Frontiers in Veterinary Science

ABSTRACT Objective: Skeletal muscle growth rate differs substantially among diverse pig breeds. In the present study, RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. CCND2 showed obvious differential expression among pig breeds. Although CCND2 is essential for cell cycle control, its biological function in skeletal muscle differentiation has rarely been reported. This work aims to identify DEGs in pig breeds with different growth rates and explore CCND2 role in porcine skeletal muscle development. Methods: RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. Weighted gene co-expression network analysis (WGCNA) was used to identify gene modules potentially associated with skeletal muscle growth and development. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis was performed to validate the role of CCND2 in skeletal muscle differentiation. Results We identified 5,416, 4,846, and 2,777 DEGs in the Duroc pig (DU) vs. Jiangquan black pig (JQ), DU vs. Laiwu pigs (LW), and JQ vs. LW comparison groups, respectively. WGCNA identified two gene modules (lightgreen and darkmagenta) potentially associated with skeletal muscle growth and development. CCND2 exhibited differential expression in comparisons between DU vs JQ and DU vs LW, with higher expression observed in Duroc pigs. qRT-PCR analysis revealed that overexpression of CCND2 at day 6 (D6) of cell differentiation significantly increased the expression levels of CCND2 gene and markers of myogenic differentiation (p < 0.05). Conversely, knockdown of CCND2 significantly decreased the expression levels of CCND2 gene and myogenic differentiation markers (p < 0.05). Conclusions This study identified breed-specific DEGs and key gene modules in porcine skeletal muscle and verified that CCND2 promotes myogenic differentiation. These findings provide a genetic theoretical basis for further investigations into skeletal muscle growth and development. Keywords pig, skeletal muscle, transcriptome, WGCNA, CCND2

Skeletal dysplasias can occur in animals, including humans, and are attributed to both environmental and genetic causes. As our understanding of the distinguishing phenotypes of different skeletal dysplasias improves, alongside elucidation of the mechanisms and genetic networks that contribute to skeletal development, identifying and controlling genetic mutations in livestock populations has become increasingly possible, including approaches beyond selective breeding alone. Within Scotland an 'achondroplasia' syndrome that was first described in the South Country Cheviot breed of sheep (OMIA 000004-9940), has continued to occur periodically within the same geographical locations, despite culling of affected lambs over many decades. Affected lambs exhibit rounded heads, short legs, a loss of hooves, abnormal stance and short twisted tails. As the condition has been observed in flocks and as progeny from specific ram and ewe matings, and cases have been co-twinned to normal siblings, this suggests a syndrome caused by a recessive genetic condition rather than environmental factors. Through homozygosity mapping and whole genome sequence analyses, we identified a 10 bp deletion in the open reading frame of the PRICKLE1 gene that encodes prickle planar cell polarity protein 1 and is essential for normal vertebrate embryonic development. We identified additional phenotypes present in affected lambs, including a loss of phalanges, neural tube defects, vertebral and articular chondrocyte defects, hair orientation differences and polycystic kidneys, consistent with a loss of PRICKLE1 function based on comparisons to mouse mutant lines. These findings enabled the development of a simple DNA test for the identified PRICKLE1 mutation that was made commercially available to facilitate the elimination of this genetic disease from sheep flocks.

The emergence of Highly Pathogenic Avian Influenza (HPAI 2.3.4.4b) in dairy herds in 2024 across 19 states in the United States of America has raised concerns regarding the potential national and global zoonotic impact. All recent modeling efforts implemented homogenous cattle-to-cattle (both intra and inter-herd) transmission models which did not capture the real-world heterogeneity in mixing of animals, individual variations in susceptibility and infectiousness and clinical incidences across pens and lactation groups. The aim of this study was to develop a heterogenous transmission model to estimate the epidemiological parameters for intra-herd HPAI transmission on Californian dairies. We developed a validated stochastic agent-based model to estimate the epidemiological parameters for intra-herd HPAI transmission on California dairies. The hierarchical agent-based model also parameterized stochastic cattle movements within-herd to simulate real dairy management practices. A cow-level SEIR transmission approach was assumed during the outbreak. A novel Bayesian Optimizer with Gaussian Process (BO-GP) was fitted to the agent-based model for validation which converged within 25-40 iterations (out of 100 per farm) with minimal loss over two distinct error metrics, namely, Poisson loss function and temporal distance metric. Our optimized simulations estimated an average R0 was around 10.7-10.8 across all farms within the first 15 days of observed outbreak on four dairy farms with a mean effective transmission rate of 4.5% per contact between susceptible and infectious cows within each pen. Our model demonstrated that the movement of cows between pens ensured localized clusters of outbreaks within the sub-herds (pen population) that prolonged the overall outbreak within farms. We estimated the total duration of infection between 14.5 and 28 days, which is higher than the estimates from the homogenous models. With an integrated hierarchical agent-based model combined with Bayesian approximation, we produced actionable insights on the epidemiology of intra-farm spread of HPAI within cow herds, thereby guiding both future model development and applied disease control strategy.

Detection of postoperative pain in mice is challenging, and there is a need for unbiased, automated methods. Home-cage monitoring systems are promising, but their ability to detect mild pain remains unclear. We evaluated whether home-cage activity measures can be used to detect pain-related changes in a plantar incision model of postoperative pain. First, we confirmed the presence of local hypersensitivity using von Frey filaments on 48 C57BL/6JRj mice (24 males, 24 females). Subsequently, we pair-housed 64 mice (32 males, 32 females) and allocated them to receive either a 4 mm plantar incision on the hind paw under anaesthesia, or anaesthesia alone. Baseline locomotion and voluntary wheel-running activity were recorded over five days, followed by four days of postprocedural monitoring in the home cages. Both procedure groups (incision and anaesthesia-only) showed reduced locomotion and running wheel activity relative to baseline. However, activity measures did not differ between incised and anaesthesia-only mice, and we detected no sex-related effects. Under these conditions, home cage activity measures did not reliably discriminate pain-related behavioural changes in the model, despite the model showing local mechanical hypersensitivity in the von Frey test. Together, these findings indicate that, given the mild and localised nature of the plantar incision mouse model, commonly used home-cage metrics cannot yet reliably detect subtle pain-related behavioural changes.

Background: Bovine respiratory disease (BRD) is a major cause of antimicrobial use in cattle, raising concerns about antimicrobial resistance (AMR). This systematic review estimated pooled AMR proportions in BRD pathogens: Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, and assessed temporal and geographic trends in resistance. Methods: Five antimicrobials commonly used for BRD treatment were evaluated: penicillin G (PEN), tetracycline (TET), florfenicol (FLO), tulathromycin (TUL), and enrofloxacin (ENR). Following PRISMA guidelines, 1,097 records were screened and 24 studies met inclusion criteria. Study quality and risk of bias were assessed, and random-effects meta-analyses estimated pooled proportions of resistant isolates by antimicrobial, continent and period. Results: A total of 13,949 bacterial isolates were analysed including P. multocida (5,615), M. haemolytica (5,585), and H. somni (2,749). TET resistance was highest across all pathogens (12-30%), followed by TUL (6-11%), PEN (4-12%), FLO (0.5-1.6%) and ENR (0.2-1.1%). TET resistance in M. haemolytica and P. multocida, and FLO resistance in P. multocida were significantly more frequent in North America than in Europe (p[&le;]0.05). TUL resistance increased significantly in P. multocida after 2013 (p=0.038), with similar non significant trends in M. haemolytica and H. somni. FLO resistance decreased significantly in H. somni after 2013 (p=0.013). Egger's test identified significant funnel plot asymmetry for ENR resistance in H. somni and PEN resistance in M. haemolytica, suggesting possible small study effects. Conclusion: These results offer insights into distribution of phenotypic resistance across pathogens and regions, informing BRD antimicrobial treatment guidelines and One-Health antimicrobial stewardship aimed at preserving the effectiveness of medically important antimicrobials.

Background: The yak (Bos grunniens) is an essential livestock species in high-altitude alpine ecosystems, serving key roles in meat, milk, and wool production as well as ecological maintenance. However, traditional yak breeding systems face several limitations, including fragmented herd data management, inefficient phenotypic collection, missing pedigree records, and high technical barriers to applying genomic technologies. These factors constrain the widespread application of modern genetic evaluation methods in yak breeding programs. Description: We developed the Yak Genomic Evaluation Platform (YGEP, https://yakbreeding.swun.edu.cn/en/), an integrated digital system for yak genetic selection and herd management. YGEP integrates three core analytical modules: pedigree reconstruction, genotype imputation and genomic breeding value estimation. Benchmarking on 706 yaks showed that GBLUP achieved a prediction accuracy of r = 0.96 for cannon bone circumference (CCB), and KBeagle reached 84.0% imputation accuracy with the combined reference panel. Conclusion: YGEP bridges the gap between advanced genomic analytics and practical yak breeding. By integrating pedigree reconstruction, genotype imputation, and GEBV estimation into a user-friendly cloud platform, YGEP effectively eliminates technical and data bottlenecks. Overall, it provides an accessible, scalable, and standardized solution to advance digital herd management and precision genetic improvement in alpine livestock.

The study of animal personality has gained increasing attention in recent years, as researchers recognize that non-human animals exhibit stable individual differences in behaviour. In dairy cattle, understanding personality traits holds potential for improving animal welfare, enhancing management practices, and supporting productivity outcomes. However, validating the behavioural tests used to assess these traits remains a significant challenge. The present study aimed to evaluate the consistency and validity of five commonly used behavioural tests in dairy cows: the Human Approach Test (HAT), Sudden Test (SUD), Novel Object Test (NOT), Open Field Test (OFT), and Novel Surface Test (NST). These tests were chosen for their potential to assess personality dimensions that parallel components of human personality, particularly Openness, Neuroticism, Extraversion, and Agreeableness. Repeated assessments were conducted across three time periods to evaluate both intra-test (temporal) and inter-test (contextual) consistency. Results revealed that only the SUD exhibited significant behavioural consistency across all periods, suggesting its potential as a reliable tool for personality assessment. Additionally, a moderate correlation between the HAT and SUD was observed, indicating that these tests may capture overlapping personality traits. In contrast, the remaining tests (NOT, OFT, NST) lacked consistent behavioural patterns over time and across contexts, raising questions about their reliability and the complexity of trait expression. These findings highlight the challenges of identifying stable personality traits in cattle and emphasize the need for more rigorous validation of behavioural tests. This research contributes to the growing field of animal personality by providing insights into trait stability, the limitations of current testing methods, and the potential application of personality assessment in future livestock management practices.

Highly pathogenic avian influenza (HPAI) is among the most significant disease threats to poultry worldwide. Modelling challenges, where independent teams address a common epidemiological scenario, can support the development of response capabilities and strengthen communication between modellers and risk managers. Despite the established benefits of these exercises, they remain uncommon in animal health, and none have previously addressed avian influenza. Here Jolly Island, an artificial landscape of 9160 poultry farms with five production types, was developed and seeded with stochastic HPAI epidemics that ran their course over a three-to-four month period. From January through April 2026, 45 registered teams across five continents investigated a selected synthetic epidemic, producing probabilistic forecasts, inferring transmission drivers, and evaluating counterfactual control policies. Here the objectives, design choices, and data generation of the HPAI Modelling Challenge are described in full, covering transmission processes, surveillance system operations, and control strategy implementation, along with the selected epidemic trajectory, the narrative situation reports supplied to the teams at each phase, and the complete phase-specific datasets released to them. As the opening paper of this special issue, here is provided the foundation upon which all subsequent contributions, where teams document their approaches and analyses, are built.

Background: Microbiome research has linked microbial community structure to host phenotype, but translating microbiome-based discovery into defined interventions with reproducible long-term host effects remains challenging. We evaluated whether a defined four-member consortium of rumen native microorganisms identified through associations with host phenotype could influence herd retention. Cull outcomes (sold or died vs. retained in herd) were analyzed across 20 controlled commercial dairy trials encompassing more than 40,000 cattle housed across 110 experimental pens, with each trial conducted for at least 5 months. Treatment pens received a defined daily dose of Galaxis Frontier (GF, Native Microbials, San Diego, CA), containing Pichia kudriavzevii, Clostridium beijerinckii, Ruminococcus bovis, and Butyrivibrio fibrisolvens, incorporated into the ration; control and treatment groups were otherwise managed equivalently. Cow-level time to culling was modeled within each trial, accounting for pen-level clustering, and trial estimates were combined using random-effects meta-analysis. Results: Daily treatment with rumen native microbes was associated with a 9% lower hazard of culling across 20 trials (hazard ratio = 0.91, 95% confidence interval: 0.86-0.96; P < 0.001). Between trial heterogeneity was negligible, and treatment effects were not significantly moderated by breed or geographic region. Detailed health records from one trial were examined to further characterize health outcomes associated with GF; treatment was associated with fewer transition-related disorders, particularly ketosis and metritis, whereas mastitis and lameness were largely unaffected. These findings suggest that the health effects associated with GF may be more pronounced for disorders linked to physiological and metabolic adaptation during the transition period than for health events more broadly. Conclusion: Across diverse commercial dairy environments, treatment with a defined consortium of rumen native microbes was associated with improved dairy cow retention. The consistency of this association across independent trials provides large scale evidence that targeted application of native microorganisms can translate into reproducible, long-term outcomes for the host. Complementary health event data suggest that improved transition period health and metabolic stability may contribute to this effect. These findings support the potential for microbiome targeted interventions to influence productive longevity under commercial conditions.

Histomonosis, caused by Histomonas meleagridis, is a severe disease in poultry with main pathological lesions in ceca and liver, leading to significant animal suffering and economic losses, with no licensed treatments available. While cecal pathology and microbiota disruption have been documented, the metabolic consequences of infection and vaccination remain poorly understood. Here, we used untargeted LC-MS metabolomics to profile cecal tissue and luminal digesta in a controlled vaccination-challenge chicken trial (n=100, 25 birds/group), including uninfected and unvaccinated but challenged controls, together with birds vaccinated either cloacally, or orally via an edible gel following challenge, across five post-challenge timepoints. Results showed that H. meleagridis infection caused extensive, time-dependent disruption of the cecal metabolome, especially at 7-14 days post-infection (DPI). At DPI 14, 325 tissue and 359 digesta metabolites were significantly altered in unvaccinated challenged birds. Infection was associated with depletion of microbiota-related metabolites, including dicarboxylic acids, tryptophan indoles, phytochemical derivatives, bilirubin catabolites, phenolics, vitamins, and secondary bile acids, alongside accumulation of microbial substrates and fermentation products. Changes in the host-associated metabolites indicated mucosal inflammation, epithelial injury, mitochondrial and amino acid metabolic disturbance, oxidative stress, and membrane lipid remodeling. Cloacal vaccination provided greater metabolic protection than oral vaccination, with 78.3% of disrupted metabolites preserved at DPI 14, compared with 60.7% vaccination by oral gel delivery, pointing towards the importance of vaccine take. By DPI 21, cloacally vaccinated birds showed nearly complete metabolic recovery across most pathway groups, whereas gel-vaccinated birds retained broader metabolic disturbance. These findings reveal histomonosis as a disruption of the cecal host-microbiota metabolic interface and provide a metabolite-level framework for future studies of pathogenesis, vaccine development, and prevention strategies.

Background Opioid-free anaesthesia (OFA) has emerged as an alternative to opioid-based anaesthesia (OBA), but its benefit over OBA for postoperative quality of recovery (QoR) remains unclear. To address this question while limiting variability inherent in clinical studies, such as analgesic regimens and patient psychosocial factors, we investigated the effects of OFA versus OBA on postoperative recovery in a controlled preclinical mouse model. Methods Adult male and female C57BL/6J mice underwent laparotomy or sham procedures under isoflurane anaesthesia, and were randomly assigned to saline (control), fentanyl (OBA), or dexmedetomidine (OFA) as intraoperative analgesic adjuncts. All mice received multimodal postoperative analgesia, including carprofen. We adapted a standardised multidimensional recovery model using six behavioural endpoints reflecting human QoR domains: body weight, food intake, locomotor activity, mechanical sensitivity, sucrose preference, and social interaction. These endpoints were assessed on postoperative days 1, 2, 3, and 7. Plasma inflammatory cytokine and brain-derived neurotrophic factor (BDNF) concentrations were also measured in parallel as potential biological correlates of recovery. Results Over the study period, we observed no treatment effect across behavioural endpoints in laparotomised mice, including body weight (P=0.157), food intake (P=0.884), locomotor activity (P=0.864), mechanical sensitivity (P=0.628), sucrose preference (P=0.615), and social interaction (P=0.442). Composite QoR scores did not differ between OFA and OBA groups (P=0.569), with no differences in postoperative circulating inflammatory cytokine or BDNF concentrations. Conclusions Dexmedetomidine-based OFA and fentanyl-based OBA produced similar postoperative behavioural recovery, circulating inflammatory cytokine and BDNF trajectories in laparotomised mice receiving multimodal postoperative analgesia.

The gut-airway axis is increasingly recognised as an important determinant of respiratory health in livestock. However, the interactions among respiratory infections, microbial communities, mucosal barrier function, and microbial metabolism that underpin this axis remain poorly understood. Here, we combined longitudinal immunological, mucosal, microbiological, and metabolic analyses to characterise host-microbiota interactions during antibiotic treatment and experimental bovine respiratory disease (BRD). We found that the bovine respiratory tract is organised as a hierarchically structured mucosal ecosystem, with compartment-specific mucin expression patterns associated with distinct microbial communities. Within this framework, increasing respiratory pathogen loads were associated with greater clinical severity, oxidative stress, acute inflammation, and targeted alterations in mucosal regulation and microbial composition, while serum amyloid A emerged as the host biomarker most closely reflecting infection intensity. Although infection altered host and microbial states, antimicrobial treatment represented the dominant ecological perturbation. Antibiotic exposure reshaped both respiratory and intestinal microbial communities, reducing diversity, increasing community drift, and driving coordinated ecological transitions across the gut-airway axis that exceeded the effects of infection alone. Importantly, these compositional changes were accompanied by profound reductions in acetate, propionate, butyrate, and valerate, identifying short-chain fatty acids as a major functional consequence of gut microbiota disruption. Integrative multi-omics analyses revealed that mucosal organisation, microbial diversity, microbial metabolism, and immune activity were embedded within a highly structured gut-airway network. Together, these findings support a holobiont view of BRD in which disease outcomes emerge not only from pathogen-host interactions but also from ecological disturbances that propagate across interconnected mucosal compartments. Notably, antimicrobial treatment affected ecosystem structure and function more than infection itself, highlighting potential trade-offs between pathogen control and microbiota stability. Preserving microbial resilience and its metabolic functions may therefore represent an important component of future strategies to improve respiratory health and disease resilience in cattle.

Land use change is widely recognized as a major driver of emerging zoonotic diseases. Yet, while forest plantations are expanding worldwide, their consequences on the circulation of infectious agents in wildlife remain poorly understood. We investigated how native pine plantations and broadleaved habitats shape rodent-associated infectious hazard in the generalist wood mouse (Apodemus sylvaticus), in southwestern France. Using a multi-season survey, we screened 424 wood mice for a broad range of infectious taxa and compared infection probability and infected-host abundance among pine plantation edges, broadleaved hedgerows embedded within pine plantations and broadleaved forests. Using a combination of linear mixed model and joint species distribution modelling, we tested whether infectious hazard differed between pine plantations and broadleaved forests, whether broadleaved hedgerows shifted these patterns towards those observed in broadleaved forests, and how these habitat-related patterns varied across seasons. We detected 22 potentially infectious taxa, including nine recognized zoonotic bacteria. Season strongly influenced infectious patterns, while habitat effects were taxa and season dependent. In spring, pine plantation edges increased infection probability for Bartonella grahamii and Neoerhlichia mikurensis compared to broadleaved forest, but their strong negative effect on wood mouse abundance resulted in consistently lower infected-host abundance for most infectious taxa. Broadleaved hedgerows showed distinct and season-dependent patterns with infectious profiles resembling those of pine edges in spring, but with higher infectious hazard than both other habitats for several taxa in autumn. Our results highlight that habitat effects on infectious hazard cannot be inferred from infection probability alone. Pine plantations may reduce rodent-associated zoonotic hazard through their strong negative effect on host abundance, despite increasing infection probability for some agents. Forest diversification and restoration initiatives, such as broadleaved hedgerows here, may have unforeseen epidemiological consequences, underscoring the need to integrate disease ecology into forest management and restoration to anticipate variation in zoonotic risks, while maximizing ecological benefits.

Neoehrlichia mikurensis is widely detected in tick populations across Europe, yet its host range beyond small rodents remains poorly understood. Large wild mammals are frequently exposed to tick vectors, but their role in the transmission cycle of this bacterium is unclear. Wild boars (Sus scrofa) are among the most abundant large mammals in southern Sweden and commonly inhabit tick-infested environments, making them a potentially relevant host species. In this study, spleen samples from 87 wild boars collected between 2023 and 2025 across southern and central Sweden were analysed for the presence of N. mikurensis DNA using quantitative polymerase chain reaction. N. mikurensis DNA was not detected in any of the analysed samples, despite sampling in regions where the bacterium is known to be prevalent in ticks. These results indicate that wild boars may have a limited role in the maintenance of N. mikurensis in Sweden, although the possibility of rare or transient infection cannot be excluded. Despite being based on negative findings, this study contributes to a more comprehensive understanding of the host range of N. mikurensis and highlights the importance of continued evaluation of wildlife species in the transmission dynamics of tick-borne pathogens.

Infection following high-energy open fractures remains a major challenge. Open fractures are exposed to environmental and skin pathogens, which, along with traumatized tissue and implanted hardware, create a favorable environment for infection. 24-83% of open fractures yield positive culture results. Despite culture-positive wounds being at higher risk for infection, culture data are rarely used in clinical decision-making. Culture-positivity in open fractures is believed to indicate higher wound bioburden, but this hypothesis remains unconfirmed. This study aimed to correlate culture positivity and quantitative wound bioburden using next-generation sequencing (NGS) and to characterize patterns of bioburden and bacterial diversity amongst patients with open fracture and Fracture Related Infection. We hypothesized that higher wound bioburden would be associated with culture positivity. This secondary analysis of the METRC Bioburden Study included 78 patients with severe open tibia fractures who underwent standardized tissue sampling at definitive wound closure and at later fracture site revision surgery. DNA extracted from intraoperative tissue was analyzed via 16S rRNA gene amplicon sequencing. Quantitative bioburden metrics included bacterial read percentage and bacteria-to-human read ratio (BHR). Associations between sequencing-based bioburden, culture results, and clinical infection (CDC-defined) were evaluated using Mann-Whitney U tests, McNemars chi-squared tests, and unsupervised clustering analyses. Culture-positive samples exhibited significantly higher bacterial read percentages and higher log(BHR) values than culture-negative samples. Optimal thresholds yielded high sensitivity and specificity for both bacterial reads and BHR for predicting culture positivity. Neither baseline culture nor NGS positivity predicted later infection. However, follow-up samples from patients with established infection showed significantly higher bioburden and distinct microbiome structures. Clustering analyses identified two infection-associated microbial profiles: one with high bioburden and high diversity (polymicrobial infection) and one with low bioburden and low diversity (single-dominant pathogen). Culture positivity in open fractures correlates strongly with increased bacterial bioburden, indicating that positive cultures may primarily reflect microbial load rather than specific pathogens. Quantitative NGS-based measures, including bacterial read proportion and BHR, may offer a biologically grounded approach to assess wound contamination and may inform infection risk. Distinct bioburden-diversity patterns suggest heterogeneous infection phenotypes that may require tailored surgical and antimicrobial strategies.

The growth and performance of cattle is dependent on efficient feed conversion, facilitated by the gut microbiome, including both prokaryotic and eukaryotic organisms. Extrinsic factors such as management practices and intrinsic factors like age and genetics can shape these communities. To characterize the relative effects of such factors on the prokaryotic and eukaryotic microbiomes, fresh fecal samples from dairy heifers (n = 8), beef heifers (n = 8), bred beef heifers (n = 8), and adult beef cows (n = 8) were subjected to paired 16S rRNA (V4) and a novel 18S rRNA (V4-V5) metabarcoding assay, and 18S rRNA amplicons were annotated using two databases in parallel. Taxonomic resolution of 18S rRNA amplicons was excellent, with SILVA and EUKARYOME databases each providing better resolution of different groups of organisms. While no differences in eukaryotic richness or alpha diversity were detected, beta diversity differed in all pairwise comparisons except between beef heifers and bred beef heifers. Prokaryotic richness was lower in adult beef cows than the other groups, and beta diversity differed in all pairwise comparisons. Adult beef cows were the most distinct, characterized by replacement of fungal organisms with protozoa and loss of thermophilic bacteria in the eukaryotic and prokaryotic compartments, respectively. Among numerous differentially abundant features, dairy heifers harbored greater abundance of Cooperia oncophora while beef heifers contained greater abundance of Buxtonella sulcata and Mucor. Correlation network analysis revealed multiple significant positive and negative associations between bacterial, fungal, and protozoal features during maturation of the fecal microbiome. Collectively, these data highlight the richness and diversity of both the prokaryotic and eukaryotic compartments of the bovine fecal microbiome, and the influence of management practices and age on both communities. From a technical standpoint, these data demonstrate the ability to resolve fungal, protozoal, and metazoan organisms, including potential parasites and pathogens, with a single metabarcoding assay. They also highlight the nuanced differences between databases and the value of parallel analyses using more than one database.

Abstract Background Liposarcoma is a rare cancer, comprising four major histological subtypes: well-differentiated, dedifferentiated, myxoid and pleomorphic liposarcoma. Therapeutic options remain limited for advanced disease, and additional biomarkers that may support biological characterization, diagnosis, or risk stratification are needed. Methods Bulk RNA sequencing (RNA-seq) was performed on paired tumour and adjacent non-tumour tissues from an analysable subset of 16 patients (22 tumour specimens) within a clinicopathological cohort of 21 patients. Differential gene expression analysis, principal component analysis, gene set enrichment (GSEA) analysis and single-sample GSEA (ssGSEA) were used to define subtype-specific transcriptional programs and imprinted-gene dysregulation. PEG10 expression was validated by RT-qPCR and RNA fluorescence in situ hybridization (FISH), and its cellular localization was explored by combined FISH and immunofluorescence for P53, vimentin, Ki67, and CD34. PEG10 expression in liposarcoma was further investigated in an external single-cell RNA-sequencing dataset of dedifferentiated liposarcoma. An exploratory survival analysis was performed in the pan-sarcoma TCGA-SARC cohort. Results Transcriptomic profiling identified distinct subtype-specific gene expression patterns and broad dysregulation of imprinted genes in liposarcoma compared with adjacent non-tumour tissue. Among all the imprinted genes, PEG10 showed a marked tumour-to-normal expression difference and good discriminatory performance between tumour and normal tissues in the discovery cohort (AUC=0.867). In the TCGA sarcoma cohort high PEG10 expression was associated with shorter overall survival. Immuno-FISH and single-cell analyses revealed that PEG10 was predominantly detected in tumour and proliferating cell populations. Importantly, PEG10 expression was higher in high-grade tumours. In bulk RNA-seq data, PEG10 expression correlated with hypoxia, extracellular matrix remodelling and invasion ssGSEA signatures. In the external single-cell RNA-seq dataset PEG10high tumours showed a reduced immune cell infiltration. Conclusions This study provides an integrated transcriptomic characterisation of liposarcoma and identifies PEG10 as a candidate tumour-associated biomarker linked to aggressive disease features. The diagnostic and prognostic value of PEG10 requires validation in larger, independent, subtype-balanced liposarcoma cohorts, and its potential therapeutic relevance requires direct functional investigation.

Antimicrobial resistance (AMR) is a critical One Health challenge at the interface of agriculture, the environment and human health. In Ireland, cattle production systems generate large volumes of manure and slurry, which are routinely applied to land. However, data on the prevalence and environmental persistence of clinically important resistance phenotypes remain limited. This study investigated the occurrence, characterisation and persistence of extended-spectrum {beta}-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CPE), as well as fluoroquinolone-resistant bacteria on Irish cattle farms. A total of 450 pooled bovine faecal samples were collected from farms across 25 counties, screened using selective culture, antimicrobial susceptibility testing, and MALDI-TOF MS identification. Carbapenemase activity in presumptive CPE isolates was confirmed using phenotypic and biochemical assays, including MALDI-TOF MBT STAR analysis to demonstrate carbapenem hydrolysis. In parallel, a controlled persistence study evaluated the survival of phenotypically resistant ESBL and CPE bacteria in bovine slurry under simulated seasonal conditions. Overall, 29.6% of farms were positive for ESBL and/or CPE, with ESBL only resistance most prevalent (13.7%), followed by combined ESBL and CPE phenotypes (7.5%). Fluoroquinolone resistance was frequently detected and commonly co-occurred with {beta}-lactam resistance, indicating multidrug resistance. Escherichia coli was the dominant carrier of both ESBL and carbapenemase phenotypes. Persistence experiments demonstrated sustained phenotypic resistance in slurry for up to nine months under simulated winter conditions and up to three months during simulated summer conditions, with resistance becoming undetectable following extended verification. These findings demonstrate that clinically important AMR phenotypes are embedded within Irish cattle production systems and can persist in agricultural waste streams, highlighting slurry as a significant environmental reservoir with implications for environmental dissemination and One Health surveillance.

Macrophages, alongside mammary epithelial cells, are major contributors to the innate immune response triggered by bacterial invasion of the mammary gland. To investigate breed-specific immune mechanisms, we stimulated monocyte-derived macrophages from Holstein and Normande cattle with Escherichia coli and Streptococcus uberis, two major mastitis pathogens. We monitored bacterial survival using [methode] and profiled gene expression via RNA-seq. E. coli exhibited significantly higher survival 6 hours post-infection compared to S. uberis (p < 0.05). Moreover, E. coli induced a robust transcriptional response, with 4403 differentially expressed genes (FDR < 0.05, |log2FC| > 1), versus only 813 for S. uberis. Qualitative differences were also observed: genes such as CCL2 and CSF1 were uniquely induced by S. uberis. Additionally, macrophages from Holstein and Normande cattle showed distinct expression profiles: 185, 45, and 174 genes were differentially expressed at steady state or after E. coli or S. uberis stimulation, respectively. These genes were enriched in immune-related pathways. Overall, our results demonstrate a stronger response to E. coli, although S. uberis specifically induces a subset of genes. The observed breed-specific differences may reflect underlying immune mechanisms that could influence disease susceptibility, warranting further functional validation.

The 2026 Andes virus (ANDV) outbreak aboard the MV Hondius cruise ship resulted in 11 confirmed cases and 3 deaths and raised questions regarding the origin of infection, with much media focus resting on a landfill in Tierra del Fuego. We evaluated competing exposure hypotheses by assembling open data on reservoir host occurrences, rodent serosurveys, and historical ANDV outbreaks along with the index case's self-documented, publicly-posted citizen-science digital record of their movements. Historical outbreaks associated with human-to-human transmission were concentrated within a restricted region spanning southern Chile and adjacent western Argentina, coinciding with the distribution of the principal reservoir host, Oligoryzomys longicaudatus, and areas identified as elevated risk by multiple ecological and genetic models. The index case was documented within this transmission focus shortly before the putative exposure period. Together, our open data approach was able to rapidly locate initial exposure within the established ANDV transmission focus and develop scenarios to prioritise further epidemiological investigation.