School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia.
BMC Genomics. 2013 Aug 28;14:585. doi: 10.1186/1471-2164-14-585.
In spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of Campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. One proposed reason for this is the presence of high genetic diversity among the genomes of C. concisus strains.
In this study the genomes of six C. concisus strains were sequenced, assembled and annotated including two strains isolated from Crohn's disease patients (UNSW2 and UNSW3), three from gastroenteritis patients (UNSW1, UNSWCS and ATCC 51562) and one from a healthy individual (ATCC 51561). The genomes of C. concisus BAA-1457 and UNSWCD, available from NCBI, were included in subsequent comparative genomic analyses. The Pan and Core genomes for the sequenced C. concisus strains consisted of 3254 and 1556 protein coding genes, respectively.
Genes were identified with specific conservation in C. concisus strains grouped by phenotypes such as invasiveness, adherence, motility and diseased states. Phylogenetic trees based on ribosomal RNA sequences and concatenated host-related pathways for the eight C. concisus strains were generated using the neighbor-joining method, of which the 16S rRNA gene and peptidoglycan biosynthesis grouped the C. concisus strains according to their pathogenic phenotypes. Furthermore, 25 non-synonymous amino acid changes with 14 affecting functional domains, were identified within proteins of conserved host-related pathways, which had possible associations with the pathogenic potential of C. concisus strains. Finally, the genomes of the eight C. concisus strains were compared to the nine available genomes of the well-established pathogen Campylobacter jejuni, which identified several important differences in the respiration pathways of these two species. Our findings indicate that C. concisus strains are genetically diverse, and suggest the genomes of this bacterium contain respiration pathways and modifications in the peptidoglycan layer that may play an important role in its virulence.
尽管空肠弯曲菌与胃肠炎和炎症性肠病有关,但从患病和健康个体中分离出空肠弯曲菌,导致其作为肠道病原体的作用存在争议。其原因之一是空肠弯曲菌菌株的基因组存在高度遗传多样性。
本研究对 6 株空肠弯曲菌菌株的基因组进行了测序、组装和注释,包括从克罗恩病患者中分离出的 2 株(UNSW2 和 UNSW3)、3 株从胃肠炎患者中分离出的(UNSW1、UNSWCS 和 ATCC51562)和 1 株从健康个体中分离出的(ATCC51561)。可从 NCBI 获得的空肠弯曲菌 BAA-1457 和 UNSWCD 基因组也包含在随后的比较基因组分析中。测序的空肠弯曲菌菌株的泛基因组和核心基因组分别由 3254 和 1556 个编码蛋白的基因组成。
根据侵袭性、粘附性、运动性和疾病状态等表型对空肠弯曲菌菌株进行分组,确定了具有特定保守性的基因。基于核糖体 RNA 序列和 8 株空肠弯曲菌宿主相关途径的串联构建的系统发育树,采用邻接法生成,其中 16S rRNA 基因和肽聚糖生物合成将空肠弯曲菌菌株按其致病表型分组。此外,在保守宿主相关途径的蛋白质中发现了 25 个非同义氨基酸变化,其中 14 个影响功能域,这些变化可能与空肠弯曲菌菌株的致病潜力有关。最后,将 8 株空肠弯曲菌的基因组与 9 株已建立的病原体空肠弯曲菌的基因组进行比较,发现这两个物种的呼吸途径存在几个重要差异。我们的研究结果表明,空肠弯曲菌菌株具有遗传多样性,并表明该细菌的基因组包含呼吸途径和肽聚糖层的修饰,这可能在其毒力中发挥重要作用。