Regionally Distinct Immune and Metabolic Transcriptional Responses in the Bovine Small Intestine and Draining Lymph Nodes During a Subclinical Mycobacterium avium subsp. paratuberculosis Infection

Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle

Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.

Modeling Paratuberculosis in Laboratory Animals, Cells, or Tissues: A Focus on Their Applications for Pathogenesis, Diagnosis, Vaccines, and Therapy Studies

Paratuberculosis is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. Paratuberculosis that affects a wide variety of domestic and wild animals. It is considered one of the diseases with the highest economic impact on the ruminant industry. Despite many efforts and intensive research, paratuberculosis control still remains controversial, and the existing diagnostic and immunoprophylactic tools have great limitations. Thus, models play a crucial role in understanding the pathogenesis of infection and disease, and in testing novel vaccine candidates. Ruminant animal models can be restricted by several reasons, related to space requirements, the cost of the animals, and the maintenance of the facilities. Therefore, we review the potential and limitations of the different experimental approaches currently used in paratuberculosis research, focusing on laboratory animals and cell-based models. The aim of this review is to offer a vision of the models that have been used, and what has been achieved or discovered with each one, so that the reader can choose the best model to answer their scientific questions and prove their hypotheses. Also, we bring forward new approaches that we consider worth exploring in the near future.

Viperin (RSAD2) gene expression in peripheral blood mononuclear cells of pregnant crossbred beef cows is altered by Bos indicus genetics

The expression of interferon (IFN) stimulated genes (ISGs) in lymphocytes has been used for pregnancy diagnosis in cattle. However, among-cow variability has yielded sub-optimal predictive accuracy. We hypothesized that the expression of ISGs (ISG15, OAS1, RSAD2, CLEC3B, and AKR1B1) in early pregnancy varies according to the proportion of Bos indicus (B. indicus) genetics on females. Multiparous cows were classified in three genetic groups, High Angus (HA; n = 45 [0-33% Brahman influence]), Angus-Brahman (AB; n = 30 [34-67%]), and High Brahman (HB; n = 19 [68-100%]) and submitted to a Select-Synch + CIDR protocol. Cows that displayed estrus (n = 94) were artificially inseminated (Day0; D0). On D19, blood samples were collected to obtain peripheral blood mononuclear cells (PBMC) and measure progesterone (P4) concentrations. On D30, pregnancy diagnosis was performed. The expression of RSAD2 in PBMC of pregnant cows was positively related to the proportion of B. indicus genetics of the groups, but not the expression of ISG15 and OAS1. In pregnant cows, the proportion of B. indicus genetics was negatively associated to circulating levels of P4 concentrations. The P4 concentrations were related positively with RSAD2 expression. ROC curve results determined that for cattle with B. indicus genetics lower than 67%, the CLEC3B and AKR1B1 combination was the most accurate option to predict the outcome of pregnancy. In cows with more than 68% of B. indicus genetics, RSAD2 provided the best accuracy. In conclusion, there is a relationship between the proportion of B. indicus genetics and the ISGs gene expression in PBMC during pregnancy.

Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria

Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases.

Impact of a Saccharomyces cerevisiae fermentation product during an intestinal barrier challenge in lactating Holstein cows on ileal microbiota and markers of tissue structure and immunity

Feeding a Saccharomyces cerevisiae fermentation product (SCFP; NutriTek, Diamond V, Cedar Rapids, IA) during periods of metabolic stress is beneficial to the health of dairy cows partially through its effect on the gut microbiota. Whether SCFP alters the ileal microbiota in lactating cows during intestinal challenges induced by feed restriction (FR) is not known. We used 16S rRNA sequencing to assess if feeding SCFP during FR to induce gut barrier dysfunction alters microbiota profiles in the ileum. The mRNA abundance of key genes associated with tissue structures and immunity was also detected. Multiparous cows (97.1 ± 7.6 days in milk (DIM); n = 7 per treatment) fed a control diet or the control plus 19 g/d NutriTek for 9 wk were subjected to an FR challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. All cows were slaughtered at the end of FR. DNA extracted from ileal digesta was subjected to PacBio Full-Length 16S rRNA gene sequencing. High-quality amplicon sequence analyses were performed with Targeted Amplicon Diversity Analysis and MicrobiomeAnalyst. Functional analysis was performed and analyzed using PICRUSt and STAMP. Feeding SCFP did not (P > 0.05) alter dry matter intake, milk yield, or milk components during FR. In addition, SCFP supplementation tended (P = 0.07) to increase the relative abundance of Proteobacteria and Bifidobacterium animalis. Compared with controls, feeding SCFP increased the relative abundance of Lactobacillales (P = 0.03). Gluconokinase, oligosaccharide reducing-end xylanase, and 3-hydroxy acid dehydrogenase were among the enzymes overrepresented (P < 0.05) in response to feeding SCFP. Cows fed SCFP had a lower representation of adenosylcobalamin biosynthesis I (early cobalt insertion) and pyrimidine deoxyribonucleotides de novo biosynthesis III (P < 0.05). Subsets of the Firmicutes genus, Bacteroidota phylum, and Treponema genus were correlated with the mRNA abundance of genes associated with ileal integrity (GCNT3, GALNT5, B3GNT3, FN1, ITGA2, LAMB2) and inflammation (AOX1, GPX8, CXCL12, CXCL14, CCL4, SAA3). Our data indicated that the moderate FR induced dysfunction of the ileal microbiome, but feeding SCFP increased the abundance of some beneficial gut probiotic bacteria and other species related to tissue structures and immunity.

Analysis of runs of homozygosity of cattle living in different climate zones

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation

Background

Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be improved through selective breeding. Using a large dataset of Holstein cows (161,253 animals including 56,766 cows with ELISA serological phenotypes and 12,431 animals with genotypes), we applied a single-step single nucleotide polymorphism (SNP) best linear unbiased prediction approach to investigate the genetic determinism underlying resistance to this disease (heritability estimate and identification of relevant genomic regions) and estimated genetic trends, reliability, and relative risk factors associated with genomic predictions.

Results

Resistance to JD was moderately heritable (0.14) and 16 genomic regions were detected that accounted for at least 0.05% of the breeding values variance (GV) in resistance to JD, and were located on chromosomes 1, 3, 5, 6, 7, 19, 20, 21, 23, 25, and 27, with the highest percentage of variance explained by regions on chromosomes 23 (0.36% GV), 5 (0.22% GV), 1 (0.14% GV), and 3 (0.13% GV). When estimated for the whole chromosomes, the autosomes with the largest overall contributions were chromosomes 3 (5.3% GV), 10 (4.8%), 23 (4.7%), 1 (3.6%), 7 (3.4%), 5 (2.9%), 12 (2.5%), 11 (2.2%), and 13 (2%). We estimated a slightly favorable genetic trend in resistance to JD over the last two decades, which can be explained by a low positive genetic correlation between resistance to JD and total merit index (+ 0.06). Finally, in a validation population of 907 cows, relatively reliable genomic predictions (reliability = 0.55) were obtained, which allowed the identification of cows at high risk of infection.

Conclusions

This study provides new insights into the genetic determinism of resistance to JD and shows that this trait can be predicted from SNP genotypes. It has led to the implementation of a single-step genomic evaluation that should rapidly become an effective tool for controlling paratuberculosis on French Holstein farms.

Local assessment of the immunohistochemical expression of Foxp3+ regulatory T lymphocytes in the different pathological forms associated with bovine paratuberculosis

Background

Mycobacterium avium subsp. paratuberculosis infected animals show a variety of granulomatous lesions, from focal forms with well-demarcated granulomas restricted to the gut-associated lymphoid tissue (GALT), that are seen in the initial phases or latency stages, to a diffuse granulomatous enteritis, with abundant (multibacillary) or scant (paucibacillary) bacteria, seen in clinical stages. Factors that determine the response to the infection, responsible for the occurrence of the different types of lesion, are still not fully determined. It has been seen that regulatory T cells (Treg) play an important role in various diseases where they act on the limitation of the immunopathology associated with the immune response. In the case of paratuberculosis (PTB) the role of Treg lymphocytes in the immunity against Map is far away to be completely understood; therefore, several studies addressing this subject have appeared recently. The aim of this work was to assess, by immunohistochemical methods, the presence of Foxp3⁺ T lymphocytes in intestinal samples with different types of lesions seen in cows with PTB.

Methods

Intestinal samples of twenty cows showing the different pathological forms of PTB were evaluated: uninfected controls (n = 5), focal lesions (n = 5), diffuse paucibacillary (n = 5) and diffuse multibacillary (n = 5) forms. Foxp3⁺ lymphocyte distribution was assessed by differential cell count in intestinal lamina propria (LP), gut-associated lymphoid tissue (GALT) and mesenteric lymph node (MLN).

Results

A significant increase in the number of Foxp3⁺ T cells was observed in infected animals with respect to control group, regardless of the type of lesion. However, when the different categories of lesion were analyzed independently, all individuals with PTB lesions showed an increase in the amount of Foxp3⁺ T lymphocytes compared to the control group but this increase was only significant in cows with focal lesions and, to a lesser extent, in animals with diffuse paucibacillary forms. The former showed the highest numbers, significantly different from those found in cows with diffuse lesions, where no differences were noted between the two forms. No specific distribution pattern was observed within the granulomatous lesions in any of the groups.

Conclusions

The increase of Foxp3⁺ T cells in focal forms, that have been associated with latency or resistance to infection, suggest an anti-inflammatory action of these cells at these stages, helping to prevent exacerbation of the inflammatory response, as occurs in diffuse forms, responsible for the appearance of clinical signs.