Kittichotirat W, Bumgarner R E, Chen C
Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok, Thailand.
Department of Microbiology, University of Washington, Seattle, USA.
J Dent Res. 2016 Jan;95(1):94-101. doi: 10.1177/0022034515608163. Epub 2015 Sep 29.
Gram-negative facultative Aggregatibacter actinomycetemcomitans is an oral pathogen associated with periodontitis. The genetic heterogeneity among A. actinomycetemcomitans strains has been long recognized. This study provides a comprehensive genomic analysis of A. actinomycetemcomitans and the closely related nonpathogenic Aggregatibacter aphrophilus. Whole genome sequencing by Illumina MiSeq platform was performed for 31 A. actinomycetemcomitans and 2 A. aphrophilus strains. Sequence similarity analysis shows a total of 3,220 unique genes across the 2 species, where 1,550 are core genes present in all genomes and 1,670 are variable genes (accessory genes) missing in at least 1 genome. Phylogenetic analysis based on 397 concatenated core genes distinguished A. aphrophilus and A. actinomycetemcomitans. The latter was in turn divided into 5 clades: clade b (serotype b), clade c (serotype c), clade e/f (serotypes e and f), clade a/d (serotypes a and d), and clade e' (serotype e strains). Accessory genes accounted for 14.1% to 23.2% of the A. actinomycetemcomitans genomes, with a majority belonging to the category of poorly characterized by Cluster of Orthologous Groups classification. These accessory genes were often organized into genomic islands (n = 387) with base composition biases, suggesting their acquisitions via horizontal gene transfer. There was a greater degree of similarity in gene content and genomic islands among strains within clades than between clades. Strains of clade e' isolated from human were found to be missing the genomic island that carries genes encoding cytolethal distending toxins. Taken together, the results suggest a pattern of sequential divergence, starting from the separation of A. aphrophilus and A. actinomycetemcomitans through gain and loss of genes and ending with the divergence of the latter species into distinct clades and serotypes. With differing constellations of genes, the A. actinomycetemcomitans clades may have evolved distinct adaptation strategies to the human oral cavity.
革兰氏阴性兼性放线共生放线杆菌是一种与牙周炎相关的口腔病原体。长期以来，人们一直认识到放线共生放线杆菌菌株之间存在遗传异质性。本研究对放线共生放线杆菌和密切相关的非致病性嗜二氧化碳嗜纤维菌进行了全面的基因组分析。利用Illumina MiSeq平台对31株放线共生放线杆菌和2株嗜二氧化碳嗜纤维菌进行了全基因组测序。序列相似性分析显示，这两个物种共有3220个独特基因，其中1550个是所有基因组中都存在的核心基因，1670个是至少在一个基因组中缺失的可变基因（辅助基因）。基于397个串联核心基因的系统发育分析区分了嗜二氧化碳嗜纤维菌和放线共生放线杆菌。后者又分为5个进化枝：进化枝b（血清型b）、进化枝c（血清型c）、进化枝e/f（血清型e和f）、进化枝a/d（血清型a和d）和进化枝e'（血清型e菌株）。辅助基因占放线共生放线杆菌基因组的14.1%至23.2%，其中大多数属于直系同源簇分类中特征不明确的类别。这些辅助基因通常被组织成具有碱基组成偏差的基因组岛（n = 387），表明它们是通过水平基因转移获得的。进化枝内菌株之间的基因含量和基因组岛的相似程度高于进化枝之间。从人类分离出的进化枝e'菌株被发现缺失携带编码细胞致死性膨胀毒素基因的基因组岛。综上所述，结果表明了一种顺序分化模式，从嗜二氧化碳嗜纤维菌和放线共生放线杆菌通过基因的获得和丢失而分离开始，到后者物种分化为不同的进化枝和血清型结束。由于基因组合不同，放线共生放线杆菌进化枝可能已经进化出了针对人类口腔的不同适应策略。
