Analysis of Gene Expression Responses to a Salmonella Infection in Rugao Chicken Intestine Using GeneChips

Effects of Probiotic Enterococcus faecium from Yak on the Intestinal Microflora and Metabolomics of Mice with Salmonella Infection

Salmonella spp. are pathogenic bacteria that cause diarrhea, abortion, and death in yak and severely harm livestock breeding. Therefore, it is vital to identify a probiotic that effectively antagonizes Salmonella. To the best of our knowledge, few prior studies have investigated the efficacy of Enterococcus faecium against Salmonella. Here, we evaluated the enteroprotective mechanism of E. faecium in a mouse Salmonella infection model using hematoxylin-eosin (H&E) staining, quantitative real-time polymerase chain reaction (Q-PCR) technology, microbial diversity sequencing, and metabonomics. Enterococcus faecium inhibited the proinflammatory cytokines IL-1β, IL-6, TNF-α, and IFN-γ and promoted the anti-inflammatory cytokine IL-10. The Firmicutes/Bacteroidota (F/B) ratio and the abundances of Firmicutes and Akkermansia were significantly higher in the E. faecium than in the Salmonella group. Metabonomics and microbial diversity sequencing disclosed five different metabolites with variable importance in the projection (VIP) > 3 that were characteristic of both the Salmonella and E. faecium groups. Combined omics revealed that Lactobacillus and Bacteroides were negatively and positively correlated, respectively, with cholic acid, while Desulfovibrio was positively correlated with lipids in both the control and Salmonella groups. Desulfovibrio was also positively correlated with lipids in both the Salmonella and E. faecium groups. Enterococcus faecium antagonizes Salmonella by normalizing the abundance of the intestinal microorganisms and modulating their metabolic pathways. Hence, it may efficaciously protect the host intestine against Salmonella infection.

Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis

Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 61 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 61, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.

Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation

BACKGROUND

Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study.

RESULTS

There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8946 differentially methylated genes (3639 hypo-methylated genes, 5307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated.

CONCLUSIONS

The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.

Transcriptome profiling analysis of caeca in chicks challenged with Salmonella Typhimurium reveals differential expression of genes involved in host mucosal immune response

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.

Changes of host DNA methylation in domestic chickens infected with Salmonella enterica

Cytosine methylation is an effective way to modulate gene transcription.However, very little is knownabout the epigenetic changes in the host that is infected with Salmonella enterica. In this study, we usedmethylatedDNA immunoprecipitation sequencing to analyse the genomewide DNA methylation changes in domestic chickens after infected with Salmonella. The level of DNA methylation was slightly higher in the genomic regions around the transcription start termination sites in a Salmonella-infected group compared to the controls. Overall, 879 peaks were differentially methylated between Salmonella-infected and control groups, among which 135 were located in the gene promoter regions. Genes including MHC class IV antigen, GABARAPL1, MR1 and KDM1B were shown to be methylated more heavily after infected with Salmonella, whereas DYNLRB2, SEC14L3 and ANKIB1 tended to have fewer methylated cytosine residues in the promoter regions.Gene interaction network analysis of differentiallymethylated genes in the promoter regions revealed extensive connections with immune-related genes, indicating the possible impact of infection with Salmonella on the epigenetic status of the host.

Corticosterone-Induced Lipogenesis Activation and Lipophagy Inhibition in Chicken Liver Are Alleviated by Maternal Betaine Supplementation

Background

We have shown previously that in ovo betaine injection can prevent nonalcoholic fatty liver induced by glucocorticoid exposure in chickens; yet it remains unknown whether feeding betaine to laying hens may exert similar effects in their progeny.

Objective

In this study, we fed laying hens a betaine-supplemented diet, and the progeny were later exposed chronically to corticosterone (CORT) to test hepatoprotective effects and further elucidate underlying mechanisms.

Methods

Rugao yellow-feathered laying hens (n = 120) were fed a basal (control, C) diet or a 0.5% betaine-supplemented (B) diet for 28 d before their eggs were collected for incubation. At 49 d of age, male chickens selected from each group were daily injected subcutaneously with solvent (15% ethanol; vehicle, VEH) or CORT (4.0 mg/kg body mass) for 7 d to establish a fatty liver model. Chickens in the 4 groups (C-VEH, C-CORT, B-VEH, and B-CORT) were killed at day 57. Plasma and hepatic triglyceride (TG) concentrations, as well as the hepatic expression of genes involved in lipogenesis and lipophagy, were determined.

Results

CORT induced a 1.6-fold increase in the plasma TG concentration (P < 0.05) and a 1.8-fold increment in the hepatic TG concentration (P < 0.05), associated with activation of lipogenic genes (70-780%). In contrast, lipophagy and mitochondrial β-oxidation genes were inhibited by 30-60% (P < 0.05) in CORT-treated chickens. These CORT-induced changes were completely normalized by maternal betaine supplementation or were partially normalized to intermediate values that were significantly different from those in the C-VEH and C-CORT groups. These effects were accompanied by modifications in CpG methylation and glucocorticoid receptor binding to the promoters of major lipogenic and lipophagic genes (P < 0.05).

Conclusions

These results indicate that maternal betaine supplementation protects male juvenile chickens from CORT-induced TG accumulation in the liver via epigenetic modulation of lipogenic and lipophagic genes.

Splenic gene expression profiling in White Leghorn layer inoculated with the Salmonella enterica serovar Enteritidis

Salmonella enterica serovar Enteritidis (SE) is a foodborne pathogen that can threaten human health through contaminated poultry products. Live poultry, chicken eggs and meat are primary sources of human salmonellosis. To understand the genetic resistance of egg-type chickens in response to SE inoculation, global gene expression in the spleen of 20-week-old White Leghorn was measured using the Agilent 4 × 44 K chicken microarray at 7 and 14 days following SE inoculation (dpi). Results showed that there were 1363 genes significantly differentially expressed between inoculated and non-inoculated groups at 7 dpi (I7/N7), of which 682 were up-regulated and 681 were down-regulated genes. By contrast, 688 differentially expressed genes were observed at 14 dpi (I14/N14), of which 371 were up-regulated genes and 317 were down-regulated genes. There were 33 and 28 immune-related genes significantly differentially expressed in the comparisons of I7/N7 and I14/N14 respectively. Functional annotation revealed that several Gene Ontology (GO) terms related to immunity were significantly enriched between the inoculated and non-inoculated groups at 14 dpi but not at 7 dpi, despite a similar number of immune-related genes identified between I7/N7 and I14/N14. The immune response to SE inoculation changes with different time points following SE inoculation. The complicated interaction between the immune system and metabolism contributes to the immune responses to SE inoculation of egg-type chickens at 14 dpi at the onset of lay. GC, TNFSF8, CD86, CD274, BLB1 and BLB2 play important roles in response to SE inoculation. The results from this study will deepen the current understanding of the genetic response of the egg-type chicken to SE inoculation at the onset of egg laying.