Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.
Centre for Integrative Biology, University of Trento, Trento, Italy.
Infect Genet Evol. 2017 Dec;56:19-25. doi: 10.1016/j.meegid.2017.10.013. Epub 2017 Oct 11.
Phylogenetic studies of bacteria have been based so far either on a single gene (usually the 16S rRNA) or on concatenated housekeeping genes. For what concerns the genus Mycobacterium these approaches support the separation of rapidly and slowly growing species and the clustering of most species in well-defined phylogenetic groups. The advent of high-throughput shotgun sequencing leads us to revise conventional taxonomy of mycobacteria on the light of genomic data. For this purpose we investigated 88 newly sequenced species in addition to 60 retrieved from GenBank and used the Average Nucleotide Identity pairwise scores to reconstruct phylogenetic relationships within this genus.
Our analysis confirmed the separation of slow and rapid growers and the intermediate position occupied by the M. terrae complex. Among the rapid growers, the species of the M. chelonae-abscessus complex belonged to the most ancestral cluster. Other major clades of rapid growers included the species related to M. fortuitum and M. smegmatis and a large grouping containing mostly environmental species rarely isolated from humans. The members of the M. terrae complex appeared as the most ancestral slow growers. Among slow growers two deep branches led to the clusters of species related to M. celatum and M. xenopi and to a large group harboring most of the species more frequently responsible of disease in humans, including the major pathogenic mycobacteria (M. tuberculosis, M. leprae, M. ulcerans). The species previously grouped in the M. simiae complex were allocated in a number of sub-clades; of them, only the one including the species M. simiae identified the real members of this complex. The other clades included also species previously not considered related to M. simiae. The ANI analysis, in most cases supported by Genome to Genome Distance and by Genomic Signature-Delta Difference, showed that a number of species with standing in literature were indeed synonymous.
Genomic data revealed to be much more informative in comparison with phenotype. We believe that the genomic revolution enabled by high-throughput shotgun sequencing should now be considered in order to revise the conservative approaches still informing taxonomic sciences.
迄今为止，细菌的系统发育研究要么基于单个基因（通常是 16S rRNA），要么基于串联的管家基因。就分枝杆菌属而言，这些方法支持快速生长和缓慢生长物种的分离，以及大多数物种在明确的系统发育群中聚类。高通量测序技术的出现促使我们根据基因组数据来修正分枝杆菌的传统分类。为此，我们除了从 GenBank 中检索到的 60 个物种外，还研究了 88 个新测序的物种，并使用平均核苷酸同一性成对评分来重建该属内的系统发育关系。
我们的分析证实了慢生菌和快生菌的分离以及 M. terrae 复合体所占据的中间位置。在快生菌中，M. chelonae-abscessus 复合体的物种属于最原始的聚类。其他主要的快生菌类群包括与 M. fortuitum 和 M. smegmatis 相关的物种，以及一个包含大多数很少从人类中分离出来的环境物种的大型聚类。M. terrae 复合体的成员似乎是最原始的慢生菌。在慢生菌中，两个深分支导致与 M. celatum 和 M. xenopi 相关的物种聚类以及一个包含大多数更频繁导致人类疾病的物种的大型聚类，包括主要的致病性分枝杆菌（M. tuberculosis、M. leprae、M. ulcerans）。以前被归类在 M. simiae 复合体中的物种被分配到许多亚群中；其中，只有包括 M. simiae 物种的亚群才能确定这个复合体的真正成员。其他亚群还包括以前不认为与 M. simiae 相关的物种。ANI 分析，在大多数情况下得到了基因组到基因组距离和基因组特征差异的支持，表明许多文献中具有地位的物种实际上是同义的。
与表型相比，基因组数据显示出更多的信息。我们相信，高通量测序技术带来的基因组革命现在应该被考虑用于修正仍然为分类学科学提供信息的保守方法。
