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  • First reported case in an Irish flock of MCF- like systemic necrotizing vasculitis in sheep associated with ovine herpesvirus 2

    Sheehan, Maresa; Pesavento, Patricia A.; Campion, Francis; Lynch, John; McGettrick, Shane; Toland, Brian; Kennedy, Aideen (2024-05-04)
    Abstract Background Ovine gammaherpesvirus 2 (OvHV-2) is the causative agent of sheep associated malignant catarrhal fever (MCF). As sheep are the adapted host for OvHV-2, it is generally presumed that infection is not associated with disease in this species. However, a recent case review combined in-situ hybridisation, PCR and histopathology and correlated the viral distribution with systemic necrotizing vasculitis and concluded OvHV-2 was the likely agent responsible for sporadic, MCF-like vascular disease in sheep. Case presentation Using similar methods this case study reports on the findings of the first reported cases in an Irish Flock of MCF- like systemic necrotizing vasculitis in sheep associated with OvHV-2. Sheep A, a 16-month-old Texel-cross hogget displayed signs of ill- thrift, Sheep B, a nine-month-old Belclare-cross lamb, was found dead having displayed no obvious symptoms. Both cases occurred on the same farm, however the animals were not related. Lymphohistiocytic vasculitis of various tissues was the predominant histopathological finding in both animals. Conclusion By combining histopathology, PCR and in-situ hybridisation results, MCF- like systemic necrotizing vasculitis associated with OvHV-2 has been diagnosed for the first time in an Irish flock.
  • The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits

    Alexa, Elena A.; Cobo-Díaz, José F.; Renes, Erica; O´Callaghan, Tom F.; Kilcawley, Kieran; Mannion, David; Skibinska, Iwona; Ruiz, Lorena; Margolles, Abelardo; Fernández-Gómez, Paula; et al. (2024-04-27)
    Abstract Background Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. Results Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. Conclusion Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract
  • Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs

    Ortiz Sanjuán, Juan M.; Argüello, Héctor; Cabrera-Rubio, Raúl; Crispie, Fiona; Cotter, Paul D.; Garrido, Juan J.; Ekhlas, Daniel; Burgess, Catherine M.; Manzanilla, Edgar G. (2024-04-16)
    Abstract Background Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. Results Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. Conclusion Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
  • An in-depth evaluation of metagenomic classifiers for soil microbiomes

    Edwin, Niranjana R.; Fitzpatrick, Amy H.; Brennan, Fiona; Abram, Florence; O’Sullivan, Orla (2024-03-28)
    Abstract Background Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. Results In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. Conclusion This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.
  • Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy

    Hourigan, David; Stefanovic, Ewelina; Hill, Colin; Ross, R. P. (2024-03-28)
    Abstract Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
  • Cutaneous application of SecurePig® FLASH, a Pig appeasing pheromone analogue, facilitates adaptation and manages social behavior during feeding in semi-extensive conditions

    Chasles, Manon; Marcet-Rius, Míriam; Chou, Jen-Yun; Teruel, Eva; Pageat, Patrick; Cozzi, Alessandro (2024-03-05)
    Abstract Background Farm animals face several challenges throughout their lives, which can affect both their welfare and their productivity. Promoting adaptation in animals is one way of limiting these consequences. In various animal species, the use of maternal appeasing pheromones is efficient to reduce aggressiveness, improve adaptation and thus ensuring better welfare and productivity. This study sought to investigate the efficiency of a treatment with a Pig Appeasing Pheromone (PAP) on the behavior of pigs reared under semi-extensive conditions and exposed to a potential conflict– collective feeding. Animals (n = 14 divided in 2 groups of 7) were subjected to 3 different phases, (A) baseline - no pigs received the PAP, (B) SP − 2 out of the 7 pigs per group received the PAP and (C) AP– all pigs received the PAP. Behaviors related to feeding, aggression and locomotion were compared between the 3 phases of the study. Results Compared to the baseline period, we observed that the number of head knocks was reduced when some pigs (p < 0.001) and all pigs (p < 0.005) received the PAP. Similarly, we observed that the number of fleeing attempts was reduced when some pigs (p < 0.001) and all pigs (p < 0.001) were treated when compared to baseline. This number was lower in the AP phase than in the SP phase (p < 0.001). When all pigs were treated (AP), we also observed that they spent less time investigating the floor than during the two other phases (p < 0.001), but they seemed more likely to leave the feeder due to the presence or behavior of another pig of the group (SP vs. AP, p < 0.05). Conclusions The PAP application improved adaptation in pigs by reducing aggressiveness and promoting conflict avoidance. Those results validate the efficiency of the pheromonal treatment under semi-extensive rearing conditions to help pigs to cope with a challenging situation. Using PAP in the pig industry seems interesting to limit unwanted consequences of farm practices on animal welfare and productivity, by promoting their adaptation.
  • An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle

    Keogh, Kate; Kenny, D. A.; Alexandre, P. A.; McGee, M.; Reverter, A. (2024-03-04)
    Abstract Background Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network. Results Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts. Conclusions Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.
  • Survey of farm, parlour and milking management, parlour technologies, SCC control strategies and farmer demographics on Irish dairy farms

    Uí Chearbhaill, Alice; Boloña, Pablo S.; Ryan, Eoin G.; McAloon, Catherine I.; Burrell, Alison; McAloon, Conor G.; Upton, John (2024-05-06)
    Abstract Background This cross-sectional study describes a survey designed to fill knowledge gaps regarding farm management practices, parlour management practices and implemented technologies, milking management practices, somatic cell count (SCC) control strategies, farmer demographics and attitudes around SCC management on a sample of Irish dairy farms. Results We categorized 376 complete responses by herd size quartile and calving pattern. The average respondent herd was 131 cows with most (82.2%) operating a seasonal calving system. The median monthly bulk tank somatic cell count for seasonal calving systems was 137,000 cells/ml (range 20,000 – 1,269,000 cells/ml), 170,000 cells/ml for split-calving systems (range 46,000 – 644,000 cells/ml) and 186,000 cells/ml for ‘other’ herds (range 20,000 – 664,000 cells/ml). The most common parlour types were swing-over herringbones (59.1%) and herringbones with recording jars (22.2%). The average number of units across herringbone parlours was 15, 49 in rotary parlours and two boxes on automatic milking system (AMS) farms. The most common parlour technologies were in-parlour feeding systems (84.5%), automatic washers on the bulk tank (72.8%), automatic cluster removers (57.9%), and entrance or exit gates controlled from the parlour pit (52.2%). Veterinary professionals, farming colleagues and processor milk quality advisors were the most commonly utilised sources of advice for SCC management (by 76.9%, 50.0% and 39.2% of respondents respectively). Conclusions In this study, we successfully utilised a national survey to quantify farm management practices, parlour management practices and technology adoption levels, milking management practices, SCC control strategies and farmer demographics on 376 dairy farms in the Republic of Ireland. Rotary and AMS parlours had the most parlour technologies of any parlour type. Technology add-ons were generally less prevalent on farms with smaller herds. Despite finding areas for improvement with regard to frequency of liner changes, glove-wearing practices and engagement with bacteriology of milk samples, we also found evidence of high levels of documentation of mastitis treatments and high use of post-milking teat disinfection. We discovered that Irish dairy farmers are relatively content in their careers but face pressures regarding changes to the legislation around prudent antimicrobial use in their herds.
  • Metagenomic comparison of the faecal and environmental resistome on Irish commercial pig farms with and without zinc oxide and antimicrobial usage

    Ekhlas, Daniel; Cobo Díaz, José F.; Cabrera-Rubio, Raúl; Alexa, Elena; Ortiz Sanjuán, Juan M.; Garcia Manzanilla, Edgar; Crispie, Fiona; Cotter, Paul D.; Leonard, Finola C.; Argüello, Héctor; et al. (Biomed Central, 2023-12-11)
    Abstract Background Antimicrobials and heavy metals such as zinc oxide (ZnO) have been commonly used on Irish commercial pig farms for a 2-week period post-weaning to help prevent infection. In 2022, the prophylactic use of antimicrobials and ZnO was banned within the European Union due to concerns associated with the emergence of antimicrobial resistance (AMR) and contamination of the environment with heavy metals. In this study, faecal and environmental samples were taken from piglets during the weaning period from ten commercial farms, of which five farms used antimicrobial or ZnO prophylaxis (AB-ZnO farms) and five which had not used antimicrobials or ZnO for the previous 3 years (AB-ZnO free farms). A total of 50 samples were compared using a metagenomic approach. Results The results of this study showed some significant differences between AB-ZnO and AB-ZnO free farms and suggested positive selection for AMR under antimicrobial and ZnO treatment. Moreover, strong differences between environmental and faecal samples on farms were observed, suggesting that the microbiome and its associated mobile genetic elements may play a key role in the composition of the resistome. Additionally, the age of piglets affected the resistome composition, potentially associated with changes in the microbiome post-weaning. Conclusions Overall, our study showed few differences in the resistome of the pig and its environment when comparing AB-ZnO farms with AB-ZnO free farms. These results suggest that although 3 years of removal of in-feed antimicrobial and ZnO may allow a reduction of AMR prevalence on AB-ZnO farms, more time, repeated sampling and a greater understanding of factors impacting AMR prevalence will be required to ensure significant and persistent change in on-farm AMR.
  • Anti-methanogenic potential of seaweeds and seaweed-derived compounds in ruminant feed: current perspectives, risks and future prospects

    McGurrin, Ailbhe; Maguire, Julie; Tiwari, Brijesh K.; Garcia-Vaquero, Marco; Irish Research Council Enterprise Partnership Scheme Postgraduate Scholarship; BlueBio ERA-NET; EPSPG/2021/154 (Biomed Central, 2023-12-02)
    Abstract With methane emissions from ruminant agriculture contributing 17% of total methane emissions worldwide, there is increasing urgency to develop strategies to reduce greenhouse gas emissions in this sector. One of the proposed strategies is ruminant feed intervention studies focused on the inclusion of anti-methanogenic compounds which are those capable of interacting with the rumen microbiome, reducing the capacity of ruminal microorganisms to produce methane. Recently, seaweeds have been investigated for their ability to reduce methane in ruminants in vitro and in vivo, with the greatest methane abatement reported when using the red seaweed Asparagopsis taxiformis (attributed to the bromoform content of this species). From the literature analysis in this study, levels of up to 99% reduction in ruminant methane emissions have been reported from inclusion of this seaweed in animal feed, although further in vivo and microbiome studies are required to confirm these results as other reports showed no effect on methane emission resulting from the inclusion of seaweed to basal feed. This review explores the current state of research aiming to integrate seaweeds as anti-methanogenic feed additives, as well as examining the specific bioactive compounds within seaweeds that are likely to be related to these effects. The effects of the inclusion of seaweeds on the ruminal microbiome are also reviewed, as well as the future challenges when considering the large-scale inclusion of seaweeds into ruminant diets as anti-methanogenic agents.
  • Potential application of phage vB_EfKS5 to control Enterococcus faecalis and its biofilm in food

    El-Telbany, Mohamed; Lin, Chen-Yu; Abdelaziz, Marwa N.; Maung, Aye T.; El-Shibiny, Ayman; Mohammadi, Tahir N.; Zayda, Mahmoud; Wang, Chen; Zar Chi Lwin, Su; Zhao, Junxin; et al. (Biomed Central, 2023-11-20)
  • Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome

    Patangia, Dhrati V.; Grimaud, Ghjuvan; O’Shea, Carol-Anne; Ryan, C. A.; Dempsey, Eugene; STANTON, CATHERINE; Ross, R. P.; European Union—FP7 (Biomed Central, 2024-02-03)
    Abstract Background Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. Methods Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort’s first week of life. Results Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). Conclusion These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures—leading to what can be an extensive and diverse resistome. Video Abstract
  • Farmers’ knowledge of Johne’s disease and opinions of the Irish Johne’s Control Programme: results of an online survey answered mostly by young farmers

    Horan, Louise; Mee, John F.; Field, Niamh L.; Walsh, Siobhán W.; Valldecabres, Ainhoa; Teagasc Walsh Scholarship programme (Biomed Central, 2023-10-20)
    Abstract A voluntary control programme for Johne’s disease, the Irish Johne’s Control Programme (IJCP) has been implemented in Ireland since 2017. The objective of this observational study was to assess Irish beef and dairy farmers’ Johne’s disease knowledge, implemented management practices and IJCP opinions. A questionnaire open to dairy and beef farmers was distributed via social media and email. In total 126 responses were used for this study; these responses came from mostly young farmers (18–25 years old) and represent a small proportion of the total number of dairy and beef farmers in Ireland whose average age is 55. Most respondents claimed to know what Johne’s disease was (73%; 92/126) and associated the disease to loss of body condition (68%; 78/114) and diarrhoea (59%; 67/114). Twenty-eight respondents (mostly dairy farmers; 22/28) reported positive cases in their premises. And 38% reported to implement management practices to prevent Johne’s disease transmission within or into their herd (i.e. management of milk for calf consumption and isolation of Johne’s test-positive or newly purchased stock; 47/124). Eighteen percent (22/125) of respondents were, at the time of questionnaire or previously, members of the IJCP. The main benefits reported by some of the participating farmers were identification of positive cases (29%; 4/14), and management of milk for calf consumption (21%; 3/14). While the main disadvantage was inaccurate testing methods (50%; 10/20). The main reasons reported for the lack of participation in the IJCP were not being aware of the programme (52%; 53/102) and not having a Johne’s disease problem on the farm (48%; 49/102). In conclusion, this study suggests that while young farmers are aware of Johne’s disease, their participation in the IJCP is limited and could benefit from further promotion. Studies representing the wider farming community in Ireland are warranted to gather non-biased input and contribute to Johne’s disease control in Ireland.
  • Is a scientific career in agri-food considered viable for girls in secondary school?

    Hyland, John; Boyle, Catriona; Ferguson, Eimear; Teagasc (Teagasc, 2023-12)
    The Festival of Farming and Food 2022 was organised by Teagasc as part of Science Week. A key finding from the previous year’s evaluation of the event was that girls viewed science as a male-dominated career. Therefore, the 2022 festival was partially evaluated through a focus group (eight participants) with Transition Year (TY) students from an all-girls school who attended the Climate and Farming event at Teagasc Moorepark. The focus group with the TY students also served to investigate perceptions of girls towards science as a career path.
  • An evaluation of the Irish Science Week Festival of Farming and Food

    Hyland, John; Boyle, Catriona (2023)
    The aim of the study was to evaluate the Festival of Farming and Food and its effectiveness of engagement with the general public as well as secondary school students.
  • Immunoproteomic analysis of the serum IgG response to cell wall-associated proteins of Staphylococcus aureus strains belonging to CC97 and CC151

    Drumm, Shauna D.; Cormican, Paul; Owens, Rebecca A.; Mitchell, Jennifer; Keane, Orla M.; Teagasc; Science Foundation Ireland; 0048GE; 12/RI/2346 (3) (2023-09-18)
    CC97 and CC151 are two of the most common Staphylococcus aureus lineages associated with bovine intramammary infection. The genotype of the infecting S. aureus strain influences virulence and the progression of intramammary disease. Strains from CC97 and CC151 encode a distinct array of virulence factors. Identification of proteins elaborated in vivo will provide insights into the molecular mechanism of pathogenesis of these lineages, as well as facilitating the development of tailored treatments and pan-lineage vaccines and diagnostics. The repertoire of genes encoding cell wall-anchored (CWA) proteins was identified for S. aureus strains MOK023 (CC97) and MOK124 (CC151); MOK023 encoded more CWA proteins than MOK124. Serum collected during an in vivo challenge trial was used to investigate whether the humoral response to cell wall proteins was strain-specific. Immunoproteomic analysis demonstrated that the humoral response in MOK023-infected cows predominantly targeted high molecular weight proteins while the response in MOK124-infected cows targeted medium or low molecular weight proteins. Antigenic proteins were identified by two-dimensional serum blotting followed by mass spectometry-based identification of immunoreactive spots, with putative antigens subsequently validated. The CWA proteins ClfB, SdrE/Bbp and IsdA were identified as immunogenic regardless of the infecting strain. In addition, a number of putative strain-specific imunogens were identified. The variation in antigens produced by different strains may indicate that these strains have different strategies for exploiting the intramammary niche. Such variation should be considered when developing novel control strategies including vaccines, therapeutics and diagnostics.
  • Analysing biomarkers in oral fluid from pigs: influence of collection strategy and age of the pig

    Ornelas, Mario A. S.; López‑Martínez, María J.; Franco-Martínez, Lorena; Cerón, José J.; Ortín-Bustillo, Alba; Rubio, Camila P.; Garcia Manzanilla, Edgar; Department of Agriculture Food and the Marine; Teagasc Walsh Scholarship Programme; Fundación Séneca, Región de Murcia (Spain); et al. (Biomed Central, 2023-08-30)
    Background and objectives Oral fluid (OF) is an easy-to-collect, inexpensive, fast and non-invasive sample to characterize health and welfare status of the pig. However, further standardisation of the collection methods is needed in order to use it regularly in veterinary practice. Cotton ropes are routinely used to collect OF for pathogen detection but they may not be optimal for biomarker analysis due to sample contamination. This study compared two methods (cotton ropes and sponges) to collect porcine OF for biomarker analysis. A panel of 11 biomarkers of stress, inflammation, sepsis, immunity, redox status and general homeostasis was studied. Materials and methods Eighteen farrow-to-finish pig farms were included in the study. In each farm, three (for sponges) or four pens of pigs (for ropes) were sampled at four age categories: the week after weaning (5 weeks), before (11–12 weeks) and after (12–13 weeks) moving to finisher facility and the week before slaughter (22–25 weeks). In total, 288 OF samples were collected with cotton ropes and 216 with sponges and analysed for the biomarkers: cortisol, alpha-amylase, oxytocin (stress), haptoglobin (inflammation), procalcitonin (sepsis), adenosine deaminase, immunoglobulin G (immune system), ferric reducing antioxidant power (redox status), and creatine kinase, lactate dehydrogenase and total protein (general homeostasis). Samples were also scored visually for dirtiness using a score from 1 (clean) to 5 (very dirty). Results Rope-collected OF had higher levels of dirtiness (3.7 ± 0.04) compared to sponge-collected OF (2.7 ± 0.15) and had higher values than sponges for cortisol, procalcitonin, oxytocin, haptoglobin, total protein, lactate dehydrogenase and ferric reducing antioxidant power. All biomarkers decreased in value with age. Immunoglobulin G did not perform well for any of the two collection methods. Discussion and conclusion The results showed a clear effect of age on the biomarkers in OF collected with both, sponges or ropes. Sponges provided a cleaner sample than cotton ropes for biomarker analysis. Both methods are easy to apply under the commercial conditions in pig farms although sponges may take more time in early weaner stages. From a practical point of view, sampling with sponges achieved the best combination of reduced sampling time and low contamination.
  • Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle

    Reding, Jason J.; van der Westhuizen, Robert R.; Berry, Donagh P.; van Marle-Köster, Este; South African Beef Genomics Project (Biomed Central, 2023-08-24)
    Background Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models. Results Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation. Conclusions This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.
  • Changes in salivary biomarkers of stress, inflammation, redox status, and muscle damage due to Streptococcus suis infection in pigs

    López-Martínez, María J.; Ornelas, Mario A. S.; Amarie, Roxana E.; Manzanilla, Edgar G.; Martínez-Subiela, Silvia; Tecles, Fernando; Tvarijonaviciute, Asta; Escribano, Damián; González-Bulnes, Antonio; Cerón, José J.; et al. (Biomed Central, 2023-07-31)
    Background Streptococcus suis (S. suis) is a Gram-positive bacteria that infects pigs causing meningitis, arthritis, pneumonia, or endocarditis. This increases the mortality in pig farms deriving in severe economic losses. The use of saliva as a diagnostic fluid has various advantages compared to blood, especially in pigs. In this study, it was hypothesized that saliva could reflect changes in different biomarkers related to stress, inflammation, redox status, and muscle damage in pigs with S. suis infection and that changes in these biomarkers could be related to the severity of the disease. Results A total of 56 growing pigs from a farm were selected as infected pigs (n = 28) and healthy pigs (n = 28). Results showed increases in biomarkers related to stress (alpha-amylase and oxytocin), inflammation (haptoglobin, inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), total protein, S100A8-A9 and S100A12), redox status (advanced oxidation protein producs (AOPP)) and muscle damage (creatine kinase (CK), CK-MB, troponin I, lactate, aspartate aminotransferase, and lactate dehydrogenase). An increase in adenosine deaminase (ADA), procalcitonin, and aldolase in infected animals were also observed, as previously described. The grade of severity of the disease indicated a significant positive correlation with total protein concentrations, aspartate aminotransferase, aldolase, and AOPP. Conclusions This report revealed that S. suis infection caused variations in analytes related to stress, inflammation, redox status, and muscle damage in the saliva of pigs and these can be considered potential biomarkers for this disease.
  • Microbiome ethics, guiding principles for microbiome research, use and knowledge management

    Lange, Lene; Berg, Gabriele; Cernava, Tomislav; Champomier-Vergès, Marie-Christine; Charles, Trevor; Cocolin, Luca; Cotter, Paul; D’Hondt, Kathleen; Kostic, Tanja; Maguin, Emmanuelle; et al. (Biomed Central, 2022-09-30)
    The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don’t Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops.

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