Céad Mile Fáilte go T-Stór (Welcome to T- Stór)

T-Stór is Teagasc’s Open Access Repository, maintained by the Teagasc Library Service. Stór is the Gaelic word for Repository or Store or Warehouse, and T-Stór is an online “store” of Teagasc Research outputs and related documents. T-Stór collects preserves and makes freely available scholarly communication, including peer-reviewed articles, working papers and conference papers created by Teagasc researchers. Where material has already been published it is made available subject to the open-access policies of the original publishers. About Teagasc

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Animal & Grassland Research & Innovation Programme [1158]
Crops, Environment & Land Use Programme [582]
Food Programme [1201]
Rural Economy & Development Programme [272]
Irish Journal of Agricultural & Food Research [317]
Other [290]
  • 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
  • Impact of birth and rearing type, as well as inaccuracy of recording, on pre-weaning lamb phenotypic and genetic merit for live weight1

    McHugh, N.; Pabiou, T.; McDermott, K.; Wall, E.; Berry, D. P. (Oxford University Press (OUP), 2017-04-01)
    The objective of the present study was to quantify the impact of the systematic environmental effects of both birth and rearing type on pre-weaning lamb live weight, and to evaluate the repercussions of inaccurate recording of birth and rearing type on subsequent genetic evaluations. A total of 32,548 birth weight records, 35,770 forty-day weight records and 32,548 records for average daily gain (ADG) between birth and 40-day weight from the Irish national sheep database were used. For each lamb, a new variable, birth-rearing type, reflecting both the birth and rearing type of a lamb was generated by concatenating both parameters. The association between birth-rearing type and birth weight, 40-day weight, and ADG was estimated using linear mixed models. The repercussions of inaccurate recording of birth type were determined by quantifying the impact on sire estimated breeding value (EBV; with an accuracy of ≥ 35%), where one of the lambs born in a selection of twin litter births was assumed to have died at birth but the farmer recorded the birth and rearing type as a singleton. The heaviest mean birth weight was associated with lambs born and subsequently reared as singles (5.47 kg); the lightest mean birth weight was associated with lambs born and reared as triplets (4.10 kg). The association between birth-rearing type and 40-day weight differed by dam parity (P < 0.001). Lambs reared by first parity dams as singles, irrespective of birth type were, on average, heavier at 40-day weighing than lambs reared as multiples, but as parity number increased, single-born lambs reared as twins outperformed triplet-born lambs reared as singles. Irrespective of the trait evaluated, the correlation between sire EBV estimated from the accurately recorded data and sire EBV estimated from the data with recording errors was strong ranging from 0.93 (birth weight) to 0.97 (ADG). The EBV for sires with progeny data manipulated were 0.14 kg, 0.34 kg and 5.56 g/d less for birth weight, 40-day weight and ADG, respectively, compared to their equivalent EBV calculated using accurately recorded data. Results from this study highlight the importance of precise recording of birth-rearing type by producers for the generation of accurate genetic evaluations.

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