Miller William G, Yee Emma, Lopes Bruno S, Chapman Mary H, Huynh Steven, Bono James L, Parker Craig T, Strachan Norval J C, Forbes Ken J
Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA.
School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom.
Genome Biol Evol. 2017 Jul 1;9(7):1843-1858. doi: 10.1093/gbe/evx093.
The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.
不耐热弯曲杆菌属物种胎儿弯曲杆菌、猪肠弯曲杆菌、鬣蜥弯曲杆菌和拉内弯曲杆菌在该属内形成一个独特的系统发育簇。这些物种主要从觅食（猪）或放牧（如牛、羊）动物中分离出来，导致偶发性且不常见的人类疾病。先前的分型研究基于多位点序列分型（MLST）或atpA序列数据，鉴定出三个假定的新型拉内弯曲杆菌相关分类单元。为了进一步表征这些假定的新型分类单元以及整个胎儿弯曲杆菌组，对76个基因组进行了测序，测序结果达到完成水平或草图水平。这些基因组代表26株拉内弯曲杆菌菌株和三个新型分类单元的50株菌株。胎儿弯曲杆菌、猪肠弯曲杆菌和鬣蜥弯曲杆菌的基因组先前已测序完成；因此，对整个胎儿弯曲杆菌组进行了比较基因组分析（包括平均核苷酸同一性分析），这支持了对这三个新型弯曲杆菌物种的初步鉴定。此外，拉内弯曲杆菌和这三个假定的新物种在胎儿弯曲杆菌组内形成一个离散的进化枝，我们将其称为拉内弯曲杆菌进化枝。该进化枝与胎儿弯曲杆菌组的其他成员的区别在于基因组大小减小和独特的CRISPR/Cas系统。此外，拉内弯曲杆菌进化枝有两个标志性特征。拉内弯曲杆菌进化枝的基因组携带4至10个不连锁且相似但不完全相同的鞭毛蛋白基因。此外，所有测序的76个拉内弯曲杆菌进化枝基因组都显示完全缺乏与硒代谢相关的基因，包括编码硒代半胱氨酸插入机制、硒蛋白和硒代半胱氨酰tRNA的基因。
