Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods
<p>Abstract</p> <p>Background</p> <p>Classification of bacteria within the genus <it>Brucella </it>has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. Ther...
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| Format: | Article |
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BMC
2010-08-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/10/249 |
| _version_ | 1819350223460237312 |
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| author | Bohlin Jon Snipen Lars Cloeckaert Axel Lagesen Karin Ussery David Kristoffersen Anja B Godfroid Jacques |
| author_facet | Bohlin Jon Snipen Lars Cloeckaert Axel Lagesen Karin Ussery David Kristoffersen Anja B Godfroid Jacques |
| author_sort | Bohlin Jon |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Classification of bacteria within the genus <it>Brucella </it>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 <it>Brucella </it>taxonomy. In the current work, we examine 32 sequenced genomes from genus <it>Brucella </it>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).</p> <p>Results</p> <p>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 <it>Brucella </it>according to host preference, the codon and amino acid frequencies based methods reflected small differences between the <it>Brucella </it>species. Only minor differences could be detected between all genera included in this study using the codon and amino acid frequencies based methods.</p> <p>Proteome comparisons were found to be in strong accordance with current <it>Brucella </it>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 <it>Brucella </it>species and <it>Ochrobactrum </it>species than between species within genus <it>Agrobacterium </it>compared to each other. In other words, proteome comparisons of species within genus <it>Agrobacterium </it>were found to be more diverse than proteome comparisons between species in genus <it>Brucella </it>and genus <it>Ochrobactrum</it>. Pan-genomic analyses indicated that uptake of DNA from outside genus <it>Brucella </it>appears to be limited.</p> <p>Conclusions</p> <p>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 <it>Brucella</it>, 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 <it>Brucella </it>showed a surprising consistency with current <it>Brucella </it>taxonomy.</p> |
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| last_indexed | 2024-12-24T19:13:00Z |
| publishDate | 2010-08-01 |
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| spelling | doaj.art-ce0188bc401c42238dae5990bd3bcae02022-12-21T16:42:58ZengBMCBMC Evolutionary Biology1471-21482010-08-0110124910.1186/1471-2148-10-249Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methodsBohlin JonSnipen LarsCloeckaert AxelLagesen KarinUssery DavidKristoffersen Anja BGodfroid Jacques<p>Abstract</p> <p>Background</p> <p>Classification of bacteria within the genus <it>Brucella </it>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 <it>Brucella </it>taxonomy. In the current work, we examine 32 sequenced genomes from genus <it>Brucella </it>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).</p> <p>Results</p> <p>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 <it>Brucella </it>according to host preference, the codon and amino acid frequencies based methods reflected small differences between the <it>Brucella </it>species. Only minor differences could be detected between all genera included in this study using the codon and amino acid frequencies based methods.</p> <p>Proteome comparisons were found to be in strong accordance with current <it>Brucella </it>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 <it>Brucella </it>species and <it>Ochrobactrum </it>species than between species within genus <it>Agrobacterium </it>compared to each other. In other words, proteome comparisons of species within genus <it>Agrobacterium </it>were found to be more diverse than proteome comparisons between species in genus <it>Brucella </it>and genus <it>Ochrobactrum</it>. Pan-genomic analyses indicated that uptake of DNA from outside genus <it>Brucella </it>appears to be limited.</p> <p>Conclusions</p> <p>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 <it>Brucella</it>, 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 <it>Brucella </it>showed a surprising consistency with current <it>Brucella </it>taxonomy.</p>http://www.biomedcentral.com/1471-2148/10/249 |
| spellingShingle | Bohlin Jon Snipen Lars Cloeckaert Axel Lagesen Karin Ussery David Kristoffersen Anja B Godfroid Jacques Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods BMC Evolutionary Biology |
| title | Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods |
| title_full | Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods |
| title_fullStr | Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods |
| title_full_unstemmed | Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods |
| title_short | Genomic comparisons of <it>Brucella </it>spp. and closely related bacteria using base compositional and proteome based methods |
| title_sort | genomic comparisons of it brucella it spp and closely related bacteria using base compositional and proteome based methods |
| url | http://www.biomedcentral.com/1471-2148/10/249 |
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