Temporal Transcriptome Following Salmonella Enteritidis Infection In Chicken Cecum

Salmonella enteritidis(SE)is a common zoonotic pathogen that not only causes gastroenteritis or death of livestock and poultry,but also poses a serious threat to human health,causing severe economic losses to the poultry industry and society.The transcriptome plays important role in regulating SE infection.The high throughput next generation sequencing technology facilitate transcriptome analysis.In the current study,cecal trancriptome was analyzed following SE infection in Jining Bairi chicken through next generation sequencing.Two-day old SE free Jining Bairi chicken was inoculated with SE.The cecum was harvested from inoculated and control groups on 1,3,7,and 14 days after infection.Total RNA was isolated from 3 samples from each of inoculated and control groups.The libraries were constructed and sequenced using Illumina Hiseq 4000.The data were analyzed through bioinformatics.The results were followings:(1)After filtering,a total of 189.7 Gb data was obtained in 24 samples,and the average data of each sample was 7.9 Gb.Differentially expressed gene was performed between the inoculated group and control group.There were 530 significantly differentially expressed genes on day 1 post infection(1dpi)(P <0.05,| log2 fold change |> 1),of which 258 genes were up-regulated and 242 genes down-regulated.The number of significantly differentially expressed genes was 1441,of which 782 genes were up-regulated and 695 genes were down-regulated;There were 476 significantly differentially expressed genes identified on7 dpi,of which 264 genes were up-regulated and 212 genes were down-regulated;a total of432 significantly differentially expressed genes were found in 14 dpi,of which 283 genes were up-regulated and 149 down-regulated.(2)Functional enrichment of signaling pathways associated with differentially expressed gene showed that differentially expressed genes were significantly enriched in neuroactive ligand-receptor interactions,phagosomes,and PPAR signaling pathways on 1dpi.The differentially expressed genes were significantly enriched in 21 pathways including cytokine-cytokine-receptor interaction,Toll-like receptor signaling pathway,and retinol metabolism on 3dpi.The differentially expressed genes were significantly enriched in 14 pathways including neuroactive ligand-receptor interactions,cell adhesion molecules(CAMs),and alpha-linolenic acid metabolism on 7dpi.The differentially expressed genes were significantly enriched in 10 pathways such as histidine metabolism and MAPK signaling pathway 14 dpi.(3)Gene ontology(GO)enrichment of differentially expressed genes showed that up-regulated genes were significantly enriched to anion transport,organic anion transport,ion transport,transporter active ion transmembrane transport activity,and carboxylic acid transmembrane transport activity and other terms;down-regulated genes were significantly enriched in multicellular tissue processes,ion transmembrane transport,cell projection,sarcomere,etc.There were also 7 ion channel related terms such as ion channel activity,ion channel activity,and gate channel activity on 1dpi.On 3dpi,the up-regulated genes were significantly enriched in a large number of immune-related terms such as immune system process,immune response,defense response,leukocyte activation,interleukin-8 receptor binding,etc.The down-regulated genes were significantly enriched in terms of ion transport and metabolism in biological processes.On 7dpi,up-regulated genes are mainly enriched in immune,cell membrane,and connection-related terms.The down-regulated genes are mainly concentrated in the outer cell membrane,heme binding,oxygen binding and other terms.On14 dpi,up-regulated genes were mainly concentrated in the signaling-related terms,while the down-regulated genes were mainly concentrated in the metabolic-related terms.(4)Weighted gene co-expression network analysis results showed that four modules of energy,non-coding processes,immunity,and development-related functions were associated with 1,3,7,and 14 dpi with 5,8,6 and 5 core genes were identified,respectively.The core genes of the module lightyellow were MAP3K14,COX5 A,UQCRQ,ELL,and HSPB11.The core genes of the module pink were KLHL12,NIP7,NOB1,ADAM9,AAAS,SCARB2,SARS,CHEK1.The core genes of the module green were GMFB,SLC2A14,TLR7,LCP1,SMAP2,TRAF2.The core genes of module green were MXRA8,CXCL14,C39A13,PODN,and ADAMTS10.(5)The results of the quantitative PCR of TLR7,CCL1,CXCL13,NCF1 C,FKBP5,and SOUL were consistent with that in the sequencing.In summary,the results demonstrated that the chicken cecal transcriptome regulation responding to Salmonella enteritidis is time-dependent.The regulation of Salmonella enteritidis infection in chickens is coordinated by multiple systems,mainly involving immunity,metabolism,and signal transduction.Immunity was induced at 3 and 7 dpi and then repressed,while metabolism was induced after 7dpi.Signal pathways such as cytokine-cytokine receptor interaction,Toll-like receptor signaling pathway,NOD-like receptor signaling pathway,intestinal immune network produced by IgA,MAPK,retinol metabolism,phagosomes,and linoleic acid metabolism play key roles in SE infection.ACE,CD28,TLR2 A,TLR7,CXCL14 and MAP3K14 play important roles in SE infection in chicken.