Limits...
Brucella microti: the genome sequence of an emerging pathogen.

Audic S, Lescot M, Claverie JM, Scholz HC - BMC Genomics (2009)

Bottom Line: 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.Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Information Génomique et Structurale, CNRS - UPR2589, Aix-Marseille University, Institut de Microbiologie de la Méditerranée (IM2, IFR-88), Parc Scientifique de Luminy, FR- 13288, Marseille cedex 09, France. stephane.audic@igs.cnrs-mrs.fr

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.

Show MeSH

Related in: MedlinePlus

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2743711&req=5

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.

Mentions: Dotplots (Figure 1) of the chromosomes of B. microti against the 8 Brucella genome sequences available at the time of writing and the genome sequence of O. anthropi show that: i) the overall genome structures of Brucella are remarkably conserved, ii) Brucella genomes are markedly different from that of O. anthropi and iii) based on this genome structure only, B. microti is more similar to B. suis 1330, B. canis and B. melitensis 16M than to the other genomes with which it has at least one major difference. Consistently, phylogenetic reconstruction based on a set of 1,486 orthologous genes clearly placed B. microti closer to B. suis 1330 than to any other Brucella (Figure 2). We thus based our subsequent analyses on the detailed comparison of B. microti and B. suis 1330.


Brucella microti: the genome sequence of an emerging pathogen.

Audic S, Lescot M, Claverie JM, Scholz HC - BMC Genomics (2009)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2743711&req=5

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.
Mentions: Dotplots (Figure 1) of the chromosomes of B. microti against the 8 Brucella genome sequences available at the time of writing and the genome sequence of O. anthropi show that: i) the overall genome structures of Brucella are remarkably conserved, ii) Brucella genomes are markedly different from that of O. anthropi and iii) based on this genome structure only, B. microti is more similar to B. suis 1330, B. canis and B. melitensis 16M than to the other genomes with which it has at least one major difference. Consistently, phylogenetic reconstruction based on a set of 1,486 orthologous genes clearly placed B. microti closer to B. suis 1330 than to any other Brucella (Figure 2). We thus based our subsequent analyses on the detailed comparison of B. microti and B. suis 1330.

Bottom Line: 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.Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Information Génomique et Structurale, CNRS - UPR2589, Aix-Marseille University, Institut de Microbiologie de la Méditerranée (IM2, IFR-88), Parc Scientifique de Luminy, FR- 13288, Marseille cedex 09, France. stephane.audic@igs.cnrs-mrs.fr

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.

Show MeSH
Related in: MedlinePlus