Comprehensive miRNA expression profiles in the ilea of Lawsonia intracellularis-infected pigs

Identification of trait-associated microRNA modules in liver transcriptome of pig fed with PUFAs-enriched supplementary diet

Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the dietary effects of PUFAs on the hepatic transcriptome and physiological pathways of two diets on two pig breeds. Polish Landrace (PL: n = 6) and six PLxDuroc (PLxD: n = 6) pigs were fed with a normal diet (n = 3) or PUFAs-enriched healthy diet (n = 3), and the hepatic miRNA profiles were studied for weighted gene co-expression network analysis biological interactions between gene networks and metabolic pathways of DE miRNA genes. The study identified trait-associated modules that were significantly associated with four phenotypic traits in the dietary groups of PL and PLxD: meat colour (a*), shoulder subcutaneous fat thickness, conductivity 24 h post-mortem (PE24), and ashes. Trait-wise, a large set of co-expressed miRNAs of porcine liver were identified in these trait-associated significant modules (9, 7, 2, and 8) in PL and PLxD. Each module is represented by a module eigengene (ME). Forty-four miRNAs out of 94 miRNAs interacted with 6719 statistically significant target genes with a target score > 90. The GO/pathway analysis showed association with pathways including regulation of metallopeptidase activity, sebaceous gland development, collagen fibril organization, WNT signalling, epithelial tube morphogenesis, etc. The study showed the differences in miRNA expression between the dietary groups of PL and PLxD breeds. Hub genes of discovered miRNA clusters can be considered predicted miRNA genes associated with PE24, meat colour, shoulder subcutaneous fat thickness, and ashes. Discovered target genes for miRNA clusters play significant roles in biological functions such as (i) muscle and body growth development, (ii) different cellular processes and developments, (iii) system development, and (iv) metabolic processes.

Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population

Understanding the pig immune function is crucial for disease-resistant breeding and potentially for human health research due to shared immune system features. Immune cell ratios, like monocyte/lymphocyte ratio (MLR) and neutrophil/lymphocyte ratio (NLR), offer a more comprehensive view of immune status compared to individual cell counts. However, research on pig immune cell ratios remains limited. This study investigated MLR and NLR in a Duroc × Erhualian F2 resource population. Heritability analysis revealed high values (0.649 and 0.688 for MLR and NLR, respectively), suggesting a strong genetic component. Furthermore, we employed an ensemble-like GWAS (E-GWAS) strategy and functional annotation analysis to identify 11 MLR-associated and 6 NLR-associated candidate genes. These genes were significantly enriched in immune-related biological processes. These findings provide novel genetic markers and candidate genes associated with porcine immunity, thereby providing valuable insights for addressing biosecurity and animal welfare concerns in the pig industry.

miRNA Regulatory Functions in Farm Animal Diseases, and Biomarker Potentials for Effective Therapies

MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in major farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.

Noncoding RNAs: Regulatory Molecules of Host-Microbiome Crosstalk

Recent emerging evidence has revealed that regulatory noncoding RNAs (microRNAs, circular RNAs) modulate host-microbe interactions and they have been proposed as potential biomarkers of the host's response to microbiome-linked pathologies such as cancers, obesity, and neurodegenerative diseases. Interactions between microRNAs and circular RNAs, however, increase the complexity of the mechanisms that modulate host-microbe interactions. Current knowledge on these noncoding RNAs (ncRNAs) is mainly generated from well controlled germ-free or knockout (small) animal models. Application of such knowledge to effective modulation outcomes in humans (and livestock) is challenging due to the complex nature of microbiome-linked pathologies in larger outbred animals that constantly interact with the changing environment. This review critically discusses the findings of regulatory noncoding RNAs and their roles in microbiome-linked pathologies in small and large animals and provides insights on their roles as potential therapeutic agents to improve human (and livestock) health.

Identification of differentially expressed miRNAs after Lactobacillus reuteri treatment in the ileum mucosa of piglets

BACKGROUND

Lactobacillus reuteri I5007 possesses many excellent probiotic characteristics in piglets. miRNA plays important role in host-microbiota interactions, but the mechanism by which L. reuteri I5007 regulates intestinal function through its influence on miRNA expression is unknown.

OBJECTIVE

This study analyzed the miRNA expression patterns in the ileum mucosa tissue of piglets by L. reuteri I5007 treatment, aim to clarify its molecular mechanism for regulating intestinal function through miRNA.

METHODS

Neonatal piglets were orally administered L. reuteri I5007 or a placebo daily starting on day 1, and differential expression of ileal miRNAs was analyzed at 10 and 20 days of age by small RNA sequencing.

RESULTS

361 known porcine miRNAs were identified, and ten miRNAs were highly expressed in the ileum mucosa in both treatments. Nineteen differentially expressed (DE) miRNAs were identified in response to L. reuteri treatment, and four DE miRNAs (ssc-miR-196a, -196b-5p, -1285 and -10386) were differentially expressed at both time points. The KEGG pathway analyses showed the targets of 19 DE miRNAs were involved in 63 significantly enriched pathways, including the PI3K-Akt and MAPK pathways, which were confirmed to play important roles in probiotic-host communication. L. reuteri I5007 exerted anti-inflammatory effects by influencing the levels of inflammatory cytokines. Suppressor of cytokine signalling 4 gene was the target gene of ssc-miR-196a/-196b-5p, overexpression of ssc-miR-196a/-196b-5p downregulated the mRNA expression of IL-1β and TNFα in IPEC-J2 cells.

CONCLUSION

Our study provides new insight into the role of miRNAs in the intestinal function of piglets after L. reuteri I5007 treatment.

Systemic cytokine response in pigs infected orally with a Lawsonia intracellularis isolate of South Korean origin

In the swine industry, Lawsonia intracellularis is one of the main enteric pathogens; it causes acute intestinal hemorrhage (proliferative hemorrhagic enteropathy) in naïve adult pigs and a wasting disease (proliferative enteropathy) in growing pigs. Among many kinds of cytokines, interferon-γ (IFN-γ) has previously been reported to play a significant role in limiting intracellular infection and increasing cellular proliferation associated with L. intracellularis. However, the levels of various circulating inflammatory cytokines, including IFN-γ, in animals infected with L. intracellularis is still an area of considerable interest for understanding immunity against this bacterium. In addition, there has been no information on cytokine response in animals infected with any L. intracellularis isolate of South Korean origin or Asian origin. To determine the relationship between the changes in the systemic inflammatory cytokine response in the peripheral blood of the host after L. intracellularis infection, we measured the levels of some pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and IFN-γ), anti-inflammatory cytokines (IL-4, IL-10, and transforming growth factor-β (TGF-β)), and a chemokine (IL-8) in pigs infected with L. intracellularis isolated from South Korea. This study demonstrated that a L. intracellularis isolate of South Korean origin induced cytokine (TNF-α, IL-6, and IFN-γ) responses in infected animals within 15 days post-infection although the circulating levels of IL-4, IL-10, IL-8 and TGF-β were induced relatively late.