Gene flow and species boundaries of the genus Salmonella.
Gene flow and species boundaries of the genus Salmonella.
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DOI：
10.1128/msystems.00292-23
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发表时间：
2023-08-31
期刊：
影响因子：
6.4
通讯作者：
中科院分区：
文献类型：
--
作者：
沙门氏菌属包括两个种，邦戈里沙门氏菌和肠沙门氏菌，这两种沙门氏菌可感染多种动物宿主。根据寄主范围、地理以及最近的遗传亲缘关系和系统发育关系等特征，将肠链霉菌内的多样性进一步划分为6-10个亚种。虽然沙门氏菌的致病力可归因于大量的获得性毒力因子，但整个物种之间的同源交换程度明显受到限制，以至于物种和亚种形成了不同的菌株簇。为了探索亚种内和亚种间基因流动的程度，并最终定义真正的生物物种，我们评估了目前归入该属的1000多个基因组的重组模式。这些沙门氏菌亚种含有足够数量的已测序基因组，以进行有意义的分析--即亚种。肠道和腹泻亚科-被发现彼此之间以及与所有其他亚种之间存在生殖性分离。根据亚种间基因组序列差异的结构，预计其他沙门氏菌亚种中的每一个也将代表一个生物物种。我们的发现反对使用规定的核苷酸同一性阈值来描述细菌物种，并认为不应忽视细菌的生物物种概念，即使是那些表现出复杂的物种模式和亚种分化的细菌，如沙门氏菌。生物物种概念(BSC)定义了基于基因交换能力的物种边界，被广泛用于有性繁殖真核生物的分类，但通常认为不适用于细菌，因为它们完全无性繁殖模式。我们表明，沙门氏菌属，其数千个被描述的血清型以前被认为是严格克隆的，经历了足够程度的同源重组，根据BSC将其归类为物种。除了两个公认的种--肠沙门氏菌和邦格里沙门氏菌外，肠沙门氏菌内的几个亚种(可能是全部)是相互生殖分离的，每个亚种都应该被认为是单独的生物物种。这些发现表明，尽管核苷酸同源性很高，但细菌中的物种屏障可能会形成，而且常用的基因组序列同一性阈值并不是细菌物种状况的可靠指标。
The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6–10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis—i.e., subsp. enterica and diarizonae—were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.
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影响因子：
4.4
作者：
Pearce ME;Langridge GC;Lauer AC;Grant K;Maiden MCJ;Chattaway MA
通讯作者：
Chattaway MA
影响因子：
3.2
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作者：
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