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Background  Classification of bacteria within the genus  Brucella  has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. Therefore, many different methods have been used to assess  Brucella  taxonomy. In the current work, we examine 32 sequenced genomes from genus  Brucella  representing the six classical species, as well as more recently described species, using bioinformatical methods. Comparisons were made at the level of genomic DNA using oligonucleotide based methods (Markov chain based genomic signatures, genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses).    Results  We found that the oligonucleotide based methods gave different results compared to that of the proteome based methods. Differences were also found between the oligonucleotide based methods used. Whilst the Markov chain based genomic signatures grouped the different species in genus  Brucella  according to host preference, the codon and amino acid frequencies based methods reflected small differences between the  Brucella  species. Only minor differences could be detected between all genera included in this study using the codon and amino acid frequencies based methods.  Proteome comparisons were found to be in strong accordance with current  Brucella  taxonomy indicating a remarkable association between gene gain or loss on one hand and mutations in marker genes on the other. The proteome based methods found greater similarity between  Brucella  species and  Ochrobactrum  species than between species within genus  Agrobacterium  compared to each other. In other words, proteome comparisons of species within genus  Agrobacterium  were found to be more diverse than proteome comparisons between species in genus  Brucella  and genus  Ochrobactrum . Pan-genomic analyses indicated that uptake of DNA from outside genus  Brucella  appears to be limited.    Conclusions  While both the proteome based methods and the Markov chain based genomic signatures were able to reflect environmental diversity between the different species and strains of genus  Brucella , the genomic codon and amino acid frequencies based comparisons were not found adequate for such comparisons. The proteome comparison based phylogenies of the species in genus  Brucella  showed a surprising consistency with current  Brucella  taxonomy.

Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods