A computer vision approach to improving cattle digestive health by the monitoring of faecal samples.

The digestive health of cows is one of the primary factors that determine their well-being and productivity. Under- and over-feeding are both commonplace in the beef and dairy industry; leading to welfare issues, negative environmental impacts, and economic losses. Unfortunately, digestive health is difficult for farmers to routinely monitor in large farms due to many factors including the need to transport faecal samples to a laboratory for compositional analysis. This paper describes a novel means for monitoring digestive health via a low-cost and easy to use imaging device based on computer vision. The method involves the rapid capture of multiple visible and near-infrared images of faecal samples. A novel three-dimensional analysis algorithm is then applied to objectively score the condition of the sample based on its geometrical features. While there is no universal ground truth for comparison of results, the order of scores matched a qualitative human prediction very closely. The algorithm is also able to detect the presence of undigested fibres and corn kernels using a deep learning approach. Detection rates for corn and fibre in image regions were of the order 90%. These results indicate the potential to develop this system for on-farm, real time monitoring of the digestive health of individual animals, allowing early intervention to effectively adjust feeding strategy.

Evaluating lifetime nitrogen use efficiency of dairy cattle: A modelling approach.

The increased nitrogen (N) use efficiency in cattle farming is proposed as a key action to improve N management and reduce the environmental impact of cattle farming systems. Most attention has been given to lactating cow nutrition, excluding the elements of fertility, disease, and the non-lactating animals within the herd. Therefore, the aim of the current study was to develop a herd-level simulation model incorporating these elements to assess dairy farm N use efficiency. We developed a cattle N use efficiency (CNE) model with six primary compartments: (i) heifer growth, (ii) heifer removal, (iii) pregnancy, (iv) cow removal, (v) disease and fertility, and (vi) milk production. The CNE model calculates N loss or gain for each compartment, and then calculates the lifetime N loss or gain taking into account the replacement rate (rep) and/or the corresponding number of lactations in a herd (Lact = 1/rep). Finally, three N use efficiencies were estimated: (i) ReplNE: replacement cattle N use efficiency, (ii) LactNE: lifetime N use efficiency for lactation, and (iii) LNE: lifetime N use efficiency. The sensitivity of the model to variation in farm- and animal-related input values was evaluated using Monte Carlo simulation. Values for a model dairy farm were used based on published data reflecting typical dairy farming practices in the United Kingdom. To assist reporting net values of main N outputs, a dairy herd of 100 lactating cows was modelled. Productive N outputs (1000s of kg) over the course of an animal's lifetime, partitioned into milk and meat, were dominated by milk production (89% of total N output). We estimated a mean ReplNE of 23.7%, affected most by the last stage of heifer growth. The Monte Carlo sensitivity analysis suggested that variation in time to first calving (T1stCal) might cause larger changes on ReplNE than variation in feed. The sensitivity analysis revealed a strong positive correlation between dietary oriented milk N use efficiency (MNE) and LactNE and LNE (r = 0.99 and 0.97 for LactNE and LNE, respectively). However, our study highlighted two other model variables that affected LNE. Variation in calving interval (CI; r = -0.15) and T1stCal (r = -0.15) may cause measurable reductions of overall LNE. The first is an indicator of lactating cattle fertility, and the second an indicator of replacement cattle growth and fertility efficiency. In conclusion, with the current study we provided a dairy cattle herd model that is sensitive in elements of diet, fertility and health. Lifetime N use efficiency of dairy cattle is dominated by MNE, but we detected specific non-diet related variables that affect ReplNE, LactNE and LNE.

Spatially explicit estimation of heat stress-related impacts of climate change on the milk production of dairy cows in the United Kingdom.

Dairy farming is one the most important sectors of United Kingdom (UK) agriculture. It faces major challenges due to climate change, which will have direct impacts on dairy cows as a result of heat stress. In the absence of adaptations, this could potentially lead to considerable milk loss. Using an 11-member climate projection ensemble, as well as an ensemble of 18 milk loss estimation methods, temporal changes in milk production of UK dairy cows were estimated for the 21st century at a 25 km resolution in a spatially-explicit way. While increases in UK temperatures are projected to lead to relatively low average annual milk losses, even for southern UK regions (<180 kg/cow), the 'hottest' 25×25 km grid cell in the hottest year in the 2090s, showed an annual milk loss exceeding 1300 kg/cow. This figure represents approximately 17% of the potential milk production of today's average cow. Despite the potential considerable inter-annual variability of annual milk loss, as well as the large differences between the climate projections, the variety of calculation methods is likely to introduce even greater uncertainty into milk loss estimations. To address this issue, a novel, more biologically-appropriate mechanism of estimating milk loss is proposed that provides more realistic future projections. We conclude that South West England is the region most vulnerable to climate change economically, because it is characterised by a high dairy herd density and therefore potentially high heat stress-related milk loss. In the absence of mitigation measures, estimated heat stress-related annual income loss for this region by the end of this century may reach £13.4M in average years and £33.8M in extreme years.

Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows?

It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.

Traditional vs modern: role of breed type in determining enteric methane emissions from cattle grazing as part of contrasting grassland-based systems.

Ruminant livestock turn forages and poor-quality feeds into human edible products, but enteric methane (CH4) emissions from ruminants are a significant contributor to greenhouse gases (GHGs) and hence to climate change. Despite the predominance of pasture-based beef production systems in many parts of Europe there are little data available regarding enteric CH4 emissions from free-ranging grazing cattle. It is possible that differences in physiology or behaviour could influence comparative emissions intensities for traditional and modern breed types depending on the nutritional characteristics of the herbage grazed. This study investigated the role of breed type in influencing CH4 emissions from growing beef steers managed on contrasting grasslands typical of intensive (lowland) and extensive (upland) production systems. Using the SF6 dilution technique CH4 emissions were estimated for a modern, fast-growing crossbred (Limousin cross) and a smaller and hardier native breed (Welsh Black) when grazing lowland perennial ryegrass (high nutritional density, low sward heterogeneity) and semi-improved upland pasture (low/medium nutritional density, high sward heterogeneity). Live-weight gain was substantially lower for steers on the upland system compared to the lowland system (0.31 vs. 1.04 kg d-1; s.e.d. = 0.085 kg d-1; P<0.001), leading to significant differences in estimated dry matter intakes (8.0 vs. 11.1 kg DM d-1 for upland and lowland respectively; s.e.d. = 0.68 kg DM d-1; P<0.001). While emissions per unit feed intake were similar for the lowland and upland systems, CH4 emissions per unit of live-weight gain (LWG) were substantially higher when the steers grazed the poorer quality hill pasture (760 vs 214 g kg-1 LWG; s.e.d. = 133.5 g kg-1 LWG; P<0.001). Overall any effects of breed type were relatively small relative to the combined influence of pasture type and location.

Simultaneous quantification of purine and pyrimidine bases, nucleosides and their degradation products in bovine blood plasma by high performance liquid chromatography tandem mass spectrometry.

Improved nitrogen utilization in cattle is important in order to secure a sustainable cattle production. As purines and pyrimidines (PP) constitute an appreciable part of rumen nitrogen, an improved understanding of the absorption and intermediary metabolism of PP is essential. The present work describes the development and validation of a sensitive and specific method for simultaneous determination of 20 purines (adenine, guanine, guanosine, inosine, 2'-deoxyguanosine, 2'-deoxyinosine, xanthine, hypoxanthine), pyrimidines (cytosine, thymine, uracil, cytidine, uridine, thymidine, 2'-deoxyuridine), and their degradation products (uric acid, allantoin, ß-alanine, ß-ureidopropionic acid, ß-aminoisobutyric acid) in blood plasma of dairy cows. The high performance liquid chromatography-based technique coupled to electrospray ionization tandem mass spectrometry (LC-MS/MS) was combined with individual matrix-matched calibration standards and stable isotopically labelled reference compounds. The quantitative analysis was preceded by a novel pre-treatment procedure consisting of ethanol precipitation, filtration, evaporation and reconstitution. Parameters for separation and detection during the LC-MS/MS analysis were investigated. It was confirmed that using a log-calibration model rather than a linear calibration model resulted in lower CV% and a lack of fit test demonstrated a satisfying linear regression. The method covers concentration ranges for each metabolite according to that in actual samples, e.g. guanine: 0.10-5.0 µmol/L, and allantoin: 120-500 µmol/L. The CV% for the chosen quantification ranges were below 25%. The method has good repeatability (CV%≤25%) and intermediate precision (CV%≤25%) and excellent recoveries (91-107%). All metabolites demonstrated good long-term stability and good stability within-runs (CV%≤10%). Different degrees of absolute matrix effects were observed in plasma, urine and milk. The determination of relative matrix effects revealed that the method was suitable for almost all examined PP metabolites in plasma drawn from an artery and the portal hepatic, hepatic and gastrosplenic veins and, with a few exceptions, also for other species such as chicken, pig, mink, human and rat.

Mixed grazing systems benefit both upland biodiversity and livestock production.

BACKGROUND: With world food demand expected to double by 2050, identifying farming systems that benefit both agricultural production and biodiversity is a fundamentally important challenge for the 21(st) century, but this has to be achieved in a sustainable way. Livestock grazing management directly influences both economic outputs and biodiversity on upland farms while contributing to potentially damaging greenhouse gas emissions, yet no study has attempted to address these impacts simultaneously. METHODS: Using a replicated, landscape-scale field experiment consisting of five management 'systems' we tested the effects of progressively altering elements within an upland farming system, viz i) incorporating cattle grazing into an upland sheep system, ii) integrating grazing of semi-natural rough grazing into a mixed grazing system based on improved pasture, iii) altering the stocking ratio within a mixed grazing system, and iv) replacing modern crossbred cattle with a traditional breed. We quantified the impacts on livestock productivity and numbers of birds and butterflies over four years. RESULTS CONCLUSION AND SIGNIFICANCE: We found that management systems incorporating mixed grazing with cattle improve livestock productivity and reduce methane emissions relative to sheep only systems. Systems that also included semi-natural rough grazing consistently supported more species of birds and butterflies, and it was possible to incorporate bouts of summer grazing of these pastures by cattle to meet habitat management prescriptions without compromising cattle performance overall. We found no evidence that the system incorporating a cattle breed popular as a conservation grazer was any better for bird and butterfly species richness than those based on a mainstream breed, yet methane emissions from such a system were predicted to be higher. We have demonstrated that mixed upland grazing systems not only improve livestock production, but also benefit biodiversity, suggesting a 'win-win' solution for farmers and conservationists.

Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation.

Balancing energy and nitrogen in the rumen is a key to both profitability and environmental sustainability. Four dairy cows were used in a Latin square experimental design to investigate the effect of severe nitrogen underfeeding (110 vs. 80% of requirements) and the type of carbohydrate consumed [neutral detergent fiber rich (FIB) vs. starch rich (STA)] on the rumen ecosystem. These dietary treatments modified both rumen fermentation and microbial populations. Compared with STA diets, consumption of FIB diets increased bacterial and fungal diversity in the rumen and also increased the concentrations of cellulolytic microorganisms, including protozoa (+38%), anaerobic fungi (+59%), and methanogens (+27%). This microbial adaptation to fiber utilization led to similar digestibility values for the 2 carbohydrate sources and was accompanied by a shift in the rumen fermentation patterns; when the FIB diets were consumed, the cows had greater ruminal pH, ammonia concentrations, and molar proportions of acetate and propionate compared with when they consumed the STA diets. Certain rumen microorganisms were sensitive to a shortage of nitrogen; rumen concentrations of ammonia were 49% lower when the low-protein (LP) diets were consumed as were total bacteria (-13%), anaerobic fungi (-28%), methanogens (-27%), protozoa (-19%), cellulolytic bacteria, and microbial diversity compared with when the high-protein (HP) diets were consumed. As a result, the digestibility of the LP diets was less than that of the HP diets. These findings demonstrated that the rumen microbial ecosystem is directly linked to the rumen fermentation pattern and, to some extent, to the efficiency of diet utilization by dairy cattle.

Oxidative phenols in forage crops containing polyphenol oxidase enzymes.

Polyphenol oxidases (PPOs) are copper-containing enzymes that catalyze oxidation of endogenous monophenols to ortho-dihydroxyaryl compounds and of ortho-dihydroxyaryl compounds to ortho-quinones. Subsequent nucleophilic addition reactions of phenols, amino acids, and proteins with the electrophilic ortho-quinones form brown-, black-, or red-colored secondary products associated with the undesired discolouration of fruit and vegetables. Several important forage plants also exhibit significant PPO activity, and a link with improved efficiency of ruminant production has been established. In ruminant animals, extensive degradation of forage proteins, following consumption, can result in high rates of excretion of nitrogen, which contributes to point-source and diffuse pollution. Reaction of quinones with forage proteins leads to the formation of protein-phenol complexes that are resistant to proteolytic activity during ensilage and during rumen fermentation. Thus, PPO in red clover (Trifolium pratense) has been shown to improve protein utilization by ruminants. While PPO activity has been demonstrated in a number of forage crops, little work has been carried out to identify substrates of PPO, knowledge of which would be beneficial for characterizing this trait in these forages. In general, a wide range of 1,2-dihydroxyarenes can serve as PPO substrates because these are readily oxidized because of the ortho positioning of the hydroxy groups. Naturally occurring phenols isolated from forage crops with PPO activity are reviewed. A large number of phenols, which may be directly or indirectly oxidized as a consequence of PPO activity, have been identified in several forage grass, legume, cereal, and brassica species; these include hydroxybenzoic acids, hydroxycinnamates, and flavonoids. In conclusion, a number of compounds are known or postulated to enable PPO activity in important PPO-expressing forage crops. Targeting the matching of these compounds with PPO activity would be a useful plant breeding approach to improve the utilization of feed nitrogen by ruminant livestock and help reduce the environmental impact of livestock agriculture in temperate countries.

Relationship between grazing lamb growth rate and blood plasma analytes as profiled by gas chromatography with time-of-flight mass spectrometry (GC-TOF/MS).

There can be considerable variation in the performance of individual lambs grazing on the same pasture. Gas chromatography with time-of-flight mass spectrometry (GC-TOF/MS) was used to profile the relative abundances of metabolites in plasma from growing lambs to determine any correlation effects between plasma metabolites and liveweight gain. Analysis of relative abundance of 336 analyte clusters and liveweight gain revealed that the growth rates of female lambs were significantly positively correlated with 5 analyte clusters and negatively correlated with 5 other analyte clusters. Growth rates of male lambs were likewise significantly positively correlated with 9 analyte clusters and negatively with 5 analyte clusters. Analytes identified as being associated with lamb growth rate included the amino acids valine, methionine, phenylalanine, cystine and asparagine, and oxalic acid, phenylacetic acid, and phosphoric acid. A number of currently unidentified analytes were significantly correlated with growth rate. Stepwise regression of the analytes on lamb growth rate yielded relationships that accounted for 48% and 58% of the variation in female and male lamb growth rates, respectively. This study demonstrated that by using GC-TOF/MS in combination with multivariate statistical techniques it is possible to correlate the presence of specific analytes in sheep plasma with growth rate.

Application of gas chromatography-mass spectrometry metabolite profiling techniques to the analysis of heathland plant diets of sheep.

Little is known about how plant biochemistry influences the grazing behavior of animals consuming heterogeneous plant communities. The biochemical profiles of grassland species are mostly restricted to major nutritional characteristics, although recent developments in analytical techniques and data analysis have made possible the detailed analysis of minor components that may influence animal feeding preferences, performance, and health. In the present study, gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF/MS) was used to profile the abundances of metabolites in nine specific heathland plant groups and in three mixed forage diets containing 10, 20, or 30% heather (Calluna vulgaris) and also in plasma and feces from sheep offered one of the three diets. Statistical and chemometric approaches, that is, principal component analysis (PCA) and hierarchical cluster analysis (HCA), were used to discriminate between these diets and between individual animals maintained on these diets. It is shown that GC-TOF/MS analysis of sheep plasma allowed distinction between the very similar diets by PCA and HCA, and, moreover, the plant metabolites responsible for the differences observed have been identified. Furthermore, metabolite markers of herbage mixtures and individual plant groups have been identified, and markers have been detected in sheep plasma and feces.