Zhang Grace, Gao Beile, Adeolu Mobolaji, Khadka Bijendra, Gupta Radhey S
Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada.
CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China.
Front Microbiol. 2016 Jun 27;7:978. doi: 10.3389/fmicb.2016.00978. eCollection 2016.
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.
双歧杆菌目包含在人类和其他动物胃肠道中发现的多种不同物种，其中一些是机会致病菌，而其他一些则具有促进健康的作用。然而，目前已知的针对双歧杆菌目或该目内特定进化枝的生化或分子特征非常少，这些特征可将它们与其他细菌区分开来。本研究报告了对来自双歧杆菌目62个基因组测序物种/菌株进行详细比较基因组学和系统发育研究的结果。在基于614个核心蛋白构建的双歧杆菌目稳健系统发育树中，观察到许多解析良好的进化枝，包括一个将与斯卡罗维亚菌属相关的菌属（斯卡罗维亚进化枝）与双歧杆菌属和加德纳菌属分开的进化枝，以及一些先前报道的双歧杆菌属物种簇。同时，我们对双歧杆菌目基因组蛋白序列的比较分析确定了许多针对这组细菌的分子标记。在这些标记中，广泛分布蛋白中的32个保守特征性插入缺失（CSIs）和10个特征蛋白是所有已测序双歧杆菌目物种的独特特征，为区分这些细菌提供了新颖且高度特异的方法。此外，还有多个其他分子特征针对以下双歧杆菌目进化枝：（i）5个特定于由与斯卡罗维亚菌属相关的菌属组成的进化枝的CSIs；（ii）3个CSIs和2个CSPs特定于由双歧杆菌属和加德纳菌属物种组成的进化枝；（iii）多个其他特征区分了许多与小行星双歧杆菌和长双歧杆菌相关的物种簇。所描述的分子标记为从分子角度区分双歧杆菌目及其一些进化枝以及对这些细菌进行分类提供了新颖且可靠的方法。在重要蛋白中发现的双歧杆菌目特异性CSIs预计在改变受影响蛋白的细胞功能中起重要作用。因此，对这些CSIs细胞功能的生化研究可能会导致发现所有双歧杆菌目或该目内特定细菌群的新特征。这些基因变化影响/修饰的一些功能对于双歧杆菌的益生菌/致病活性也可能很重要。
