Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades.
Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades.
复制标题
双歧杆菌基因组的系统基因组分析和比较研究：双歧杆菌目及其不同亚支特异分子特征的鉴定。
DOI：
10.3389/fmicb.2016.00978
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发表时间：
2016
影响因子：
5.2
通讯作者：
Gupta RS
中科院分区：
文献类型：
--
作者：
Zhang G;Gao B;Adeolu M;Khadka B;Gupta RS
双歧杆菌目包括在人类和其他动物的胃肠道中发现的各种物种，其中一些是机会性病原体，而另一些则表现出促进健康的作用。然而，目前已知的双歧杆菌目或该目中特定的分支的生化或分子特征很少，这是它们与其他细菌的区别。本研究报告了来自双歧杆菌目的62个种/菌株的详细比较基因组和系统发育研究结果。在基于614个核心蛋白构建的双歧杆菌属系统发育树中，观察到了一些分辨良好的分支，包括将Scarodvia相关属(Scardovia Clade)与双歧杆菌属和加德纳氏菌属分开的一个分支，以及一些以前报道的双歧杆菌属簇。同时，我们对双歧杆菌基因组中的蛋白质序列进行了比较分析，发现了许多针对这类细菌的分子标记。在这些标记中，分布广泛的蛋白质中的32个保守签名INDELs(CSI)和10个签名蛋白质是所有测序的双歧杆菌物种的显著特征，为区分这些细菌提供了新的和高度特异的手段。此外，多个其他分子标记是双歧杆菌属以下分支所特有的：(I)5个CSIS，专用于由Scardovia相关属组成的一个分支；(Ii)3个CSIS和2个CSP，专用于由双歧杆菌和加德纳氏菌组成的一个分支；(Iii)多个其他标记，用于区分星状双歧杆菌和长双歧杆菌相关物种的若干簇。所描述的分子标记为从分子上区分双歧杆菌和它们的若干分支以及对这些细菌进行分类提供了新的可靠的手段。在重要蛋白质中发现的双歧杆菌特异性CSI，被预测在改变受影响蛋白质的细胞功能方面发挥重要作用。因此，对这些CSI的细胞功能的生化研究可能会导致发现所有双歧杆菌或该目中特定细菌群的新特征。受这些基因变化影响/修改的一些功能对双歧杆菌的益生菌/致病活性也可能是重要的。
The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.