Methane (CH4) emissions present a significant challenge to both environmental sustainability and energy efficiency in ruminants, including beef cattle that are born in dairy herds. Although numerous approaches, including alterations in feed and the use of additives, are under investigation to mitigate these emissions, the genetic selection of animals that produce lower levels of methane offers the potential for enduring and cumulative advantages. Transcriptome analysis represents a crucial advancement in elucidating the networks and mechanisms through which the ruminant genome influences methane emissions. In the present study, methane emissions were measured using a GreenFeed system in beef-on-dairy cattle (n = 11). High-throughput RNA sequencing was conducted on animal blood samples, followed by differential gene expression analysis using methane production (g/d) as a continuous trait. The analysis identified eleven differentially expressed genes (DEGs), including six downregulated (KIAA1211L, LOC107131224, OSCP1, IL12B, LOC618859, FREM1) and five upregulated (DSCAML1, OSBP2, ACAN, PRSS16, CD1B) genes (Padj < 0.05) with one gene exhibiting potential biomarker characteristics. Gene and cell enrichment, as well as pathway analysis, suggested that nervous, immune, and endocrine systems may be involved in ruminal methane production by beef-on-dairy cattle. These findings highlight the potential of transcriptomic biomarkers to guide genetic selection strategies, offering a sustainable pathway to reduce methane emissions and enhance both environmental and agricultural efficiency.

Abstract Background With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows. Methods Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes. Results Values are reported as mean ± SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7% ± 2.8%, P = 0.032; HC: 54.5% ± 3.4%, P = 0.048) compared to the Control (48.2% ± 3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81 ± 0.06 (Control) to 0.58 ± 0.05 for AP (P = 0.012) and 0.64 ± 0.05 for HC (P = 0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P < 0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways (P = 0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P = 0.0075) and methane emissions per unit of dry matter intake (CH4/DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P = 0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P = 0.035), alongside a significant reduction in methane intensity (CH4/DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments (P > 0.05). Conclusions In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.

Nutrition, healthcare and management of the rearing environment all interact and have an impact on the performance and feed efficiency of pre-weaned dairy calves. In a survey of 54 dairy farms in Northern Ireland, average daily gain (ADG) of 369 pre-weaned calves was assessed. Dietary and nutritional information detailing intake of milk or calf milk replacer (CMR) and the composition of milk/CMR and solid feed diets was collected. Environmental and hygiene-related parameters within calf rearing facilities were recorded. It was hypothesised that suboptimal environmental management conditions would negatively affect calf performance and cause the observed average daily gain and retained energy to fall below values predicted from nutritional intake alone. Factors that tended to be negatively associated with the observed calf ADG were increased time (>50%) below lower critical temperature (LCT), increased time (>10%) above 0.4 m/s airspeed and reduced straw dry matter (<70%). Potential calf ADG was predicted using the young calf model from the Nutrient Requirements of Dairy Cattle (8th Edition). The predicted and observed calf ADG and retained energy (RE) were compared to assess whether the individual observed calf ADG was greater, equal to or less than that predicted by the model. Environmental factors associated with calf ADG or RE being less than the model prediction included: greater than 30 animals housed in the calf house, increased time (>10%) above 0.4 m/s airspeed and where coliforms were detected in ≤50% of milk samples on that farm. These results demonstrate the relevance of management of the rearing environment in optimising pre-weaned calf performance and feed efficiency.

Minimising methane (CH4) emissions from livestock production is a global priority, and feed modifications, such as supplementing diets with microalgae, have previously been shown to help reducing enteric CH4 production. This study explored blood-derived host gene expression profiles from twenty lambs supplemented with increasing levels of microalgae oil to investigate their transcriptional responses associated with varying microalgae oil levels while also exploring the host systemic responses towards varied CH4 productions. Findings revealed no significant changes in CH4 production with increasing levels of microalgae oil intake through phenotypic analysis (P = 0.18). However inter-individual variations in CH4 production ranged from 27.02 to 47.86 g/day throughout the study period. Blood RNA-Sequencing identified 64 significant genes including DHCR7, DHCR24, HMGCS1, INSIG1, LSS, MSMO1, and SQLE, which were involved in lipid metabolism, and steroid biosynthesis that became enriched alongside increasing microalgae oil intake levels thereby contributing to a positive impact on lambs’ metabolic functions. Additionally, seven significant blood-expressed host genes (NME4, MARCHF3, PLXNB3, LOC132657460, LOC121819234, LOC105603087, LOC101116551) functionally enriched in nucleotide metabolic pathways and immune responses were identified to have significant positive associations with increasing CH4 production. Importantly, this study found no overlap between genes associated with microalgae oil intake and those linked to CH4 emissions. Findings suggest that microalgae oil intake and inter-individual variations in CH₄ production are associated with distinct blood-derived transcriptional responses. Although such signals should be interpreted as proxies for systemic host responses rather than direct measures of rumen-specific processes, these results emphasise the importance of considering host-associated molecular variations alongside dietary CH₄-mitigation strategies.

Methane (CH4) is a potent gas produced by ruminants and new measurement techniques are required to generate large datasets suitable for genetic analysis. One such technique are portable accumulation chambers (PAC), a short-term sampling method. The objectives of the current study were to explore the relationship between CH4 and carbon dioxide (CO2) output measured using both PAC and respiration chambers (RC) in growing lambs, and separately investigate the relationship among CH4, CO2 and measured ad libitum DM intake (DMI). Methane, CO2 and DMI were measured on 30 Suffolk and 30 Texel ewe lambs (age 253 ± 12 days) using the RC and PAC sequentially. The experiment was conducted over a 14-day period, with DMI measured from day 1 to 14; measurements in RC were conducted from day 10 to 12, while measurements in PAC were taken twice, the day immediately prior to the lambs entering the RC (day 9; PAC Pre-RC) and on the day lambs exited the RC (day 13; PAC Post-RC). Greater CH4 and CO2 output was measured in the RC than in the PAC (P<0.01); similarly mean CH4 yield was greater when measured in the RC (15.39 ± 0.452 g CH4/kg DMI) compared to PAC (8.01 ± 0.767 g CH4/kg DMI). A moderate correlation of 0.37 was found between CH4 output measured in PAC Pre-RC and the RC, the corresponding regression coefficient of CH4 output measured in the RC regressed on CH4 output measured in PAC Pre-RC was close to unity (0.74; SE 0.224). The variance of CH4 and CO2 output within measurement technique did not differ from each other (P>0.05). Moderate to strong correlations were found between CH4 and CO2 per kg of live-weight and CH4 and CO2 yield. Results from this study highlight the suitability of PAC as a ranking tool to rank animals based on their gaseous output when compared to the RC. However, repeated measurements separated by several days may be beneficial if precise rankings are required. Given the close to unity regression coefficient of CH4 output measured in the RC regressed on CH4 output measured in PAC Pre-RC suggests that PAC could also be potentially used to estimate absolute CH4 output, however further research is required to substantiate this claim. When DMI is unknown, CH4 and CO2 per kg of live-weight are a suitable alternative to the measurement of CH4 and CO2 yield.

Pre-weaned dairy calves are very susceptible to disease in the first months of life due to having a naïve immune system and because of the numerous physiological stressors they face. Hygiene management is a key element in minimizing enteric disease risk in calves by reducing their exposure to pathogens. Samples of milk, concentrate feed and drinking water, boot swabs of bedding and swabs of feed equipment were collected from 66 dairy farms as part of a survey of calf rearing practice and housing design. All the samples were cultured to determine total viable counts (TVC), total coliforms (TCC) and Escherichia coli as indicators of hygiene. Target ranges for levels of TVC, TCC and E. coli were defined from the literature and the sample results compared against them. The TVC targets in milk, MR and water were <4.0 log10 CFU/mL. TCC and E. coli targets of <1.1 log10 CFU/mL (the detection limit) were used for milk, MR, concentrate feed and feeding equipment. For water, the TCC and E. coli targets were <1.0 log10 CFU/100 mL. The targets used for bedding boot swabs were <6.3 log10 TVC CFU/mL and <5.7 log10 TCC or E. coli CFU/mL. Farm management factors were included as fixed effects in a generalized linear mixed model to determine the probability of samples being within each hygiene indicator target range. Milk replacer samples obtained from automatic feeders were more likely to be within the TVC target range (0.63 probability) than those prepared manually (0.34) or milk samples taken from the bulk tank (0.23). Concentrate feed samples taken from buckets in single-calf pens were more likely to have E. coli detected (0.89) than samples taken from group pen troughs (0.97). A very small proportion of water samples were within the indicator targets (TVC 9.8%, TCC 6.0%, E. coli 10.2%). Water from self-fill drinkers had a lower likelihood of being within the TVC target (0.03) than manually filled buckets (0.14), and water samples from single pens were more likely to be within TCC target ranges (0.12) than those from group pens (0.03). However, all self-fill drinkers were located in group pens so these results are likely confounded. Where milk feeders were cleaned after every feed, there was a greater likelihood of being within the TVC target range (0.47, compared with 0.23 when not cleaned after every feed). Detection of coliforms in milk replacer mixing utensils was linked with reduced probability of TVC (0.17, compared with 0.43 when coliforms were not detected) and TCC (0.38, compared with 0.62), which was within target in feeders. Key factors related to increased probability of bedding samples being within TCC target range were use of group calf pens (0.96) rather than single-calf pens (0.80), use of solid floors (0.96, compared with 0.76 for permeable floors) and increased space allowance of calves (0.94 for pens with ≥2 m2/calf, compared with 0.79 for pens with <2 m2/calf). Bedding TVC was more likely to be within the target range in group (0.84) rather than in single pens (0.66). The results show that hygiene levels in the calf rearing environment vary across farms and that management and housing design impact hygiene.

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

The objective of this study was to investigate the impact of sire on variation in methane (CH4) production and dry matter intake (DMI). Methane emissions were measured on 60 Suffolk and Texel ewe lambs from 20 sires using respiration chambers (RC) and portable accumulation chambers (PAC). Daily DMI was measured on lambs fed an ad libitum grass pellet diet. The mean CH4 output was 13.65±2.63 g/day (PAC Pre-RC), 28.07±4.96 g/day (RC) and 13.53±3.83 g/day (PAC Post-RC). Methane production differed by sire (P<0.05) and varied from 20.70 to 40.25 g/day in the RC. A strong correlation (0.68) was observed between CH4 output measured in PAC Pre-RC and RC. Dry matter intake differed by sire (P<0.05). Methane production did not differ by breed (P>0.05), however, DMI differed by breed (P<0.05), with greater intakes associated with Suffolk (2.14 kg DM/day) compared to Texel lambs (2.01 kg DM/day).

Cattle production necessitates potentially dangerous human–animal interactions. Cattle are physically strong, large animals that can inflict injuries on humans accidentally or through aggressive behaviour. This study provides a systematic review of literature relating to farm management practices (including humans involved, facilities, and the individual animal) associated with cattle temperament and human’s on-farm safety. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) was used to frame the review. Population, Exposure, and Outcomes (PEO) components of the research question are defined as “Bovine” (population), “Handling” (exposure), and outcomes of “Behaviour”, and “Safety”. The review included 17 papers and identified six main themes: actions of humans; human demographics, attitude, and experience; facilities and the environment; the animal involved; under-reporting and poor records; and mitigation of dangerous interactions. Cattle-related incidents were found to be underreported, with contradictory advice to prevent injury. The introduction of standardised reporting and recording of incidents to clearly identify the behaviours and facilities which increase injuries could inform policy to reduce injuries. Global differences in management systems and animal types mean that it would be impractical to impose global methods of best practice to reduce the chance of injury. Thus, any recommendations should be regionally specific, easily accessible, and practicable.

Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million deaths annually. Agricultural and soil environments act as antimicrobial resistance gene (ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing and dissemination of resistance genes. Due to the close interactions between humans and agricultural environments, these AMR gene reservoirs are a major risk to both human and animal health. In this study, we aimed to identify the resistance gene reservoirs present in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with those from soil. This large study brings together every poultry, swine, ruminant, and soil shotgun metagenomic sequence available on the NCBI sequence read archive for the first time. We use the ResFinder database to identify acquired antimicrobial resistance genes in over 5,800 metagenomes. ARGs were diverse and widespread within the metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance genes were the most widespread in the livestock GI microbiomes, including tet(W)_1, tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were “real” and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were shared by the four microbiomes, with 11 ARGs actively expressed in two or more microbiomes. By using all available metagenomes we were able to mine a large number of samples and describe resistomes in 37 countries. This study provides a global insight into the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes.

Abstract The aim of this study was to assess the effects of feeding immunized egg proteins (IEP) on the health and performance of newborn dairy calves. Sixty‐four Holstein calves, both male and female, were divided over two treatments. Calves either received IEP or a placebo (PCB) in their colostrum and calf milk replacer (CMR) for the first 14 days of their life. Until day 49, CMR was offered at 15% of birth weight (BW), at 10% on days 49–57 and at 5% on days 57–63. In addition, calves received starter concentrate, chopped straw and water from 3 days old until 70 days old at the end of study. Individual CMR and concentrate intake were measured daily whilst BW was recorded weekly. Visual faecal scoring and health observations were conducted daily. Faecal samples were collected weekly up to 4 weeks and during the first 4 days of scouring to screen for presence of Cryptosporidium parvum, rotavirus, coronavirus, E. coli and Salmonella. Results indicated that feeding IEP increased BW (p < .05) at 42 and 56 days old, and BW also tended (p = .06) to be higher after weaning at 63–70 days old compared to the PCB group. When analysed using a repeated measures model, compared to feeding PCB, feeding IEP increased total concentrate consumption (p = .001) by 3.6kg/calf. Over the entire study, daily water intake was higher (p = .002) for the IEP group when compared with the PCB group. In the IEP group, 12 calves were scored as scouring whereas there were 14 calves in the PCB group. There were no significant differences between treatments in faecal pathogen load of neither healthy nor scouring calves. In conclusion, supplementing IEP during the first 14 days of calf life improved the performance of newborn calves. Further work is warranted to understand the mode of action of IEP in calves.

The first few months of life are of great importance to the longevity and lifetime performance of dairy cows. The nutrition, environment and healthcare management of heifer calves must be sufficient to minimise exposure to stress and disease and enable them to perform to their genetic potential. Lack of reporting of farm management practices in Northern Ireland (NI) makes it difficult to understand where issues impacting health, welfare and performance may occur in the rearing process. The objective of this study was to investigate housing design and management practices of calves on 66 dairy farms across NI over a 3-month period and also identify areas that may cause high risk of poor health and performance in dairy calves. An initial survey was used to detail housing and management practices, with two subsequent visits to each farm used to collect animal and housing-based measurements linked to hygiene management, animal health and performance. Large variations in key elements such as weaning criteria and method, calf grouping method used, nutritional feed plane, and routine hygiene management were identified. The specification of housing, in particular ventilation and stocking density, was highlighted as a potential limiting factor for calf health and performance. Lack of measurement of nutritional inputs, hygiene management practices and calf performance was observed. This poses a risk to farmers' ability to ensure the effectiveness of key management strategies and recognise poor calf performance and health.

This study aimed to use a range of non-invasive monitoring technologies to investigate the behavioural and physiological responses of individually housed dairy calves to age at change in milk replacer (MR) feeding frequency. Forty-eight Holstein Friesian calves were individually penned and fed MR (625 g/d) as solids in one of three feeding regimes: (i) once-a-day feeding commencing at age 14 d (OAD14), (ii) once-a-day feeding commencing at age 28 d (OAD28) and (iii) twice-a-day feeding (TAD). Several behavioural (automatic activity sensors), physiological (infrared [IR] thermography and heart rate variability [HRV]) and haematological indicators were used to examine calf responses. Reduction in milk feeding frequency at 14 or 28 d of age increased daily concentrate intakes and drinking water consumption throughout the pre-wean period. Calf lying behaviour was unaffected by reduction in milk feeding frequency; however, TAD calves recorded a significant decrease in total daily lying time during the post-wean period compared with OAD28s. There was no effect of treatment on IR eye or rectal temperature throughout the experiment; however, there was an effect of age, with IR temperature decreasing as calf age increased. OAD14 calves tended to have decreased HRV at days 14 and 16, which is suggestive of an increased stress load. The findings suggest that under high levels of animal husbandry and whilst maintaining the same amount of milk powder/d (625 g/d), reduction in milk feeding frequency from twice to once daily at 28 d can occur without significant impact to behavioural, performance and physiological parameters assessed here.