Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars
Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars
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DOI：
10.1128/jb.00056-12
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发表时间：
2012-08-01
影响因子：
3.2
通讯作者：
Ehrlich, Garth D.
中科院分区：
文献类型：
--
作者：
Ahmed, Azad;Earl, Josh;Ehrlich, Garth D.
阴道加德纳菌与一系列临床状况有关，表明在染色物中存在高度的遗传异质性。17个阴道芽孢杆菌分离株进行了一系列比较基因组分析，以确定它们的亲缘关系水平。在23种至少有8个基因组可用的病原菌中，阴道芽孢杆菌菌株之间的差异程度最高。基因组大小为1.491 ~ 1.716 Mb；GC含量范围为41.18% ~ 43.40%；核心基因组仅由746个基因组成，平均只占每个菌株基因组的51.6%，只占物种超基因组的27%。利用分布基因占有数据和核心基因等位基因数据进行邻居分组分析，分别鉴定出两组主要菌株，每组由两组组成。4个类群各有其特有的基因组大小、GC比值，核心基因含量大大扩展，使得各类群的基因组多样性对于其他菌种而言都在一定范围内。为了检验这4个群体是否对应于基因分离的分支，我们推断了每个分布基因的系统发育，这些基因至少在两个菌株中存在，至少在两个菌株中不存在；该分析发现了组内频繁的同源重组，但组间或组间没有。阴道支原体似乎包括四个具有不同基因库和基因组特性的非重组生物群/分支，这可能赋予不同的生态特性。因此，将这四组作为单独的物种来对待可能是合适的。
Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.