Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
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DOI：
10.1186/1471-2148-10-249
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发表时间：
2010-08-13
影响因子：
3.4
通讯作者：
Godfroid, Jacques
中科院分区：
文献类型：
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作者：
Bohlin, Jon;Snipen, Lars;Godfroid, Jacques
背景资料：尽管表型存在明显差异，但对布氏杆菌属内的细菌进行分类一直很困难，部分原因是不同物种和生物群之间存在相当大的基因组同质性。因此，许多不同的方法已被用于评估布鲁氏菌分类。在目前的工作中，我们研究了32个测序的基因组从布鲁氏菌属代表的6个经典物种，以及最近描述的物种，使用生物信息学方法。在基因组DNA水平上，采用基于寡核苷酸的方法（基于Markov链的基因组特征、基于基因组密码子和氨基酸频率的比较）和蛋白质组的方法（全对全BLAST蛋白质比较和泛基因组分析）进行比较。在所使用的基于寡核苷酸的方法之间也发现了差异。虽然基于马尔可夫链的基因组签名根据宿主偏好将布鲁氏菌属中的不同物种分组，但基于密码子和氨基酸频率的方法反映了布鲁氏菌物种之间的微小差异。只有微小的差异，可以检测到在本研究中使用的密码子和氨基酸频率为基础的方法之间的所有属。蛋白质组比较被发现是在强烈符合目前的布鲁氏菌分类表明基因的获得或损失之间的显着关联，一方面和标记基因的突变，另一方面。基于蛋白质组学的方法发现布鲁氏菌属物种和苍白杆菌属物种之间的相似性大于农杆菌属内物种之间的相似性。换句话说，发现农杆菌属内物种的蛋白质组比较比布鲁氏菌属和苍白杆菌属物种之间的蛋白质组比较更加多样化。泛基因组分析表明，摄取的DNA从外属布鲁氏菌似乎是limited.Conclusions：虽然蛋白质组为基础的方法和马尔可夫链为基础的基因组签名是能够反映不同物种和菌株之间的环境多样性属布鲁氏菌，基因组密码子和氨基酸频率为基础的比较没有发现足够的这种比较。基于蛋白质组比较的布鲁氏菌属物种的同源性显示出与当前布鲁氏菌分类学惊人的一致性。
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.