Temporal regulation of global gene expression in the caeca of chickens infected with Salmonella Typhimurium has not been investigated previously. In this study, we performed the transcriptome analysis of the caeca of Salmonella Typhimurium challenged chicks to understand the regulation of the mucosal immune system in a temporal manner. The Salmonella infection resulted in the activation of the caecal immune system by the upregulation of the differentially expressed genes (DEGs; false discovery rate (FDR) < 0.05; log2 fold change > 1) involved in biological pathways such as Toll-like receptor signaling pathway, Salmonella infection, cytokine-cytokine receptor interaction, phagosome, apoptosis and intestinal immune network for IgA production. The activation of biological pathways such as RIG-I-like receptor signaling pathway, ErbB signaling pathway and cellular senescence showed a time-dependent response of the host immune system. A 49% increase in the DEGs on day 7 compared with day 3 post-infection (p.i.) suggested a time-dependent role of multiple genes such as AvBD1, AvBD2, AvBD7, IL2, IL10, IL21, SIVA1, CD5, CD14 and GPR142 in the regulation of the immune system. Nested network analysis of the individual biological pathways showed that IL6 played a significant role in the immune system regulation by activating the pathways, including Toll-like receptor signaling pathway, Salmonella infection, intestinal immune network for IgA production and C-type lectin receptor signaling pathway. The downregulated DEGs (FDR < 0.05; log2 fold change < -1) showed that Salmonella challenge affected the functions of pathways, such as tryptophan metabolism, retinol metabolism, folate biosynthesis and pentose and glucoronate interconversions, suggesting the disruption of cellular mechanisms involved in nutrient synthesis, absorption and metabolism. Overall, the immune response was temporally regulated through the activation of Toll-like signaling receptor pathway, cytokine-cytokine interactions and Salmonella infection, where IL6 played a significant role in the modulation of caecal immune system against Salmonella Typhimurium. KEY POINTS: • The immune response to Salmonella Typhimurium challenge was temporally regulated in the caeca of chickens. • Many newly identified genes have been shown to be involved in the activation of the immune system. • Toll-like receptors and interleukins played a key role in immune system regulation.

中文翻译：

---

鼠伤寒沙门氏菌攻击的雏鸡盲肠的转录组谱分析表明，参与宿主粘膜免疫反应的基因差异表达。

以前尚未研究感染鼠伤寒沙门氏菌的鸡的盲肠中全局基因表达的时间调控。在这项研究中，我们进行了鼠伤寒沙门氏菌攻击小鸡盲肠的转录组分析，以了解粘膜免疫系统的调控。沙门氏菌感染通过上调涉及Toll样受体信号通路等生物途径的差异表达基因（DEGs;错误发现率（FDR）<0.05; log2倍变化> 1）导致盲肠免疫系统激活。 ，沙门氏菌感染，细胞因子与细胞因子受体的相互作用，吞噬体，细胞凋亡和产生IgA的肠道免疫网络。诸如RIG-I样受体信号传导途径等生物途径的激活，ErbB信号通路和细胞衰老表明宿主免疫系统的时间依赖性反应。与感染后第3天（pi）相比，第7天的DEG增加了49％，这表明多个基因（例如AvBD1，AvBD2，AvBD7，IL2，IL10，IL21，SIVA1，CD5，CD14和GPR142）具有时间依赖性调节免疫系统。对单个生物途径的巢式网络分析表明，IL6通过激活包括Toll样受体信号传导途径，沙门氏菌感染，IgA产生的肠道免疫网络和C型凝集素受体信号传导途径在内的途径，在免疫系统调节中发挥了重要作用。 。下调的DEGs（FDR <0.05； log2倍数变化<-1）表明沙门氏菌挑战影响了色氨酸代谢，视黄醇代谢，叶酸的生物合成以及戊糖和葡萄糖酸根的相互转化，表明破坏了参与营养素合成，吸收和代谢的细胞机制。总体而言，免疫反应是通过激活Toll样信号受体途径，细胞因子与细胞因子的相互作用以及沙门氏菌感染而暂时调节的，其中IL6在调节针对盲肠沙门氏菌的盲肠免疫系统中起着重要作用。要点：•鸡盲肠对鼠伤寒沙门氏菌攻击的免疫反应在时间上受到调节。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。表明破坏了参与营养素合成，吸收和代谢的细胞机制。总体而言，免疫反应是通过激活Toll样信号受体途径，细胞因子与细胞因子的相互作用以及沙门氏菌感染而暂时调节的，其中IL6在调节针对盲肠沙门氏菌的盲肠免疫系统中起着重要作用。要点：•鸡盲肠对鼠伤寒沙门氏菌攻击的免疫反应在时间上受到调节。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。表明破坏了参与营养素合成，吸收和代谢的细胞机制。总体而言，免疫反应是通过激活Toll样信号受体途径，细胞因子与细胞因子的相互作用以及沙门氏菌感染而暂时调节的，其中IL6在调节针对盲肠沙门氏菌的盲肠免疫系统中起着重要作用。要点：•鸡盲肠对鼠伤寒沙门氏菌攻击的免疫反应在时间上受到调节。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。免疫反应在时间上通过激活Toll样信号受体途径，细胞因子-细胞因子相互作用和沙门氏菌感染而受到调节，其中IL6在调节针对鼠伤寒沙门氏菌的盲肠免疫系统中起着重要作用。要点：•鸡盲肠对鼠伤寒沙门氏菌攻击的免疫反应在时间上受到调节。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。免疫反应在时间上通过激活Toll样信号受体途径，细胞因子-细胞因子相互作用和沙门氏菌感染而受到调节，其中IL6在调节针对鼠伤寒沙门氏菌的盲肠免疫系统中起着重要作用。要点：•鸡盲肠对鼠伤寒沙门氏菌攻击的免疫反应在时间上受到调节。•已显示许多新鉴定的基因与免疫系统的激活有关。•Toll样受体和白介素在免疫系统调节中起关键作用。•鸡盲肠在时间上调节了对鼠伤寒沙门氏菌攻击的免疫反应。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。•鸡盲肠在时间上调节了对鼠伤寒沙门氏菌攻击的免疫反应。•许多新发现的基因已显示参与免疫系统的激活。•Toll样受体和白介素在免疫系统调节中起关键作用。