Integrating heterogeneous across-country data for proxy-based random forest prediction of enteric methane in dairy cattle.

Direct measurements of methane (CH4) from individual animals are difficult and expensive. Predictions based on proxies for CH4 are a viable alternative. Most prediction models are based on multiple linear regressions (MLR) and predictor variables that are not routinely available in commercial farms, such as dry matter intake (DMI) and diet composition. The use of machine learning (ML) algorithms to predict CH4 emissions from across-country heterogeneous data sets has not been reported. The objectives were to compare performances of ML ensemble algorithm random forest (RF) and MLR models in predicting CH4 emissions from proxies in dairy cows, and assess effects of imputing missing data points on prediction accuracy. Data on CH4 emissions and proxies for CH4 from 20 herds were provided by 10 countries. The integrated data set contained 43,519 records from 3,483 cows, with 18.7% missing data points imputed using k-nearest neighbor imputation. Three data sets were created, 3k (no missing records), 21k (missing DMI imputed from milk, fat, protein, body weight), and 41k (missing DMI, milk fat, and protein records imputed). These data sets were used to test scenarios (with or without DMI, imputed vs. nonimputed DMI, milk fat, and protein), and prediction models (RF vs. MLR). Model predictive ability was evaluated within and between herds through 10-fold cross-validation. Prediction accuracy was measured as correlation between observed and predicted CH4, root mean squared error (RMSE) and mean normalized discounted cumulative gain (NDCG). Inclusion of DMI in the model improved within and between-herd prediction accuracy to 0.77 (RMSE = 23.3%) and 0.58 (RMSE = 31.9%) in RF and to 0.50 (RMSE = 0.327) and 0.13 (RMSE = 42.71) in MLR, respectively than when DMI was not included in the predictive model. When missing DMI records were imputed, within and between-herd accuracy increased to 0.84 (RMSE = 18.5%) and 0.63 (RMSE = 29.9%), respectively. In all scenarios, RF models out-performed MLR models. Results suggest routinely measured variables from dairy farms can be used in developing globally robust prediction models for CH4 if coupled with state-of-the-art techniques for imputation and advanced ML algorithms for predictive modeling.

Variability in Enteric Methane Emissions among Dairy Cows during Lactation.

The aim of this study was to investigate variability in enteric CH4 emission rate and emissions per unit of milk across lactations among dairy cows on commercial farms in the UK. A total of 105,701 CH4 spot measurements were obtained from 2206 mostly Holstein-Friesian cows on 18 dairy farms using robotic milking stations. Eleven farms fed a partial mixed ration (PMR) and 7 farms fed a PMR with grazing. Methane concentrations (ppm) were measured using an infrared CH4 analyser at 1s intervals in breath samples taken during milking. Signal processing was used to detect CH4 eructation peaks, with maximum peak amplitude being used to derive CH4 emission rate (g/min) during each milking. A multiple-experiment meta-analysis model was used to assess effects of farm, week of lactation, parity, diet, and dry matter intake (DMI) on average CH4 emissions (expressed in g/min and g/kg milk) per individual cow. Estimated mean enteric CH4 emissions across the 18 farms was 0.38 (s.e. 0.01) g/min, ranging from 0.2 to 0.6 g/min, and 25.6 (s.e. 0.5) g/kg milk, ranging from 15 to 42 g/kg milk. Estimated dry matter intake was positively correlated with emission rate, which was higher in grazing cows, and negatively correlated with emissions per kg milk and was most significant in PMR-fed cows. Mean CH4 emission rate increased over the first 9 weeks of lactation and then was steady until week 70. Older cows were associated with lower emissions per minute and per kg milk. Rank correlation for CH4 emissions among weeks of lactation was generally high. We conclude that CH4 emissions appear to change across and within lactations, but ranking of a herd remains consistent, which is useful for obtaining CH4 spot measurements.

Short-Term Variations of C18:1 Trans Fatty Acids in Plasma Lipoproteins and Ruminal Fermentation Parameters of Non-Lactating Cows Subjected to Ruminal Pulses of Oils.

The objective of this study was to evaluate short-term variations of trans fatty acids (TFA) in plasma lipoproteins and ruminal fermentation parameters of non-lactating cows subjected to ruminal pulses of vegetable oils. Three non-lactating, non-pregnant Holstein cows, each with a ruminal cannula, were arranged in a 3 × 3 Latin square design with three-day pulsing periods and four-day washout intervals between treatments. Cows were treated with single ruminal pulses of: (1) control (skimmed milk (SM); 500 mL); (2) soybean oil (SO; 250 g/d in 500 mL of SM) and (3) partially-hydrogenated vegetable oil (PHVO; 250 g/d in 500 mL of SM). Time changes after infusion in TFA contents were only observed for plasma C18:1 trans-4, trans-5 and trans-12, and high-density lipoprotein fraction C18:1 trans-9. After ruminal pulses, concentration of acetate decreased linearly; molar concentrations of propionate and valerate increased linearly; molar concentrations of butyrate and isovalerate changed quadratically and were greater at 1 h than at other times. There was an accumulation of several C18:1 TFA in plasma and lipoproteins, especially on the third day of pulsing. Overall, naturally occurring C18:1 TFA isomers (produced during ruminal biohydrogenation of SO) and preformed TFA (supplied by PHVO) elicited differential TFA partitioning and transport in plasma and lipoproteins.

Inclusion of Wheat Dried Distillers' Grains with Solubles from Bioethanol Plants in Diets for Dairy Cows.

Dried distillers' grains with solubles (DDGS) from bioethanol production can replace soya in diets for dairy cows, but the optimum inclusion level of European wheat DDGS (wDDGS) is unknown. Two batches of wDDGS from different UK bioethanol plants were fed to 44 (Experiment 1) and 40 (Experiment 2) cows in a Latin square design. Each wDDGS replaced soya and rapeseed at four inclusion levels (g/kg of diet dry matter (DM): 0, 80, 160 and 240-Experiment 1; 0, 75, 150 and 225-Experiment 2). Diets were balanced for metabolisable energy (ME) and protein (MP), and for minimum starch and saturated fat in Experiment 2. In Experiment 1, DM intake (29 kg/day) and milk yield (42.3 kg/day) were unaffected by wDDGS inclusion up to 160 g/kg but were lower than control with 240 g/kg inclusion, which was attributed to the low proportion of solubles in this wDDGS batch. In Experiment 2, DM intake (22.4 kg/day) and milk yield (32.1 kg/day) were unaffected by wDDGS inclusion up to 225 g/kg. ME content of wDDGS, determined in vivo (MJ/kg DM) was 12.1 (Experiment 1) and 13.4 (Experiment 2). It is concluded that the optimum inclusion level of wDDGS is at least 225 g/kg DM in diets balanced for minimum starch and saturated fat as well as ME and MP supplies.

Detection of Methane Eructation Peaks in Dairy Cows at a Robotic Milking Station Using Signal Processing.

The aim of this study was to investigate the use of signal processing to detect eructation peaks in CH4 released by cows during robotic milking, and to compare recordings from three gas analysers (Guardian SP and NG, and IRMAX) differing in volume of air sampled and response time. To allow comparison of gas analysers using the signal processing approach, CH4 in air (parts per million) was measured by each analyser at the same time and continuously every second from the feed bin of a robotic milking station. Peak analysis software was used to extract maximum CH4 amplitude (ppm) from the concentration signal during each milking. A total of 5512 CH4 spot measurements were recorded from 65 cows during three consecutive sampling periods. Data were analysed with a linear mixed model including analyser × period, parity, and days in milk as fixed effects, and cow ID as a random effect. In period one, air sampling volume and recorded CH4 concentration were the same for all analysers. In periods two and three, air sampling volume was increased for IRMAX, resulting in higher CH4 concentrations recorded by IRMAX and lower concentrations recorded by Guardian SP (p < 0.001), particularly in period three, but no change in average concentrations measured by Guardian NG across periods. Measurements by Guardian SP and IRMAX had the highest correlation; Guardian SP and NG produced similar repeatability and detected more variation among cows compared with IRMAX. The findings show that signal processing can provide a reliable and accurate means to detect CH4 eructations from animals when using different gas analysers.

Effects of dietary polyunsaturated fatty acid sources on expression of lipid-related genes in bovine milk somatic cells.

The objective of this study was to compare the effect of contrasting sources of dietary n-6 and n-3 PUFA on expression of genes related to lipid metabolism in dairy cows. During 63 days, fifteen lactating cows were assigned to a control or basal diet containing no added lipid (n = 5 cows); and treatment diets supplemented with SO (n = 5 cows; unrefined soybean oil; 2.9% of DM) or FO (n = 5 cows; fish oil manufactured from salmon oil; 2.9% of DM). Plasma for fatty acid (FA) analysis and milk somatic cells (MSC) were obtained from all cows at the beginning of the study (day 0) and on days 21, 42 and 63. Plasma was used to determine FA transport dynamics. Compared with control and FO, plasma from SO had increased contents of C18:1 cis-9, C18:1 trans-11, C18:2 cis-9, trans-11 and total monounsaturated FA. On the other hand, compared with control and SO, FO increased plasma contents of C20:3 n-3, C20:3 n-6, C20:4 n-6, C20:5 n-3, C22:6 n-3 and total polyunsaturated FA. Moreover, plasma C18:3 n-3 and C20:5 n-3 increased over time for all diets. Compared with control, SO downregulated ACACA, INSIG1, and DGAT1, whereas FO downregulated ACACA, PPARGC1, LPIN1 and FABP3 on day 63, in MSC. At different time-points, SO and FO downregulated genes related to synthesis and intracellular transport of FA, synthesis of triglycerides, and transcription factors.

Comparison of Methods to Measure Methane for Use in Genetic Evaluation of Dairy Cattle.

Partners in Expert Working Group WG2 of the COST Action METHAGENE have used several methods for measuring methane output by individual dairy cattle under various environmental conditions. Methods included respiration chambers, the sulphur hexafluoride (SF6) tracer technique, breath sampling during milking or feeding, the GreenFeed system, and the laser methane detector. The aim of the current study was to review and compare the suitability of methods for large-scale measurements of methane output by individual animals, which may be combined with other databases for genetic evaluations. Accuracy, precision and correlation between methods were assessed. Accuracy and precision are important, but data from different sources can be weighted or adjusted when combined if they are suitably correlated with the 'true' value. All methods showed high correlations with respiration chambers. Comparisons among alternative methods generally had lower correlations than comparisons with respiration chambers, despite higher numbers of animals and in most cases simultaneous repeated measures per cow per method. Lower correlations could be due to increased variability and imprecision of alternative methods, or maybe different aspects of methane emission are captured using different methods. Results confirm that there is sufficient correlation between methods for measurements from all methods to be combined for international genetic studies and provide a much-needed framework for comparing genetic correlations between methods should these become available.

Long-Term Effects of Dietary Olive Oil and Hydrogenated Vegetable Oil on Expression of Lipogenic Genes in Subcutaneous Adipose Tissue of Dairy Cows.

The objective of this study was to characterize the long-term transcriptomic effects of lipogenic genes in subcutaneous adipose tissue (SAT) of dairy cows supplemented with unsaturated (olive oil; OO) and saturated (hydrogenated vegetable oil; HVO) lipids. Cows were fed a control diet with no added lipid, or diets containing OO or HVO (n = 5 cows/group) for 63 days. SAT was obtained from the tail-head area at the onset of the study and after 21, 42, and 63 days of supplementation. Treatments had minor effects on expression of measured genes. Both fat supplements reduced expression of PPARG, HVO decreased transcription of the desaturase FADS2 and lipid droplet formation PLIN2, and OO increased transcription of FABP3. Both lipid treatments decreased expression of the transcription regulator SREBF1 and its chaperone (SCAP) during the first 21 days of treatment. Our data indicated that long-term feeding of OO and HVO have a relatively mild effect on expression of lipogenic genes in SAT of mid-lactating cows.

Effect of Feeding Cows with Unsaturated Fatty Acid Sources on Milk Production, Milk Composition, Milk Fatty Acid Profile, and Physicochemical and Sensory Characteristics of Ice Cream.

The objective of this study was to evaluate the effects of supplementation of dairy cows with different fatty acid sources (soybean oil (SO) and fish oil (FO)) on milk production, milk composition, milk fatty acid profile, and physicochemical and sensory characteristics of ice cream. During 63 days, fifteen Holstein cows averaging 198 ± 35 days in milk were assigned to three groups: control diet with no added lipid (n = 5 cows); and supplemented diets with SO (n = 5 cows; unrefined SO; 30 g/kg DM) or FO (n = 5 cows; FO from unrefined salmon oil; 30 g/kg DM). Milk production, milk fat, and milk protein were not affected by treatments. Saturated fatty acids in milk fat were decreased with SO and FO compared with control. C18:2 cis-9, cis-12 was increased with SO whereas C18:2 cis-9, trans-11, C20:3n-3, C20:3n-6, C20:5n-3, and C22:6n-3 were the highest with FO. Draw temperature and firmness were higher in SO compared to control and FO ice creams. Melting resistance was higher in FO compared with control and SO ice creams. Supplementation of cow diets with SO and FO did not have detrimental effects on milk production, or ice cream physicochemical and sensory characteristics.

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions.

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.

Effect of different exogenous fatty acids on the cytosolic triacylglycerol content in bovine mammary cells.

The objective of this study was to determine how cytosolic triacylglycerols (TAG) are stored in mammary cells and whether this depends on the individual chemical configuration of fatty acids (FA). This objective was accomplished by addition of different FA to a FA-free medium used to culture mammary alveolar cells-large T antigen cells (MAC-T). Treatments consisted of adding FA (palmitate, stearate, oleate, linoleate, rumenic acid [CLA], elaidate and vaccinate) solutions to the medium at 100, 200, 300 and 400 mmol/L concentrations for a 24-h incubation period. At the end of each incubation period, cytosolic TAG, DNA and protein contents were measured. Palmitate, vaccenate, linoleate and CLA increased (P < 0.05) cytosolic TAG (µg/mg protein). Palmitate and CLA increased (P < 0.05) cytosolic TAG adjusted for DNA content. Overall, effects on cytosolic TAG accumulation depended on individual FA structure (chain length, degree of saturation, and number and orientation of FA double bonds). In addition, the long-chain FA used in this study did not have a detrimental effect on MAC-T cells as indicated by cytosolic protein and DNA contents reflecting their biological role in lipid accumulation.

Effects of Dietary Vegetable Oils on Mammary Lipid-Related Genes in Holstein Dairy Cows.

This study analyzed effects of vegetable oils fed to dairy cows on abundance of genes related to lipid metabolism in milk somatic cells (MSC). During 63 days, 15 cows were allocated to 3 treatments: a control diet with no added lipid the same diet supplemented with olive oil (OO, 30 g/kg DM) or hydrogenated vegetable oil (HVO, 30 g/kg DM). On days 21, 42 and 63, MSC were obtained from all cows. Relative abundance of genes involved in lipid metabolism in MSC from cows fed control on days 42 and 63 was compared with relative abundance at day 21 to evaluate fold-changes. Those genes without changes over the time were selected to analyze effects of OO and HVO. Compared with control, on day 42, PLIN2 and THRSP were upregulated by OO. Compared with control, on day 21, HVO up regulated ACACA, down regulated FABP3, and on day 63 THRSP and FABP4 were down regulated. Dietary oil supplementation (3% DM) had a modest nutrigenomic effect on different biological functions such as acetate and FA activation and intra-cellular transport, lipid droplet formation, and transcription regulation in MSC.

Effect of Soybean Oil and Fish Oil on Lipid-Related Transcripts in Subcutaneous Adipose Tissue of Dairy Cows.

The objective of this study was to determine the effect of long-term supplementation of unsaturated oil on lipid metabolism and transcription of genes involved in lipid metabolism in subcutaneous adipose tissue (SAT) of mid-lactating dairy cows. The objective was achieved by supplementing dairy cows with soybean oil (SO; high in linoleic acid) or fish oil (FO; high in EPA and DHA) for 63 days (nine weeks). Cows were fed a control diet with no added lipid, or diets containing SO or FO (n = 5 cows/group). At the onset of the experiment (day 0) and on days 21, 42, and 63 of supplementation, blood and SAT samples were collected from each animal. Oil supplementation increased cholesterol and NEFA in plasma, with a greater effect of SO compared to FO. Concentration of BUN was lower in SO compared to control and FO at the end of the trial. Transcription of few genes was affected by dietary lipids: FABP4 had lowest expression in FO followed by SO and control. ACACA and FASN had higher expression in FO. Transcription of SCAP was higher but expression of INSIG1 was lower in SO. Overall, results revealed that compared to control, SO and FO had lipogenic effect in SAT.

The environmental costs and benefits of high-yield farming.

How we manage farming and food systems to meet rising demand is pivotal to the future of biodiversity. Extensive field data suggest impacts on wild populations would be greatly reduced through boosting yields on existing farmland so as to spare remaining natural habitats. High-yield farming raises other concerns because expressed per unit area it can generate high levels of externalities such as greenhouse gas (GHG) emissions and nutrient losses. However, such metrics underestimate the overall impacts of lower-yield systems, so here we develop a framework that instead compares externality and land costs per unit production. Applying this to diverse datasets describing the externalities of four major farm sectors reveals that, rather than involving trade-offs, the externality and land costs of alternative production systems can co-vary positively: per unit production, land-efficient systems often produce lower externalities. For GHG emissions these associations become more strongly positive once forgone sequestration is included. Our conclusions are limited: remarkably few studies report externalities alongside yields; many important externalities and farming systems are inadequately measured; and realising the environmental benefits of high-yield systems typically requires additional measures to limit farmland expansion. Yet our results nevertheless suggest that trade-offs among key cost metrics are not as ubiquitous as sometimes perceived.

Effect of dietary vegetable oils on the fatty acid profile of plasma lipoproteins in dairy cows.

The aim of this study was to elucidate the effect of dietary supplementation of soybean oil (SO) and hydrogenated palm oil (HPO) on the transport of fatty acids (FA) within plasma lipoproteins in lactating and non-lactating cows. Three lactating and three non-lactating Holstein cows were used in two different 3 × 3 Latin square experiments that included three periods of 21 d. Dietary treatments for lactating cows consisted of a basal diet (control; no fat supplement) and fat-supplemented diets containing SO (500 g/d per cow) or HPO (500 g/d per cow). For non-lactating cows, dietary treatments consisted of a basal diet (control; no fat supplement) and fat-supplemented diets containing SO (170 g/d per cow) or HPO (170 g/d per cow). Compared with the control and SO diet, HPO addition increased (p < 0.05) the concentration of C16:0, C18:0, C18:2cis-9,12, C18:3cis-9,12,15 and total saturated and polyunsaturated FA in the plasma of lactating cows. In non-lactating cows, the SO addition increased the plasma concentration of C18:1trans-11. In lactating cows, concentrations of C16:0, C18:0 and total saturated FA were increased (p < 0.05) by HPO addition in the high-density lipoprotein (HDL). Total saturated FA were increased (p < 0.05) by HPO in very-low-density lipoprotein (VLDL). In non-lactating cows, the concentration of C18:0 was increased (p < 0.05) by HPO in HDL, whereas C18:1trans-11 was increased (p < 0.05) by SO in the low-density lipoprotein. Overall, it was found that distribution and transport of FA within the bovine plasma lipoproteins may be influenced by chain length and degree of unsaturation of dietary lipids. Also, the distribution of individual FA isomers such as C18:1trans-11 and C18:2cis-9,trans-11 may vary depending on the physiological state of the cow (lactating or non-lactating), and are increased in plasma (lactating cows) and the HDL (non-lactating cows) when cows are fed SO.

A mathematical model of the bovine oestrous cycle: simulating outcomes of dietary and pharmacological interventions.

A mathematical model was constructed to simulate the bovine oestrous cycle by using nonlinear differential equations to describe the biological mechanisms which regulate the cycle. The model predicts circulating concentrations of gonadotrophin-releasing hormone, follicle-stimulating hormone, luteinizing hormone, oestradiol, inhibin and progesterone. These hormones collectively provide control and feedback mechanisms between the hypothalamus, pituitary gland and ovaries, which regulate ovarian follicular dynamics, corpus luteum function and ovulation. When follicular growth parameters are altered, the model predicts that cows will exhibit either two or three follicular waves per cycle, as seen in practice. Changes in other parameters allow the model to simulate: effects of nutrition on follicle recruitment and size of the ovulatory follicle; effects of negative energy balance on postpartum anoestrus; and effects of pharmacological intervention on hormone profiles and timing of ovulation. It is concluded that this model provides a sound basis for exploring factors that influence the bovine oestrous cycle in order to test hypotheses about nutritional and hormonal influences which, with further validation, should help to design dietary or pharmacological strategies for improving reproductive performance in cattle.

Oocyte quality in lactating dairy cows fed on high levels of n-3 and n-6 fatty acids.

Different fatty acid (FA) sources are known to influence reproductive hormones in cattle, yet there is little information on how dietary FAs affect oocyte quality. Effects of three dietary sources of FAs (supplying predominantly palmitic and oleic, linoleic (n-6) or linolenic (n-3) acids) on developmental potential of oocytes were studied in lactating dairy cows. A total of 12 Holstein cows received three diets containing rumen inert fat (RIF), soyabean or linseed as the main FA source for three periods of 25 days in a Latin-square design. Within each period, oocytes were collected in four ovum pick-up sessions at 3-4 day intervals. FA profiles in plasma and milk reflected profiles of dietary FA sources, but major FAs in granulosa cells were not affected. Dietary FA source did not affect plasma concentrations of leptin, insulin, IGF1, GH, or amino acids. RIF led to a higher proportion of cleaved embryos than soya or linseed, but blastocyst yield and embryo quality were not affected. It is concluded that the ovary buffers oocytes against the effects of fluctuations in plasma n-3 and n-6 FAs, resulting in only modest effects on their developmental potential.

Modelling responses to nutritional, endocrine and genetic strategies to increase fertility in the UK dairy herd.

The United Kingdom, as in most countries using intensive dairy management programmes, is facing serious challenges in terms of dairy cow fertility, as highlighted by a rapidly increasing calving interval (CI). A mechanistic, mathematical model is described that predicts the size of the future national dairy herd required to supply domestic requirements and its inherent sustainability in terms of production of replacement female numbers. The results from the model suggest that continuing use of current management strategies may result in the national dairy herd being unsustainable due to increasing CI and reduced fertility in as few as 10years. Adoption of nutritional, endocrine and genetic techniques that increase fertility can effectively and rapidly reverse this trend and reduce the required size of the national herd, thereby reducing methane emissions from dairy production.

Factors influencing biohydrogenation and conjugated linoleic acid production by mixed rumen fungi.

The objective of this study was to evaluate the effect of soluble carbohydrates (glucose, cellobiose), pH (6.0, 6.5, 7.0), and rumen microbial growth factors (VFA, vitamins) on biohydrogenation of linoleic acid (LA) by mixed rumen fungi. Addition of glucose or cellobiose to culture media slowed the rate of biohydrogenation;only 35-40% of LA was converted to conjugated linoleic acid (CLA) or vaccenic acid (VA) within 24 h of incubation, whereas in the control treatment, 100% of LA was converted within 24 h. Addition of VFA or vitamins did not affect biohydrogenation activity or CLA production. Culturing rumen fungi at pH 6.0 slowed biohydrogenation compared with pH 6.5 or 7.0. CLA production was reduced by pH 6.0 compared with control (pH 6.5), but was higher with pH 7.0. Biohydrogenation of LA to VA was complete within 72 h at pH 6.0, 24 h at pH 6.5, and 48 h at pH 7.0. It is concluded that optimum conditions for biohydrogenation of LA and for CLA production by rumen fungi were provided without addition of soluble carbohydrates, VFA or vitamins to the culture medium; optimum pH was 6.5 for biohydrogenation and 7.0 for CLA production.