Institute of Environmental Science and Research Ltd, P.O. Box 29181, Christchurch 8540, New Zealand.
School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia.
Syst Appl Microbiol. 2021 May;44(3):126187. doi: 10.1016/j.syapm.2021.126187. Epub 2021 Feb 20.
Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237 and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237 and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
虽然已经有充分的证据证明弯曲菌属中的紧密型弯曲杆菌至少存在两个遗传上不同的群体或基因组种，但尚未确定其分化的表型，因此尚未正式描述为独立的种。弯曲菌属中的紧密型弯曲杆菌已从人体的各种部位分离出来，包括健康和腹泻个体的唾液和粪便样本。我们使用收集的 190 个弯曲菌属中的紧密型弯曲杆菌基因组，评估了一系列基于全基因组的工具区分两种弯曲菌属中的紧密型弯曲杆菌基因组种（GS）的能力。一些分析中包括了相关弯曲菌属种的 9 个基因组，以提供背景信息。结合多个核糖体基因的序列分析进行的分析与全基因组比较产生了相似水平的弯曲菌属中的紧密型弯曲杆菌 GS 区分能力。弯曲菌属中的紧密型弯曲杆菌基因组形成了两个群体；GS1 由 ATCC 33237 代表，GS2 由 CCUG 19995 代表。两种弯曲菌属中的紧密型弯曲杆菌 GS 与 9 个相关种的基因组分离。GS1 和 GS2 之间的 G+C 含量也存在差异，中位数分别为 37.56%和 39.51%。这两个群体与之前建立的 GS 一致，并得到 DNA 重配结果的支持。使用 MUMmer（ANIm）和全基因组 BLAST 距离系统发育（针对 ATCC 33237 和 CCUG 19995）生成的平均核苷酸同一性（ANI）和基因组杂交（in silico DNA-DNA hybridization，isDDH），再加上 G+C 含量提供了独立于聚类的 GS 区分方法，适合常规使用。泛基因组分析鉴定了 GS1 和 GS2 特有的基因。WGS 数据和基因组物种鉴定方法支持弯曲菌属中的紧密型弯曲杆菌存在两种 GS。这些数据为菌株鉴定到基因组种水平提供了基因组水平的度量标准。
