Brucella microti: the genome sequence of an emerging pathogen

Abstract

Background: Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly pathogenic facultative intracellular bacteria. In contrast to all other Brucella species, B. microti is a fast growing and biochemically very active microorganism with a phenotype more similar to that of Ochrobactrum, a facultative human pathogen. The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum.

Results: The genome is composed of two circular chromosomes of 2,117,050 and 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of B. microti is almost identical to that of Brucella suis 1330 with an overall sequence identity of 99.84% in aligned regions. The most significant structural difference between the two genomes is a bacteriophage-related 11,742 base pairs insert only present in B. microti. However, this insert is unlikely to have any phenotypical consequence. Only four protein coding genes are shared between B. microti and Ochrobactrum anthropi but impaired in other sequenced Brucella. The most noticeable difference between B. microti and other Brucella species was found in the sequence of the 23S ribosomal RNA gene. This unusual variation could have pleiotropic effects and explain the fast growth of B. microti.

Conclusion: Contrary to expectations from the phenotypic analysis, the genome sequence of B. microti is highly similar to that of known Brucella species, and is remotely related to the one of O. anthropi. How the few differences in gene content between B. microti and B. suis 1330 could result in vastly different phenotypes remains to be elucidated. This unexpected finding will complicate the task of identifying virulence determinants in the Brucella genus. The genome sequence of B. microti will serve as a model for differential expression analysis and complementation studies. Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.

Figure 1

Dotplots of 7 Brucella and Ochrobactrum anthropi genomes against the two chromosomes of B. microti. B. microti chromosomes are in abscissa of each plot and the corresponding chromosomes of target genomes are in ordinate. In chromosome 2 plots, the 12 kbp region specific to B. microti is circled. Plots for B. abortus S19 and B. abortus 9–941 are not shown because of their similarity to the plot for B. melitensis biovar abortus 2308. In the case of O. anthropi, the dotplots of the two chromosomes of B. microti against the 2 large chromosomes of O. anthropi are shown. O. anthropi plasmids are not shown as they have no similarity with B. microti chromosomes.

Figure 2

Phylogenetic representation of the alignment of 1,486 groups of orthologous genes from 8 available Brucella genome sequences and that of O. anthropi. The long branch leading to O. anthropi has been shortened. Even though B. suis and B. microti are not found within the same clade, they both exhibit a slower evolution rate than most other Brucella species (as shown by their short branch length) resulting in a high overall similarity at the genome sequence level.

Figure 3

Alignment of the region around intervening sequence (IVS I) in selected Brucella and O. anthropi. Fragments of the alignment where all sequences are identical are not shown. The whole alignment with numbering is given in Additional file 5. Sequence fragments shared by B. microti and Brucella sp. B01 are in blue. Sequence fragments shared by B. microti and O. anthropi are in green. Other regions are in red. Fragments of the alignment highlighted in yellow correspond to the terminal nucleotides of the secondary structures represented in Figure 4.

Figure 4

Predicted secondary structure of the intervening sequence (IVS I). The predicted secondary structure of the intervening sequences (IVS I) of the 23S ribosomal RNA in B. microti and Brucella sp. B01 (left), B. suis (middle) and O. anthropi (right). Arrows with a dark head represent conserved cleavage sites. Arrows with a thin head represent unconserved cleavage sites. In O. anthropi, only the lower part of the cleavage motif is present.