A high quality draft assembly of the genome of a second  L. ruminis  strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of  L. ruminis  and  L. salivarius  identified a lack of long-range synteny between these closely related species. Comparison of the  L. salivarius  clade core proteins with those of nine other  Lactobacillus  species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group.    Conclusions  The genome of  L. ruminis  provides a comparative tool for directing functional analyses of other members of the  L. salivarius  clade, and it increases understanding of the divergence of this distinct  Lactobacillus  lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli .

Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts