Comparison of NCTC 11168 isolate vs. genome-sequenced variant, microaerobic and anaerobic conditions. Campylobacter jejuni

Transcriptional analysis (RNA hybridization) for 11168-G (genome sequenced) vs. 11168-O (original), cultured microaerobically or anaerobically (published as "severely O2-limited). Published in Gaynor et al, J. Bacteriology 186:503-517 The genome sequence of the enteric bacterial pathogen Campylobacter jejuni NCTC 11168 (11168-GS) was published in 2000, providing a valuable resource for the identification of C. jejuni-specific colonization and virulence factors. Surprisingly, the 11168-GS clone was subsequently found to colonize 1-day-old chicks following oral challenge very poorly compared to other strains. In contrast, we have found that the original clinical isolate from which 11168-GS was derived, 11168-O, is an excellent colonizer of chicks. Other marked phenotypic differences were also identified: 11168-O invaded and translocated through tissue culture cells far more efficiently and rapidly than 11168-GS, was significantly more motile, and displayed a different morphology. Serotyping, multiple high-resolution molecular genotyping procedures, and subtractive hybridization did not yield observable genetic differences between the variants, suggesting that they are clonal. However, microarray transcriptional profiling of these strains under microaerobic and severely oxygen-limited conditions revealed dramatic expression differences for several gene families. Many of the differences were in respiration and metabolism genes and operons, suggesting that adaptation to different oxygen tensions may influence colonization potential. This correlates biologically with our observation that anaerobically priming 11168-GS or aerobically passaging 11168-O caused an increase or decrease, respectively, in colonization compared to the parent strain. Expression differences were also observed for several flagellar genes and other less well-characterized genes that may participate in motility. Targeted sequencing of the sigma factors revealed specific DNA differences undetected by the other genomic methods An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs Overall design: Computed本数据集为空肠弯曲杆菌（Campylobacter jejuni）NCTC 11168的两株菌的转录组分析（RNA hybridization）数据：分别为已完成基因组测序的11168-G，以及其原始临床分离株11168-O。菌株分别在微需氧或厌氧（文献中表述为“严重氧限制”）条件下培养。该项研究由Gaynor等人发表于《细菌学杂志》（Journal of Bacteriology）186卷第503-517页。 食源性细菌病原菌空肠弯曲杆菌NCTC 11168（简称11168-GS）的基因组序列于2000年发表，为鉴定空肠弯曲杆菌特异性定殖与毒力因子提供了宝贵的研究资源。令人意外的是，后续研究发现，11168-GS克隆株经口攻毒后对1日龄雏鸡的定殖能力远弱于其他菌株。与之相反，本研究发现11168-GS的原始亲本菌株11168-O则是雏鸡的高效定殖株。 此外还鉴定到其他显著表型差异：11168-O侵袭并穿过组织培养细胞的效率与速度均远高于11168-GS，运动能力显著更强，且形态存在明显差异。血清分型（serotyping）、多种高分辨率分子基因分型（molecular genotyping）技术以及消减杂交（subtractive hybridization）均未在这两个变异株间检测到可观测的遗传差异，提示二者为克隆同源株。 然而，在微需氧与严重氧限制条件下对两株菌开展的芯片转录组分析（microarray transcriptional profiling）显示，多个基因家族的表达存在显著差异。其中多数差异涉及呼吸与代谢相关基因及操纵子（operons），提示适应不同氧分压环境可能影响菌株的定殖潜能。这与本研究的生物学观察结果一致：对11168-GS进行厌氧预培养，或对11168-O进行有氧传代，分别会使其相较于亲本菌株的定殖能力上升或下降。 此外，多个鞭毛基因及其他功能尚未明确的运动相关基因也存在表达差异。对σ因子（sigma factors）的靶向测序（targeted sequencing）则发现了其他基因组学方法未能检测到的特异性DNA序列差异。 全配对实验设计指将所有标记提取物与其余所有标记提取物逐一进行比较的实验设计类型。 关键词：全配对 实验设计：已完成计算