Eveline M Ibeagha-Awemu

Agriculture and Agri-Food Canada | AAFC · Sherbrooke Research and Development Centre

The study investigated the role of gut microbiome in PPR disease in WAD goats

Research on the role of nasal microbiome on the pathogenesis of PPR viral disease in goats

Staphylococcus chromogenes (SC) is a common coagulase-negative staphylococcus described as an emerging mastitis pathogen and commonly found in dairy farms. This study investigated the potential involvement of DNA methylation in subclinical mastitis caused by SC. The whole-genome DNA methylation patterns and transcriptome profiles of milk somatic ce...

After the groundbreaking eradication of rinderpest, peste des petits ruminants (PPR) is currently the target for global eradication by 2030. Understanding the factors affecting its prevalence is imperative for effective, evidence-based planning for the eradication of the disease. Genetic and non-genetic factors affecting PPR prevalence in sheep and...

Staphylococcus aureus is one of the most prevalent contagious bacterial pathogen of bovine mastitis. The subclinical mastitis it causes has long-term economic implications and it is difficult to control. To further understanding of the genetic basis of mammary gland defense against S. aureus infection, the transcriptomes of milk somatic cells from...

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, disc...

Peste des petits ruminants (PPR) causes severe economic losses to many countries of the world where the disease is endemic. It has been targeted for global eradication by 2030 following the successful eradication of rinderpest in 2011. The proposed eradication program would benefit from efficient and relatively reliable diagnostic tools for early P...

Abstract Background Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing)...

Background Long noncoding RNAs (lncRNAs) are now proven as essential regulatory elements, playing diverse roles in many biological processes including mammary gland development. However, little is known about their roles in the bovine lactation process. Results To identify and characterize the roles of lncRNAs in bovine lactation, high throughput...

Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms. A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lacta...

Johne’s Disease (JD), caused by Mycobacterium avium subsp paratuberculosis (MAP), is an incurable disease of ruminants and other animal species and is characterized by an imbalance of gut immunity. The role of MAP infection on the epigenetic modeling of gut immunity during the progression of JD is still unknown. This study investigated the DNA meth...

Epigenetic factors respond to environmental factors and underlying genotypes to influence livestock phenotypic expression (e.g., milk yield, wool quality, disease resistance, growth, and development, etc.). • Epigenetic alterations are associated with livestock traits and with differences in livestock product yields. • A window is opened for explor...

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative infectious agent of Johne’s disease (JD), an incurable granulomatous enteritis affecting domestic livestock and other ruminants around the world. Chronic MAP infections usually begin in calves with MAP uptake by Peyer’s patches (PP) located in the jejunum (JE) and ileum (IL). Determ...

Milk fat and protein content are among key elements of milk quality, and they are attracting more attention in response to consumers′ demand for high-quality dairy products. To investigate the potential regulatory roles of DNA methylation underlying milk component yield, whole genome bisulfite sequencing was employed to profile the global DNA methy...

Bovine mastitis, commonly caused by bacteria, is one of the most devastating diseases for the dairy industry worldwide, with high economic, social, and public health impacts. Among the pathogenic bacteria, Staphylococcus aureus is one of the leading pathogens in most countries. Success rate of antibiotic treatment is low such that effective control...

Milk protein content is attracting considerable attention due to increasing demand for high-quality products. Epigenetic marks including DNA methylation have demonstrated considerable potential to contribute to the achievement of increased gain in bovine milk traits. To investigate potential roles of DNA methylation in regulating milk protein produ...

Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-cod...

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 sequen...

The accumulated and annual levels of inbreeding and their effects on growth traits of lambs were investigated using data collected over 11 years at the National Animal Production Research Institute Zaria. Inbreeding level averaged 1.313% per year, cumulating to 14.45% over the years. Average individuals inbreeding coefficients of offspring from sir...

Background: Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne's disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple interacting factors, including the genetic predisposition to a dysregulation of the immune system. The endemic situation in c...

Background Long noncoding RNAs (lncRNAs) are now proven as essential regulatory elements, playing diverse role in many biological processes including mammary gland development. However, little is known about their roles in bovine lactation process. There are very few reports available to date on the role of lncRNAs in lactation physiology and mamma...

The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to inc...

Genomic selection methodologies and genome-wide association studies use powerful statistical procedures that correlate large amounts of high-density SNP genotypes and phenotypic data. Actual 305-d milk (MY), fat (FY), and protein (PY) yield data on 695 cows and 76,355 genotyping-by-sequencing-generated SNP marker genotypes from Canadian Holstein da...

Several investigations on disease progression of Mycobacterium avium subsp. paratuberculosis (MAP) infection in dairy cows have revealed molecular mechanisms including genes and pathways implicated in MAP pathogenesis. Epigenetic processes including DNA methylation are known to regulate the expression of genes and many biological processes. However...

Paratuberculosis is an incurable disease caused by Mycobacterium avium spp. paratuberculosis (MAP). Variability in the definition of a true infection could explain the lack of consensus in published results on host genetic susceptibility to MAP. The objective of this study was to identify quantitative trait loci (QTL) for susceptibility to paratube...

Johne’s Disease (JD), caused by Mycobacterium avim spp paratuberculosis (MAP), is a chronic and incurable disease of ruminants with devastating consequences to the dairy industry. MAP can alter the expression of genes and biological processes during the progression of JD. While some studies have examined the role of gene expression regulators like...

Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) foll...

Innate responses provide the first line of defense against viral infections, including the influenza virus at mucosal surfaces. Communication and interaction between different host cells at the early stage of viral infections determine the quality and magnitude of immune responses against the invading virus. The release of membrane-encapsulated ext...

An autosomal recessive defect caused by a loss of function mutation in the bovine apolipoprotein B (APOB) gene causes cholesterol deficiency with strong effects on calf survival and development. This study examined the distribution of cholesterol deficiency haplotype (CDH) in the APOB gene in Canadian Holstein cows and their impact on milk producti...

Background: Exploration of the bioactive components of bovine milk has gained global interest due to their potential applications in human nutrition and health promotion. Despite advances in proteomics profiling, limited studies have been carried out to fully characterize the bovine milk proteome. This study explored the milk proteome of Jersey an...

High blood cholesterol concentration, mainly caused by high dietary cholesterol, is a potential risk factor for human health. Dairy products are important sources of human dietary cholesterol intake. Therefore, monitoring bovine milk cholesterol concentration is important for human health benefit. Genetic selection for improvement of cow milk chole...

Background: MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-m...

Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a chronic intestinal disease affecting ruminants worldwide. This study investigated miRNA expression in jejunal intestine (JE) and jejunal lymph nodes (JELN), and the potential regulatory roles of miRNAs during JD progression. JE and JELN tissues were col...

Paratuberculosis or Johne’s disease (JD), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic inflammatory disorder of the intestinal tract of ruminants. The mechanisms of JD pathogenesis remain unclear but MAP can cause chronic inflammatory lesions in the terminal small intestine of cattle. Using microRNA (miRNA) transcriptom...

Johne’s disease (JD) is a chronic enteric disease of ruminants caused by Mycobacterium avium subsp. Paratuberculosis (MAP) but immune and metabolic mechanisms affecting JD progression have not been clearly elucidated. MicroRNAs (miRNA) have been reported to play important roles in numerous biological processes by regulating gene expression. In this...

Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR...

Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR...

MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in milk exosomes and potential markers for quality control of milk infected by Staphylococcus aureus (S. aureus). Total RNA from milk exosomes was collected from healthy cows (n=3) and S. aureus infected cows (n=6). Two h...

Lactation persistency (LP), defined as the ability of a cow to maintain milk production at a high level after milk peak, is an important phenotype for the dairy industry. In this study, we used a targeted genotyping approach to scan for potentially functional single nucleotide polymorphisms (SNPs) within 57 potential candidate genes derived from ou...

MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in milk exosomes and potential markers for quality control of milk infected by Staphylococcus aureus (S. aureus). Total RNA from milk exosomes was collected from healthy cows (n=3) and S. aureus infected cows (n=6). Two h...

The objective of this study was to characterize GnRHR gene in Sokoto (n = 70) and Kalahari Red (n = 70) goats. Three SNPs, (g.-29T > G, g.48 G > A and g.209 T > G), were detected in Sokoto Red (SR) and one (g.48 G > A) in Kalahari Red (KR) goats. All the mutations occurred within the 5′UTR and Exon one of the gene and the g.209 T > G was non-synony...

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor instit...

Jersey and Kashmiri cattle are important dairy breeds that contribute significantly to the total milk production of the Indian northern state of Jammu and Kashmir. The Kashmiri cattle germplasm has been extensively diluted through crossbreeding with Jersey cattle with the goal of enhancing its milk production ability. However, crossbred animals are...

Enriched pathways by differentially expressed genes in (a) Kashmiri cattle and (b) Jersey cattle using GO consortium database (PANTHER). (XLSX)

Read mapping statistics. (DOCX)

Expression levels (FPKM values) of genes in mammary epithelial cells of Kashmiri and Jersey cattle1 at three different stages of lactation (a); expressed genes at different stages of lactation (D15, D90 and D250) in (b) Kashmiri and (c) Jersey cattle. (XLSX)

Differentially expressed genes between (a) D15 vs D90, (b) D15 vs D250 and (c) D90 vs D250 in Kashmiri cattle; and (d) D15 vs D90, (e) D15 vs D250 and (f) D90 vs D250 in Jersey cattle; and (g) D15 vs D15, (h) D90 vs D90 and (i) D250 vs D250 between Kashmiri and Jersey cattle. (XLSX)

Protein-Protein interaction between top 20 differentially expressed major milk candidate genes at each lactation stage comparison in (a) Kashmiri and (b) Jersey cattle using STRING database. (XLSX)

Genes and primer sequences for purity check of isolated mammary epithelial cells (a). Genes and primer sequences used for validation of RNA-Seq data by qPCR (b). (DOCX)

Enriched gene ontology (GO) terms by differentially expressed genes in (a) Kashmiri cattle and (b) Jersey cattle using GO consortium database (PANTHER). (XLSX)

Non-coding RNAs (ncRNAs) are a class of untranslated RNA molecules that have emerged as new regulators of gene expression. The roles of ncRNAs including small interfering RNA, microRNA (miRNA), PIWI-interacting RNA, small nucleolar RNA, long non-coding RNA (lncRNA) and circular RNA, in the regulation of traits of economic importance in livestock ar...

Johne’s disease (JD) is a contagious and chronic disease in ruminants caused by Mycobacterium avium ssp. paratuberculosis(MAP). It is known that MAP manipulates gut macrophages as a strategy to spare the host and ensure survival. Genetic variations in macrophages from susceptible cows were identified using a MAP infection assay. Primary monocyte-de...

Mycobacterium avium ssp. paratuberculosis (MAP) causes Johne’s disease (JD) in ruminants. The mechanisms of JD pathogenesis are still unclear, but it is known that this obligatory bacterium manipulates macrophages for its survival and long-term infection success in its host. A comparative transcriptomic analysis (next-generation RNA sequencing) was...

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD). MAP infects ruminants and resides in the intestinal submucosa, macrophages/dendritic cells causing progressive weight loss and decreased productivity. The molecular mechanisms by which MAP subverts host immune system causing extensive formation of granul...

Johne’s disease (JD), caused by Mycobacterium avium ssp. paratuberculosis (MAP), is an important economic disease of dairy cows. However, little is known about the mechanisms underlying JD development. Here, we combined weighted gene coexpression network (WGCNA) and enrichment analyses to identify important genes, pathways and transcription factors...

Direct-fed microbials (DFM) like Lactobacillus acidophilus (LA) can influence the composition of the gastrointestinal tract (GIT) microbiota of ruminants resulting in beneficial effects on health and productivity. In this study, the GIT microbiota of 16 calves (8/treatment) fed LA BT1386 (2.5 × 10⁸ CFU/L milk replacer + 1 × 10⁹ CFU/kg starter feed)...

The gastrointestinal tract (GIT) microbiota has attracted much attention due to its impact on animal health and productivity. This study characterized the GIT bacterial communities of calves (8/treatment) supplemented with Saccharomyces cerevisiae boulardii CNCM1-1079 (SCB) (7.5x108CFU/L milk replacer + 3x109CFU/kg feed) or an antibiotic (ATB) (chl...

This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented wi...

This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented wi...

Abstract This study investigated the effect of supplementing the diet of calves with two direct fed microbials (DFMs) (Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) and Lactobacillus acidophilus BT1386 (LA)), and an antibiotic growth promoter (ATB). Thirty-two dairy calves were fed a control diet (CTL) supplemented with SCB or LA or ATB for...

This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencin...

This study aimed to identify single nucleotide polymorphisms (SNPs) associated with milk cholesterol (CHL) content via a genome wide association study (GWAS). Milk CHL content was determined by gas chromatography and expressed as mg of CHL in 100 g of fat (CHL_fat) or in 100 mg of milk (CHL_milk). GWAS was performed with 1,183 cows and 40,196 SNPs...