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

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 Computed

本数据集包含对11168-G（已完成基因组测序）与11168-O（原始临床分离株）的转录组分析（RNA杂交（RNA hybridization）），菌株分别在微需氧及厌氧（文献中称为‘严重限氧（severely O₂-limited）’）条件下培养。该数据发表于Gaynor等人于《细菌学杂志（Journal of Bacteriology）》第186卷第503-517页的研究。
2000年，肠道致病菌空肠弯曲杆菌（Campylobacter jejuni）NCTC 11168（即11168-GS）的基因组序列得以发表，为鉴定空肠弯曲杆菌特异性定殖与毒力因子提供了重要资源。令人意外的是，后续研究发现，与其他菌株相比，11168-GS克隆株经口攻毒后对1日龄雏鸡的定殖能力极弱。与之相反，本研究发现，11168-GS的原始临床分离株11168-O对雏鸡具有优异的定殖能力。同时还发现了其他显著的表型差异：11168-O入侵并穿透组织培养细胞的效率与速度均远高于11168-GS，其运动能力显著更强，且形态也存在差异。血清型鉴定、多种高分辨率分子基因分型技术及消减杂交（subtractive hybridization）均未在这两个变体间检测到可观测的遗传差异，提示二者为克隆同源株。然而，在微需氧与严重限氧条件下对这两株菌进行的芯片转录组分析（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（operon），提示对不同氧张力的适应可能影响菌株的定殖潜能。这与本研究的生物学观测结果一致：对11168-GS进行厌氧预培养，或对11168-O进行有氧传代，分别可使其相较于亲本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不明确的潜在运动相关基因也存在表达差异。对σ因子（sigma factors）进行靶向测序后，发现了其他基因组学方法未检测到的特异性DNA序列差异。本数据集采用全配对实验设计（all pairs experiment design），即所有标记样本间均进行两两比对。关键词：all_pairs（全配对），计算所得。