The Impact of Increasing Anthelmintic Resistance on Ruminant Performance and Greenhouse Gas Emissions

We are unlikely to see reductions in greenhouse gas (GHG) emissions from ruminants in the UK without changes to the way we farm. However, there are many ways in which emissions can be reduced, without reducing our meat and milk output (which raises the risk of displacement of production and emissions). Improving productivity often leads to reductions in emissions intensity (EI, the kg of GHG emitted per kg of output), thereby enabling emissions to be reduced while maintaining output. One way of improving productivity is to improve ruminant health. Helminth parasites (roundworms and fluke) are among the most important production-limiting pathogens of grazing livestock in the UK. However, there is also evidence of increasing anthelmintic resistance (AR) among some important parasites, which could render current treatments less effective. In this case study, we review the evidence on trends in ruminant emissions and explain why health status is an important determinant of GHG emissions. We then review trends in AR and outline options for tackling it

Private or Public? Farmer Preferences and Identities in Agri‐Environmental Contract Implementation

This study investigates farmer preferences for publicly and privately financed agri‐environmental contracts. Using a labelled Discrete Choice Experiment with 366 German grassland farmers, we examine trade‐offs between payment schemes (public/private), payment criteria (practice‐based/result‐based), collaboration options, and advisory services. Our results show that farmers require higher compensation for privately financed contracts compared to public ones. On average, respondents prefer practice‐based over result‐based payments and value free advisory services, particularly in private schemes. Preferences for collaborative implementation indicate a strong desire for autonomy. A key contribution of this study lies in integrating farmer identity into the analysis. Drawing on a psychometric scale of ‘good farmer’ attributes, we identify three latent identities—productivist, environmentalist and civic‐minded—and show that these significantly explain heterogeneity in preferences and land enrolment decisions. Productivist farmers demand higher compensation and commit less land, while environmentalist and civic‐minded farmers are more inclined to participate and enrol larger areas, even at lower compensation levels. These findings highlight the importance of tailoring agri‐environmental contracts to farmers' identities through for example framing of agri‐environmental contracts accordingly. Privately financed schemes, such as those based on crowdfunding platforms, must address perceived risks, offer advisory support and develop communication strategies that resonate with different identity profiles. Recognising farmer identity as a behavioural driver can enhance participation in both public and private agri‐environmental schemes and inform more effective contract design

Deep Learning-Based Classification of Stress in Sows Using Facial Images

Stress in pigs is a significant factor contributing to poor health, increased antimicrobial usage, and the subsequent risk of antimicrobial resistance (AMR), which poses a major challenge for the global pig farming industry. In this paper, we propose using deep learning (DL) methods to classify stress levels in sows based on facial features captured from images. Early identification of stress can enable targeted interventions, potentially reducing health risks and mitigating AMR concerns. Our approach utilizes convolutional neural network (CNN) models, specifically YOLO8l-cls, to classify the stress levels of sows (pregnant pigs) into low-stressed and high-stressed categories. Experimental results demonstrate that YOLO8l-cls outperforms other classification methods, with an overall F1-score of 0.74, Cohen’s Kappa of 0.63, and MCC of 0.60. This highlights the model’s effectiveness in accurately identifying stress levels and its potential as a practical tool for stress management in pi g farming, with benefits for animal welfare, the farming industry, and broader efforts to minimize AMR risk

Feed additives for methane mitigation: Regulatory frameworks and scientific evidence requirements for the authorization of feed additives to mitigate ruminant methane emissions

This article describes the regulatory and evidence requirements necessary for the authorization of antimethanogenic feed additives (AMFA) aimed at mitigating enteric methane (CH ) emissions from ruminants. It outlines the legislation and legal procedures in Australia, Canada, the European Union, New Zealand, South Korea, the United Kingdom, and the United States as illustrative examples, offering insights for applicants seeking authorization. Additionals objectives are to highlight consequential similarities and differences in regulations and evidence requirements and offer recommendations for scientists and applicants. The pivotal role that scientific evidence plays in the evaluation and approval processes is emphasized, along with the need for applicants and researchers to understand and adhere to the specific regulations of each jurisdiction. Feed additives are regulated to ensure their safety for animals, humans, and the environment, and to verify their effectiveness for the intended use of enteric CH mitigation. Regulations cover various aspects, including ingredient safety, manufacturing practices, product labeling, and the establishment of permissible limits for certain substances to ensure their safe use in animal feed. Compliance with these regulations is mandatory, and they are enforced by regulatory agencies within each jurisdiction, aiming to protect animal health, promote food safety, and prevent misleading claims and unsafe practices. The assessment processes involve evaluating scientific evidence submitted by applicants, along with evaluations of quality control procedures, and record-keeping practices. The major difference in regulations is that each jurisdiction developed unique criteria to legally classify AMFA, making it challenging to satisfy all legal classifications with a single set of criteria for scientific evidence. However, numerous similarities and a universal reliance on the concept of intended use indicate consistency across all jurisdictions on the need for robust evidence for efficacy, safety, and product quality and documentation even if the type, size, duration, and location of the studies they require differ. Recommendations are made for both scientists and applicants, emphasizing the importance of designing, conducting, and reporting scientific evaluations transparently, using validated standards and methods, and communicating with regulatory bodies to ensure compliance with regulations and evidence requirements. [Abstract copyright: The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Novel adaptive immune systems in pristine Antarctic soils

Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes

Impact of Implementing Female Genomic Selection and the Use of Sex-Selected Semen Technology on Genetic Gain in a Dairy Herd in New Zealand

Genomic selection (GS) has changed cattle breeding, but its use so far has been in selecting superior bulls for breeding. However, its farm-level impact, particularly on female selection, remains less explored. This study aimed to investigate the impact of implementing GS to identify superior cows and using artificial mating of those cows with sex-selected semen in a New Zealand Holstein-Friesian (HF) dairy herd (n = 1800 cows). Heifers (n = 2061) born over four consecutive years between 2021 and 2024 were genotyped and their genomic breeding values (GBVs) were estimated. These heifers were ranked based on the Balanced Performance Index (BPI; DataGene, Dairy Australia) Lower-performing cows producing less than 15 L/day (or 20 L/day for older cows) and those with severe mastitis were culled. Cows were mated with HF genetics based on production and udder breeding values, while lower-performing cows were mated to beef genetics. Milking adult cows were mated to bulls with similar BPI value. Annual genetic change was measured using Australian breeding values (ABVg) for milk fat production (FAT), protein production (PROT), fertility (FER), Mastitis Resistance (MAS), and BPI. The genetic merits of the heifers improved annually, with BPI increasing from 136 to 184 between 2021 and 2023, corresponding to a financial gain of NZD 17.53 per animal per year. The predicted BPI gain from 2023 to 2026 is expected to rise from 184 to 384, resulting in a financial gain of NZD 72.96 per animal per year. Using sex-selected semen on the top 50% of BPI-rated heifers in 2024 further accelerated genetic gain. Predicted BPI values for progeny born in 2025 and 2026 are 320 and 384, respectively. These findings revealed that the female GS, combined with sex-selected semen from genomically selected bulls, significantly accelerates genetic gain by improving the intensity and accuracy of selection. The approach achieves genetic progress equivalent to what traditionally would have required eight years of breeding without female GS, and has potential to improve dairy herd performance and profitability.</p

Impact of Implementing Female Genomic Selection and the Use of Sex-Selected Semen Technology on Genetic Gain in a Dairy Herd in New Zealand

Genomic selection (GS) has changed cattle breeding, but its use so far has been in selecting superior bulls for breeding. However, its farm-level impact, particularly on female selection, remains less explored. This study aimed to investigate the impact of implementing GS to identify superior cows and using artificial mating of those cows with sex-selected semen in a New Zealand Holstein-Friesian (HF) dairy herd (n = 1800 cows). Heifers (n = 2061) born over four consecutive years between 2021 and 2024 were genotyped and their genomic breeding values (GBVs) were estimated. These heifers were ranked based on the Balanced Performance Index (BPI; DataGene, Dairy Australia) Lower-performing cows producing less than 15 L/day (or 20 L/day for older cows) and those with severe mastitis were culled. Cows were mated with HF genetics based on production and udder breeding values, while lower-performing cows were mated to beef genetics. Milking adult cows were mated to bulls with similar BPI value. Annual genetic change was measured using Australian breeding values (ABVg) for milk fat production (FAT), protein production (PROT), fertility (FER), Mastitis Resistance (MAS), and BPI. The genetic merits of the heifers improved annually, with BPI increasing from 136 to 184 between 2021 and 2023, corresponding to a financial gain of NZD 17.53 per animal per year. The predicted BPI gain from 2023 to 2026 is expected to rise from 184 to 384, resulting in a financial gain of NZD 72.96 per animal per year. Using sex-selected semen on the top 50% of BPI-rated heifers in 2024 further accelerated genetic gain. Predicted BPI values for progeny born in 2025 and 2026 are 320 and 384, respectively. These findings revealed that the female GS, combined with sex-selected semen from genomically selected bulls, significantly accelerates genetic gain by improving the intensity and accuracy of selection. The approach achieves genetic progress equivalent to what traditionally would have required eight years of breeding without female GS, and has potential to improve dairy herd performance and profitability.</p

The use of ruminal metabolic information to select microbial genes for microbiome-driven breeding to mitigate methane emissions from beef cattle

ApplicationThe identified animal genetic effects on ruminal metabolites concentrations and on theabundances of microbial genes together with their genetic correlations with methaneemissions are expected to improve the accuracy of microbiome-driven breeding to reducethis highly potent greenhouse gas efficiently and cost-effectively by reliable selection of lowemitting cattle.IntroductionVolatile fatty acids (VFAs) in the rumen are the primary energy source for cattle and areknown to be phenotypically related to CH4 emissions. Our research aimed to investigate howthese ruminal metabolites are animal genomically influenced and genetically correlated withCH4 emissions. Additionally, we were interested in identifying microbial genes that are closelygenetically correlated with both metabolites and CH4 emissions. The identification of the mostinformative biomarkers (VFAs, microbial genes) is essential for the microbiome-drivenbreeding strategy (Roehe et al., 2016; Martinez-Alvaro et al., 2022) and for improving ourunderstanding of the functional regulation of the ruminal metabolite metabolism and CH4production.Materials and MethodsThe animal trials were conducted following the UK Animals Act 1986 and were approved bythe Animal Experiment Committee of SRUC. The data comprised of 363 steers that weredeeply phenotyped (including CH4 emissions measured using respiration chambers) andgenotyped using a 50k SNP chip. The animals were tested at SRUC’s Beef Research Centreacross five trials and represented four breed types, with two basal diets (480:520 and 920:80forage:concentrate ratios). In two of the trials, the feed additives nitrate and rapeseed oilwere investigated. In addition, whole metagenome sequencing data of microbial DNA fromrumen fluid samples taken at slaughter were available. Aligning the ruminal metagenomicsequence reads to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database resultedin the identification of 3362 microbial genes. For a subset of these animals (n = 137), VFAconcentrations in the rumen fluid, collected at slaughter, were determined using HPLC.Bayesian genomic analyses were applied to estimate the heritabilities of the ruminalmetabolites and their genetic correlations with CH4 emissions as well as with functionalmicrobial KEGG genes. The genomic model included fixed environmental effects and theanimal’s random genomic effects, considering 36780 SNPs. Fixed effects in the model formetabolites included trial, breed, basal diet, feed additives and as a covariable age atslaughter, whereas for CH4 emissions and microbial KEGG genes, fixed effects were thecombined trial-breed-diet effects with additional consideration of a covariable, either the ageentering the respiration chambers or age at slaughter, respectively.ResultsEstimated heritabilities of molar proportion of (iso)butyrate were at high magnitude, whereasthose of acetate, propionate and (iso)valerate were at moderate level, indicating a hostgenomic influence on the ruminal microbial metabolism of VFAs (Table 1). The geneticcorrelations of the main VFAs with daily CH4 emissions (CH4d) were moderate in magnitudeand associated with probabilities (P0) of more than 80% to be different from zero. Thedirection of the correlations indicates that higher molar proportions of acetate and butyratein the rumen were genetically associated with increased CH4d. In contrast, higher proportionsof propionate and valerate were genetically correlated with decreased CH4d. The geneticcorrelations of isobutyrate and isovalerate were close to zero, indicating that they did notrelate to CH4 metabolism. The magnitude of the genetic correlations between VFAs and CH4emissions per kg dry matter intake (CH4y) were similar to those emissions obtained on a dailybasis.One interesting microbial gene group that was moderately to highly genetically correlatedwith the concentration of the main ruminal metabolites was anaerobic sulphite reductase(asr) subunits. The abundance of the microbial KEGG gene asrC showed genetic correlationswith acetate, propionate, butyrate, and valerate of -0.74, 0.87, -0.67 and 0.77, respectively,which were associated with P0 in the range of 0.95 to 0.98. Genetic correlations of equaldirection and similar magnitude were also found for asr subunits A and B. The abundance ofthe asr genes were negatively genetically correlated with CH4d between -0.23 to -0.41 withP0 ranging from 0.77 to 0.90. These results indicate that selection for increased abundancesof the asr genes will decrease CH4 emissions by favouring ruminal propionate and valeratemetabolism compared to acetate and butyrate production.Table 1.Heritabilities (h2) of ruminal metabolites and their genetic correlations (rg) with daily CH4emissions and CH4 yieldTrait h2 SD1 rg withCH4d2P0 rg withCH4drg withCH4y3P0 rg withCH4y4Acetate 0.22 0.18 0.51 0.84 0.37 0.75Propionate 0.34 0.24 -0.57 0.88 -0.62 0.89Butyrate 0.51 0.26 0.43 0.82 0.52 0.87Isobutyrate 0.46 0.27 -0.09 0.58 0.24 0.67Valerate 0.36 0.26 -0.50 0.83 -0.41 0.77Isovalerate 0.32 0.24 -0.01 0.50 0.26 0.681Standard deviation of the posterior distribution of h2 (SD); 2daily methane emissions (g/d)(CH4d); 3methane yield (g/kg dry matter intake) (CH4y); 4probability that the geneticcorrelation is different from zero (P0). Heritabilities of CH4d and CH4y were 0.46 (±0.19) and0.43 (±0.20), respectively.ConclusionsThe molar proportions of ruminal VFAs were found to be heritable and genetically correlatedwith CH4 emissions. These VFAs could be combined with the microbial gene-basedmicrobiome-driven breeding strategy to improve its accuracy to estimate breeding values forCH4 emissions. In addition, key microbial genes (asrsubunits), genetically correlated with bothVFAs and CH4 emissions were identified, which are of high value to be directly included intomicrobiome driven breeding to mitigate CH4 emissions. The asr genes are involved in thereduction of sulphite to sulphide and might compete with methanogenic archaea formolecular hydrogen (H2).AcknowledgmentsThis research was funded by the Scottish Government and based on data generated fromexperiments funded by the Scottish Government, BBSRC (BB/N01720X/1, BB/N016742/1,BB/S006567/1, and BB/S006680/1), AHDB, and QMS.ReferencesMartínez-Álvaro, M., Auffret, M.D., Duthie, C.-A., Dewhurst, R.J., Cleveland, M.A., Watson,M., and Roehe, R. 2022. Communications Biology 5, 350.Roehe, R., Dewhurst, R.J., Duthie, C.A., Rooke, J.A., McKain, N., Ross, D.W., Hyslop, J.J.,Waterhouse, A., Freeman, T.C., Watson, M. and Wallace, R.J. 2016. PLOS Genetics 12,e1005846

Cross-cultural variation in understanding of animal welfare principles and animal management practices among veterinary and animal welfare professionals in the UK and Japan

The World Organisation for Animal Health describes animal welfare as a “complex and multifacetedsubject with scientific, ethical, economic, cultural, social, religious and politicaldimensions.” In this study, an online survey in English and Japanese was developed based onthe Five Freedoms, with the aim of investigating attitudes of veterinarians and behaviour/welfarescientists in the United Kingdom (UK) and Japan toward management of companion, farmed,experimental, zoo and wildlife animals. Respondents from the UK (n = 212) were more familiarwith the Five Freedoms than those from Japan (n = 321) but both countries tended to prioritise‘survival-related’ attributes (health and nutrition) over ‘situation-related’ attributes (behaviour)and the environmental impacts (discomfort). In Japan, however, fewer respondents recognisedthe ‘Freedom to express normal behaviour’ as important for domesticated animals compared toUK respondents. When considering vignettes with practical situations of cat management anddog euthanasia, UK respondents considered the provision of outdoor access to represent bettermanagement for cat welfare while most Japanese respondents thought cats should be managedentirely indoors, although the benefits and risks of going outdoors were similarly recognised inboth countries. For the vignette of dog pain relating to an incurable tumour, severe pain and thedog’s mental stress motivated respondents from both countries to consider euthanasia. However,for Japanese respondents, the data suggested a perception that mental stress did not have anassociation with the dog’s inabilities to express normal behaviour. These data highlighted theimportance of understanding the manner in which people perceive animals in different contextsand the value of considering different cultural approaches

Timing, risk factors, and causes of foetal and preweaning lamb mortality in lowland production systems involving a range of ewe genotypes

Reducing lamb mortality has production, economic and animal welfare benefits. The timing and causes of death and associated risk factors were investigated in a study conducted over 2 consecutive years (involving 1 103 and 1 038 ewes in 2017 and 2018, respectively) in three prolific (average litter size 1.91) indoor-lambing, lowland flocks (in Ireland) that consisted of a range of genotypes, managed in grass-based systems of production. Data were collected from all foetuses and lambs that died (between ∼120 days gestation and weaning at 14 weeks of age); 221 cases in 2017 and 241 cases in 2018. All cases were submitted to a Regional Veterinary Laboratory for necropsy examination using standardised protocols that were developed in advance of case submissions. The majority (60%) of lamb mortality occurred prior to or within 24 h of birth: 46% at or prior to birth and 14% within the first 24 h. Infection (32%) and dystocia (20%) accounted for over half of the mortality. Chlamydia abortus was detected more often in lambs from 2-year-old ewes lambing for the first time than in lambs from older ewes. Dystocia accounted for a statistically significant higher proportion of deaths among purebred lambs born to Texel ewes (49.4%, 95%CI (confidence interval) 36.0 – 62.9) compared to purebred lambs born to Belclare ewes (12.8, 95%CI 2.2 – 23.5). More lambs failed to yield a diagnosis of the cause of death when born to Belclare ewes (29.2%, 95%CI 17.8 – 40.6) than to Suffolk-X ewes (7.4%, 95%CI 0.1 – 14.8). About one−third of lamb mortality cases were adjudged to be preventable through more consideration of management factors during pregnancy, parturition and early postpartum. The use of good hygiene practices at lambing time and optimising lamb birth weight should reduce the level of preweaning lamb mortality in indoor lambing flocks.</p