Methods for assessing dairy cattle welfare, such as the gold standard Qualitative Behaviour Assessment (QBA), require training and are time consuming in a sector facing labour constraints and staffing shortages. This research explores whether automated measurements from existing animal-mounted sensors can be used as a basis for objective welfare assessment in dairy cattle, supporting consumer, processor and farmer needs by demonstrating positive welfare on farm. Data (mean standing and lying duration, mean standing and lying bout frequency, mean standing and lying bout duration, mean maximum standing and lying bout duration, mean lying and standing bout frequency, mean step count) were acquired from commercially available ankle-mounted accelerometers intended for oestrus detection and compared to 20 QBA metrics from 107 animals at pasture and during housing on four dairy farms. Our analysis showed that sensor data was significantly correlated with QBA data, suggesting that sensor data can be used to accurately characterise animal behaviour. Although sensor data was influenced by location (housed and pasture), data obtained from ankle-mounted pedometers showed high accuracy (61

Two 10-day in vitro experiments were conducted to investigate the relationship between nitrogen (N) isotope discrimination (delta 15N) and ammonia (NH3) emissions from sheep manure. In Exp. 1, three different manure mixtures were set up: control (C); C mixed with lignite (C + L); and grape marc (GM), with 5, 4 and 5 replications, respectively. For C, urine and faeces were collected from sheep fed a diet of 550 g lucerne hay/kg, 400 g barley grain/kg and 50 g faba bean/kg; for C + L, urine and faeces were collected from sheep fed the C diet and 100 g ground lignite added to each incubation system at the start of the experiment; for GM, urine and faeces were collected from sheep fed a diet consisting of C diet with 200 g/kg of the diet replaced with GM. In Exp. 2, three different urine-faeces mixtures were set up: 2U:1F, 1.4U:1F and 1U:1F with urine to faeces ratios of 2:1, 1.4:1 and 1:1, respectively, each with 5 replications. Lignite in C + L led to significantly lower cumulative manure-N loss by 81 and 68% in comparison with C and GM groups, respectively (P = 0.001). Cumulative emitted manure NH3-N was lower in C + L than C and GM groups by 35 and 36%, respectively (P = 0.020). Emitted manure NH3-N was higher in 2U:1F compared to 1.4U:1F and 1U:1F by 18 and 26%, respectively (P < 0.001). This confirms the relationship between manure delta 15N and cumulative NH3-N loss reported by earlier studies, which may be useful for estimating NH3 losses.

Background Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage. Results By analysing longitudinal body weights during the finishing period and genomic and metagenomic data from 359 beef cattle, our study demonstrates that the influence of the host genome on the functional rumen microbiome contributes to the temporal variation in average daily gain (ADG) in different months (ADG 1 , ADG 2 , ADG 3 , ADG 4 ). Five hundred and thirty-three additive log-ratio transformed microbial genes ( alr -MG) had non-zero genomic correlations (r g ) with at least one ADG-trait (ranging from |0.21| to |0.42|). Only a few alr -MG correlated with more than one ADG-trait, which suggests that a differential host-microbiome determinism underlies ADG at different stages. These alr -MG were involved in ribosomal biosynthesis, energy processes, sulphur and aminoacid metabolism and transport, or lipopolysaccharide signalling, among others. We selected two alternative subsets of 32 alr -MG that had a non-uniform or a uniform r g sign with all the ADG-traits, regardless of the r g magnitude, and used them to develop a microbiome-driven breeding strategy based on alr -MG only, or combined with ADG-traits, which was aimed at shaping the rumen microbiome towards increased ADG at all finishing stages. Combining alr -MG information with ADG records increased prediction accuracy of genomic estimated breeding values (GEBV) by 11 to 22% relative to the direct breeding strategy (using ADG-traits only), whereas using microbiome information, only, achieved lower accuracies (from 7 to 41%). Predicted selection responses varied consistently with accuracies. Restricting alr -MG based on their r g sign (uniform subset) did not yield a gain in the predicted response compared to the non-uniform subset, which is explained by the absence of alr -MG showing non-zero r g at least with more than one of the ADG-traits. Conclusions Our work sheds light on the role of the microbial metabolism in the growth trajectory of beef cattle at the genomic level and provides insights into the potential benefits of using microbiome information in future genomic breeding programs to accurately estimate GEBV and increase ADG at each finishing stage in beef cattle.

Currently, the dairy industry is facing many challenges that could affect its sustainability, including climate change and public perception of the industry. As a result, interest is increasing in the concept of identifying resilient animals, those with a long productive lifespan, as well as good reproductive performance and milk yield. There is much evidence that events in utero, that is, the developmental origins of health and disease hypothesis, alter the life-course health of offspring and we hypothesized that these could alter resilience in calves, where resilience is identified using lifetime data. The aim of this study was to quantify lifetime resilience scores (LRS) using an existing scoring system, based on longevity with secondary corrections for age at first calving and calving interval, and to quantify the effects of in utero events on the LRS using 2 datasets. The first was a large dataset of cattle on 83 farms in Great Britain born from 2006 to 2015 and the second was a smaller, more granular dataset of cattle born between 2003 and 2015 in the Langhill research herd at Scotland's Rural College. Events during dam's pregnancy included health events (lameness, mastitis, use of an antibiotic or anti-inflammatory medication), the effect of heat stress as measured by temperature-humidity index, and perturbations in milk yield and quality (somatic cell count, percentage fat, percentage protein and fat: protein ratio). Daughters born to dams that experienced higher temperature-humidity indexes while they were in utero during the first and third trimesters of pregnancy had lower LRS. Daughter LRS were also lower where milk yields or median fat percentages in the first trimester were low, and when milk yields were high in the third trimester. Dam LRS was positively associated with LRS of their offspring; however, as parity of the dam increased, LRS of their calves decreased. Similarly, in the Langhill herd, dams of a higher parity produced calves with lower LRS. Additionally, dams that recorded a high maximum locomotion score in the third trimester of pregnancy were negatively associated with lower calf LRS in the Langhill herd. Our results suggest that events that occur during pregnancy have lifelong consequences for the calf's lifetime performance. However, experience of higher temperature-humidity indexes, higher dam LRS, and mothers in higher parities explained a relatively small proportion of variation in offspring LRS, which suggests that other factors play a substantial role in determining calf LRS. Although "big data" can contain a considerable amount of noise, similar findings between the 2 datasets indicate it is likely these findings are real.

The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal stability of rumen microbiomes considering taxonomic and functional aspects across the 7-month growing-finishing phase spanning 6 timepoints. We identified a temporally stable core microbiome, encompassing 515 microbial genera (e.g., Methanobacterium) and 417 microbial KEGG genes (e.g., K00856-adenosine kinase). The temporally stable core microbiome profiles collected from all timepoints were strongly associated with production traits with substantial economic and environmental impact (e.g., average daily gain, daily feed intake, and methane emissions); 515 microbial genera explained 45-83%, and 417 microbial genes explained 44-83% of their phenotypic variation. Microbiome profiles influenced by the bovine genome explained 54-87% of the genetic variation of bovine traits. Overall, our results provide evidence that the temporally stable core microbiome identified can accurately predict host performance traits at phenotypic and genetic level based on a single timepoint sample taken as early as 7 months prior to slaughter.

To meet the objectives of the Paris Agreement, which aims to limit the increase in global temperature to 1.5°C, significant greenhouse gas (GHG) emission reductions will be needed across all sectors. This includes agriculture which accounts for a significant proportion of global GHG emissions. There is therefore a pressing need for the uptake of new technologies on farms to reduce GHG emissions and move towards current policy targets. Recently, precision livestock farming (PLF) technologies have been highlighted as a promising GHG mitigation strategy to indirectly reduce GHG emissions through increasing production efficiencies. Using Scotland as a case study, average data from the Scottish Cattle Tracing System (CTS) was used to create two baseline beef production scenarios (one grazing and one housed system) and emission estimates were calculated using the Agrecalc carbon footprinting tool. The effects of adopting various PLF technologies on whole farm and product emissions were then modelled. Scenarios included adoption of automatic weigh platforms, accelerometer-based sensors for oestrus detection (fertility sensors) and accelerometer-based sensors for early disease detection (health sensors). Model assumptions were based on validated technologies, direct experience from farms and expert opinion. Adoption of all three PLF technologies reduced total emissions (kg CO2e) and product emissions (kg CO2e/kg deadweight) in both the grazing and housed systems. In general, adoption of PLF technologies had a larger impact in the housed system than in the grazing system. For example, while health sensors reduced total emissions by 6.1% in the housed system, their impact was slightly lower in the grazing system at 4.4%. The largest reduction in total emissions was seen following the adoption of an automatic weight platform which reduced the age at slaughter by 3 months in the grazing system (6.8%) and sensors for health monitoring in the housed system (6.1%). Health sensors also resulted in the largest reduction in product emissions for both the housed (12.0%) and grazing systems (10.5%). These findings suggest PLF could be an effective GHG mitigation strategy for beef systems in Scotland. Although this study utilised data from beef farms in Scotland, comparable emission reductions are likely attainable in other European countries with similar farming systems.

Precision livestock farming (PLF) tools are increasingly used in daily herd management to improve health, welfare, and overall production. While not intended to reduce greenhouse gas (GHG) emissions on farm, PLF tools can do so indirectly by improving overall efficiency, thereby reducing the emissions per unit of product. This work modelled the potential effects of commercially available PLF tools on whole enterprise and product emissions of two average Scottish dairy farm systems (an 8,000 L and 10,000 L herd) using the Agrecalc carbon footprinting tool. Scenarios modelled included an improvement in fertility and an improvement in fertility and yield from the introduction of an accelerometer-based sensor, and an improvement in health from introduction of an accelerometer-based sensor, with and without the use of management interventions. Use of a sensor intended to improve fertility had the largest reduction in total emissions (kg CO2e) of −1.42% for a 10,000 L farm, with management changes applied. The largest reduction in emissions from milk production (kg CO2e) of −2.31% was observed via fertility technology application in an 8,000 L farm, without management changes. The largest reduction in kg CO2e per kg fat and protein corrected milk of −6.72% was observed from an improvement in fertility and yield in a 10,000 L herd, with management changes. This study has highlighted the realistic opportunities available to dairy farmers in low and high input dairy systems to reduce their emissions through adoption of animal mounted PLF technologies.

Agriculture is the largest source of methane globally, and enteric methane accounts for 32% of methane emissions globally. Dairy–beef is an increasingly important contributor to the beef industry. The objective of this study was to investigate if supplementation with a blend of essential oils (Agolin Ruminant) reduced enteric methane emissions from dairy-bred steers. Methane was measured from thirty-six Holstein Friesian steers (18 control and 18 treatment) in open-circuit respiration chambers, at three time-points relative to the introduction of Agolin Ruminant: (i) −3 (pre-additive introduction co-variate), (ii) 46 days after introduction, and (iii) 116 days after introduction. A significantly lower methane yield was observed in treated animals compared to control animals at both 46 days (p < 0.05) and 116 days (p < 0.01) after the introduction of Agolin Ruminant, although there was no difference in methane production (g/day). Control animals appeared to be more affected by isolation in respiration chambers than animals receiving Agolin Ruminant, as indicated by a significant reduction in dry matter intake by control animals in respiration chambers.

Rumen microbial protein synthesis (MPS) provides at least half of the amino acids for the synthesis of milk and meat protein in ruminants. As such, it is fundamental to global food protein security. Estimating microbial protein is central to diet formulation, maximising nitrogen (N)-use efficiency and reducing N losses to the environment. Whilst factors influencing MPS are well established in vitro, techniques for in vivo estimates, including older techniques with cannulated animals and the more recent technique based on urinary purine derivative (UPD) excretion, are subject to large experimental errors. Consequently, models of MPS used in protein rationing are imprecise, resulting in wasted feed protein and unnecessary N losses to the environment. Newer ‘omics’ techniques are used to characterise microbial communities, their genes and resultant proteins and metabolites. An analysis of microbial communities and genes has recently been used successfully to model complex rumen-related traits, including feed conversion efficiency and methane emissions. Since microbial proteins are more directly related to microbial genes, we expect a strong relationship between rumen metataxonomics/metagenomics and MPS. The main aims of this review are to gauge the understanding of factors affecting MPS, including the use of the UPD technique, and explore whether omics-focused studies could improve the predictability of MPS, with a focus on beef cattle.

Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.

The temporal stability of rumen microbiome composition is very important for microbiome-driven breeding of host performance traits because it helps to identify the number of samples needed over time and best timepoints to obtain highly informative samples. Therefore, we investigated the temporal stability of the abundances of host-genomically influenced microbial genes throughout the finishing phase in beef cattle, and their associations with estimated breeding values (EBVs) of host traits such as feed conversion efficiency and methane emissions. Our results indicate that rumen microbiome profiles generated from different timepoints throughout the finishing phase are remarkably stable, with pairwise correlations of 0.74 or higher, and that their associations with EBVs of host traits were stable and strong throughout. Based on these results, we concluded that microbiome profiles at any sampling timepoint are representative of the finishing phase and can be used to predict EBVs of performance traits at similar accuracy.

In this study, 18 animals were fed two forage-based diets: red clover (RC) and grass silage (GS), in a crossover-design experiment in which methane (CH4) emissions were recorded in respiration chambers. Rumen samples obtained through naso-gastric sampling tubes were analysed by NMR. Methane yield (g/kg DM) was significantly lower from animals fed RC (17.8 ± 3.17) compared to GS (21.2 ± 4.61) p = 0.008. In total 42 metabolites were identified, 6 showing significant differences between diets (acetate, propionate, butyrate, valerate, 3-phenylopropionate, and 2-hydroxyvalerate). Partial least squares discriminant analysis (PLS-DA) was used to assess which metabolites were more important to distinguish between diets and partial least squares (PLS) regressions were used to assess which metabolites were more strongly associated with the variation in CH4 emissions. Acetate, butyrate and propionate along with dimethylamine were important for the distinction between diets according to the PLS-DA results. PLS regression revealed that diet and dry matter intake are key factors to explain CH4 variation when included in the model. Additionally, PLS was conducted within diet, revealing that the association between metabolites and CH4 emissions can be conditioned by diet. These results provide new insights into the methylotrophic methanogenic pathway, confirming that metabolite profiles change according to diet composition, with consequences for CH4 emissions.

•We aimed to establish common guidelines for experimental studies with cattle.•A book on “Methods in cattle physiology and behaviour research” was published.•The book is designed as an open-access living handbook and is open to everyone.•Citing the book saves space and avoids repetitions in scientific journals.•Referencing guidelines reduces apparent plagiarism among authors.