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Simple Summary: Salmonella enterica is a zoonotic pathogen in humans that causes gastrointestinal infections or more serious infections. Second only to poultry, pigs are the most common source of zoonotic Salmonella enterica infections. Although current pig farm disinfection is very strict, its positive detection rate is still very high. Resistance to commonly used antibiotics has been observed in various bacteria in recent decades, requiring the use of alternative strategies to control pathogens. Therefore, comprehension of the pathogenic mechanism of Salmonella enterica in the pig gut is imperative, as it will greatly facilitate the advancement of preventive and therapeutic approaches for combating Salmonella enterica. By exploring the transcriptional regulation of intestinal cells in response to Salmonella enterica infection, we can find the key genes and pathways of host cells in resistance to Salmonella enterica infection, which will provide theoretical support for disease resistance breeding in pigs. Pigs can be colonized with Salmonella enterica and become established carriers. However, the mechanisms of the host's response to Salmonella enterica infection are largely unclear. This study was constructed with the Salmonella enterica infection model in vitro using porcine intestinal epithelial cells (IPEC-J2). Transcriptome profiling of IPEC-J2 cells was carried out to characterize the effect of Salmonella enterica infection and lipopolysaccharide (LPS) treatment, in which LPS-induced inflammation was a positive control. At first, Salmonella enterica infection increased the cell apoptosis rate and induced an inflammation response in IPEC-J2. Then, the up-regulated genes were enriched in metabolic pathways, such as those for bile secretion and mineral absorption, while down-regulated genes were enriched in immune-related pathways, such as the Toll-like receptor signaling and p53 signaling pathways. Moreover, we found 368 up-regulated genes and 101 down-regulated genes in common. Then, an integrative analysis of the transcriptomic profile under Salmonella enterica infection and LPS treatment was conducted, and eight up-regulated genes and one down-regulated gene were detected. Among them, AQP8 is one critical gene of the bile secretion pathway, and its mRNA and protein expression were increased significantly under Salmonella enterica infection and LPS treatment. Thus, the AQP8 gene and bile secretion pathway may be important in IPEC-J2 cells under Salmonella enterica infection or LPS treatment. [ABSTRACT FROM AUTHOR]

Deoxynivalenol (DON) is a type of mycotoxin that threatens human and livestock health. Right open reading frame kinase 2 (RIOK2) is a kinase that has a pivotal function in ribosome maturation and cell cycle progression. This study aims to clarify the role of the RIOK2 gene in DON-induced cytotoxicity regulation in porcine intestinal epithelial cells (IPEC-J2). Cell viability assay and flow cytometry showed that the knockdown of RIOK2 inhibited proliferation and induced apoptosis, cell cycle arrest, and oxidative stress in DON-induced IPEC-J2. Then, transcriptome profiling identified candidate genes and pathways that closely interacted with both DON cytotoxicity regulation and RIOK2 expression. Furthermore, RIOK2 interference promoted the activation of the MAPK signaling pathway by increasing the phosphorylation of ERK and JNK. Additionally, we performed the dual-luciferase reporter and ChIP assays to elucidate that the expression of RIOK2 was influenced by the binding of transcription factor Sp1 with the promoter region. Briefly, the reduced expression of the RIOK2 gene exacerbates the cytotoxic effects induced by DON in IPEC-J2. Our findings provide insights into the control strategies for DON contamination by identifying functional genes and effective molecular markers. [ABSTRACT FROM AUTHOR]

Simple Summary: The aim of this study is to investigate the relationship between fecal microbiota and the backfat thickness of pigs by 16S rRNA gene sequencing. Our study found that there were significant differences in the composition of microbiota at the species level, characterized by a higher abundance of Lactobacillus reuteri (L. reuteri) in pigs with low-backfat thickness. Additionally, functional profiling of microbial communities indicated that the isoquinoline alkaloid biosynthesis, arachidonic acid metabolism, and styrene degradation were significantly different between low- and high-backfat thickness groups. Furthermore, feeding L. reuteri reduced the intake-to-gain ratio and had the potential to reduce backfat thickness. These findings show that microbiota could alter the production performance of pigs. The backfat thickness of pigs not only affects the physical properties and taste of meat, but it also closely relates to the reproduction performance of sows. Accumulating evidence indicates that, apart from genetic factors, gut microbiota can also modulate the fat deposition and muscle growth. However, the differential microbiota in pigs with different backfat thickness, and whether microbiota affects backfat thickness, remains elusive. Firstly, 16S ribosomal RNA (16S rRNA) gene sequencing was performed on 62 fecal samples from pigs with different backfat thicknesses, and the compositions of microbiota among different groups with different backfat thicknesses were different. The abundance of Lactobacillus. reuteri (L. reuteri) and Prevotella sp RS2 was significantly higher in pigs with low-backfat thickness than that in pigs with middle and high-backfat thickness; meanwhile, the abundance of Desulfovibrio piger was significantly lower (p < 0.05) in pigs with low-backfat thickness. Furthermore, the functional profiling of microbial communities suggested that the abundance of isoquinoline alkaloid biosynthesis and styrene degradation were significantly lower (p < 0.05) in the low-backfat thickness group than that in middle and high-backfat thickness groups. Finally, L. reuteri fed to Meishan piglets was capable of improving the production performance and had the potential to reduce backfat thickness. This study provides new evidence that microbiota can regulate the phenotype of the host, and dietary supplementation with L. reuteri can improve the production performance of piglets. [ABSTRACT FROM AUTHOR]

To enrich the map of genomic variations in swine, we randomly sequenced 13 domestic and wild individuals from China and Europe. We detected approximately 28.1 million single nucleotide variants (SNVs) and 3.6 million short insertions and deletions (INDELs), of which 2,530,248 SNVs and 3,456,626 INDELs were firstly identified compared with dbSNP 143. Moreover, 208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs, potentially accounting for phenotypic differences between Chinese and European pigs. Furthermore, significantly high correlation between SNV and INDEL was witnessed, which indicated that these two distinct variants may share similar etiologies. We also predicted loss of function genes and found that they were under weaker evolutionary constraints. This study gives interesting insights into the genomic features of the Chinese pig breeds. These data would be useful in the establishment of high-density SNP map and would lay a foundation for facilitating pig functional genomics study. [ABSTRACT FROM AUTHOR]

Simple Summary: Porcine epidemic diarrhea virus causes serious diarrhea in suckling piglets, resulting in huge economic losses in the pig industry. A better understanding of porcine epidemic diarrhea virus (PEDV) pathogenesis and identification of the responsive genes will contribute to controlling PEDV infection. Therefore, screening and identifying PEDV-resistance functional genes and then implementing disease resistance breeding have important scientific significance. This study explores the regulatory roles of the GLP-2 gene in regulating PEDV infection and in repairing the intestinal mucosa damage associated with PEDV infection. The findings may contribute to the identification of resistant genes or genetic markers for disease resistance breeding in pigs. Porcine epidemic diarrhea virus (PEDV) infects intestinal epithelial cells, destroys the intestinal mucosal barrier and then causes diarrhea in piglets. Glucagon-like peptide-2 (GLP-2) is a specific intestinal growth hormone that promotes the repair of damaged intestinal mucosa and improves the intestinal barrier. In this study, we investigated the functions of porcine GLP-2 gene in regulating PEDV infection. The intestinal tissues with damaged intestinal structures caused by PEDV infection were first confirmed and collected. Expression analysis indicated that the GLP-2 gene was expressed in the duodenum, jejunum and ileum tissues, and the mRNA level was significantly down-regulated in jejunum and ileum of piglets with damaged intestinal mucosa. Infection of PEDV to porcine small intestinal epithelial cells in vitro showed that GLP-2 gene was significantly decreased, which was consistent with the expression pattern in intestinal tissues. In addition, we silenced the GLP-2 gene by shRNA interfering and found that the copy numbers of PEDV were remarkably increased in the GLP-2 gene silencing cells. Our findings suggest that the GLP-2 gene was potentially involved in regulating PEDV infection and in maintaining the integrity of the intestinal mucosal barrier structure, which could contribute to our understanding of the mechanisms of PEDV pathogenesis and provide a theoretical basis for the identification and application of resistant genes in pig selective breeding for porcine epidemic diarrhea. [ABSTRACT FROM AUTHOR]

• We constructed a APN -knockout IPEC-J2 cell line using the CRISPR/Cas 9 technology. • APN knockout seemed to have caused G1 phase blockage, inhibiting cell proliferation. • APN knockout improved the resistance of IPEC-J2 cells to PEDV. • A SNP in the APN promoter region participated in gene expression regulation. The expression level of aminopeptidase N (APN) is evidently correlated with porcine epidemic diarrhea virus (PEDV) infectivity. This study aims to examine the mechanisms regulating APN expression level in response to PEDV infection. Quantitative real time PCR was performed herein to detect gene expression dynamics at various timepoints after PEDV infection. Subsequently, CRISPR/Cas9 gene editing technology was used to generate a APN -knockout IPEC-J2 cell line, exploring the effects of APN on cell proliferation by propidium iodide staining and anti-PEDV activity by indirect immunofluorescence assay. Ultimately, the effects of single nucleotide polymorphisms (SNPs) and methylation in the APN promoter region on gene expression were analyzed by using bisulfite sequencing PCR and dual luciferase reporter gene assay. APN expression was significantly upregulated within 4–24 h post-infection. The cytoactivity of the APN -knockout IPEC-J2 cell line was markedly suppressed at different timepoints. Further, cell cycle analyses indicated an increase in the number of G1-phase cells and a significant decrease in that of S-phase cells. Moreover, key cyclical factors regulating the G1 phase were highly expressed in APN -knockout cells. The RNA copies of viral particles and mRNA levels of antiviral genes and inflammatory cytokines in APN-knockout cells were markedly decreased within 24 h of PEDV infection. Similarly, indirect immunofluorescence assay confirmed that the number of PEDV particles was significantly decreased. Sequence analysis revealed two CpG islands in the APN promoter region. However, there was no evident correlation between the methylation status of APN promoter and mRNA levels. Dual luciferase reporter gene assay showed that the SNP rs326030589 (G/A) significantly increased the promoter activity of APN. These results suggested that APN knockout enhanced the resistance of IPEC-J2 cells to PEDV. Moreover, rs326030589 in the APN promoter region participated in gene transcription regulation. Our results provide a reference for studying the mechanisms regulating APN and may contribute to the application of APN gene in resistance breeding of swine epidemic diarrhea. [ABSTRACT FROM AUTHOR]