It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.

To understand how foraging decisions impact individual fitness of herbivores, nutritional ecologists must consider the complex in vivo dynamics of nutrient–nutrient interactions and nutrient–toxin interactions associated with foraging. Mathematical modeling has long been used to make foraging predictions (e.g. optimal foraging theory) but has largely been restricted to a single currency (e.g. energy) or using simple indices of nutrition (e.g. fecal nitrogen) without full consideration of physiologically based interactions among numerous co-ingested phytochemicals. Here, we describe a physiologically based model (PBM) that provides a mechanistic link between foraging decisions and demographic consequences. Including physiological mechanisms of absorption, digestion and metabolism of phytochemicals in PBMs allows us to estimate concentrations of ingested and interacting phytochemicals in the body. Estimated phytochemical concentrations more accurately link intake of phytochemicals to changes in individual fitness than measures of intake alone. Further, we illustrate how estimated physiological parameters can be integrated with the geometric framework of nutrition and into integral projection models and agent-based models to predict fitness and population responses of vertebrate herbivores to ingested phytochemicals. The PBMs will improve our ability to understand the foraging decisions of vertebrate herbivores and consequences of those decisions and may help identify key physiological mechanisms that underlie diet-based ecological adaptations.

With the advancement of high-throughput sequencing technologies, the amount of available sequencing data is growing at a pace that has now begun to greatly challenge the data processing and storage capacities of modern computer systems. Removing redundancy from such data by clustering could be crucial for reducing memory, disk space and running time consumption. In addition, it also has good performance on reducing dataset noise in some analysis applications. In this study, we propose a high-performance short sequence classification algorithm (HSC) for next generation sequencing (NGS) data based on efficient hash function and text similarity. First, HSC converts all reads into k-mers, then it forms a unique k-mer set by merging the duplicated and reverse complementary elements. Second, all unique k-mers are stored in a hash table, where the k-mer string is stored in the key field, and the ID of the reads containing the k-mer are stored in the value field. Third, each hash unit is transformed into a short text consisting of reads. Fourth, texts that satisfy the similarity threshold are combined into a long text, the merge operation is executed iteratively until there is no text that satisfies the merge condition. Finally, the long text is transformed into a cluster consisting of reads. We tested HSC using five real datasets. The experimental results showed that HSC cluster 100 million short reads within 2 hours, and it has excellent performance in reducing memory consumption. Compared to existing methods, HSC is much faster than other tools, it can easily handle tens of millions of sequences. In addition, when HSC is used as a preprocessing tool to produce assembly data, the memory and time consumption of the assembler is greatly reduced. It can help the assembler to achieve better assemblies in terms of N50, NA50 and genome fraction.

Herbivores are found in a variety of ecosystems all over the world. Permanent pastures and meadows cover about 25% of global land. We currently count one domesticated herbivore for two people in the world and the number is growing. Production systems and products are highly diverse. This high diversity is the result of thousands of years of natural selection and human-controlled breeding, as well as migration and trade. Because of the high diversity of domestic herbivore genetic resources, herders have been able to live in regions where no alternative for income generation exists. Meat and milk from domestic herbivores provide 16% and 8% of the global protein and kilocalorie consumption, respectively. They also provide a variety of essential micronutrients but can contribute to overweight and obesity when consumed in excess. Domestic herbivores also make significant contribution to food security through the production of manure, draught power and transport and the generation of income at household and national level. They have a key role to play in women’s empowerment and gender equality, both in rural and urban areas.

Demand for meat and milk is increasing because of population growth, rising incomes and urbanisation. This trend is expected to continue, especially in Latin America, South Asia and China. The sustainable development of domestic herbivore production needs to address the feed/food and the efficiency of herbivores in turning forages into protein. It also needs to address the contribution of herbivores to greenhouse gas emissions, especially of ruminants through enteric fermentation, and their mitigation potential, including through carbon sequestration. Animal genetic resources have a key role to play in mitigating and adapting to climate change. The role of ruminants in the circular bioeconomy needs to be enhanced, promoting the use of by-products and waste as livestock feed and the recycling of manure for energy and nutrients. Finally, the role of domestic herbivores in providing secure livelihoods and economic opportunities for millions of smallholder farmers and pastoralists needs to be enhanced. The sustainable development of the sector therefore requires adequate policies, and there are already a variety of mechanisms available, including regulations, cross-compliance systems, payments for environmental services and research and development. Priority areas for policy makers should be aligned with the global framework of the Sustainable Development Goals and include: (i) food security and nutrition, (ii) economic development and livelihoods, (iii) animal and human health and finally, (iv) environment, climate and natural resources.

Estrus synchronization is important for optimal management of gilt reproduction in pig farms. Hormonal treatments, such as synthetic progestogens, are used on a routine basis, but there is a growing demand for non-hormonal alternative breeding tools. Before puberty, gilts exhibit a ‘waiting period,’ related to the ovarian development and gonadotrophin secretions, during which external stimulations, such as boar exposure, could induce and synchronize first ovulation. Practical non-invasive tools for identification of this period in farms are lacking. During this period, urinary oestrone levels are high, but urine sampling is difficult in group-housed females. The aim of this work was to search for specific biomarkers of the ‘waiting period’ in saliva and urine. In total, nine 144- to 147-day-old Large White gilts were subjected to trans-abdominal ultrasonography three times a week for 5 weeks until puberty detection (week –5 to week –1 before puberty). Urine and saliva samples were collected for oestrone assay to detect the ‘waiting period’ and for metabolome analysis using 1H-nuclear magnetic resonance spectroscopy to detect potential biomarkers of the ‘waiting period.’ Gilts were slaughtered 7 days after puberty detection for puberty confirmation. Results were consistent with ultrasonography data for six gilts. Urine and saliva samples from these six gilts were analyzed. Urinary estrone concentration significantly increased 2 weeks before puberty detection. Metabolome analysis of urine samples allowed the identification of 78 spectral bins, among them, 42 low-molecular-weight metabolites were identified. Metabolome analysis of salivary samples allowed the identification of 59 spectral bins, among them, 23 low-molecular-weight metabolites were detected and 17 were identified. No potential biomarker was identified in urinary samples. In saliva, butyrate and 2HOvalerate, 5.79 ppm (putatively uridine), formate, malonate and propionate could be biomarker candidates to ascertain the pre-puberty period in gilt reproduction. These results confirm that non-invasive salivary samples could allow the identification of the physiological status of the gilts and presumably the optimal time for application of the boar effect. This could contribute to synchronize puberty onset and hence to develop non-hormonal breeding tools.

In equines, Cr2O3 is widely accepted as an indigestible marker, but there are health concerns regarding the carcinogenic properties of Cr2O3. Recently, TiO2 has been suggested to be an alternative digestibility marker in equines. However, a comparison between Cr2O3 and TiO2 has not been made in equines. Six Welsh pony geldings (initial BW: 254±3 kg; 7 years of age) fed chopped alfalfa hay were used to evaluate the use of TiO2 (Ti) and Cr2O3 (Cr) as markers for calculating apparent digestibility and to investigate the effect of frequency of marker administration on the measurement of digestibility values. Diets contained 4.65 kg dry matter (DM) chopped alfalfa hay supplemented with minerals, vitamins, TiO2 (3.3 g Ti/day) and Cr2O3 (3.2 g Cr/day). Ponies were dosed with either 3.3 g Ti and 3.2 g Cr once daily (DF1) or with 1.65 g Ti and 1.60 g Cr twice daily (DF2). After adaptation to the diets and procedures for 14 days, voluntary voided faeces were collected quantitatively over 7 days and analysed for moisture, ash, Ti and Cr. Apparent total tract DM digestibility (DMD) and organic matter digestibility (OMD) were calculated using the total faecal collection (TFC) and marker method (Ti and Cr). The overall mean cumulative faecal recovery of Cr and Ti (as % of intake) were 102.0% and 96.6%, respectively. Mean daily faecal recoveries of Cr as well as of Ti were not different (P=0.323; P=0.808, respectively) between treatments. Overall daily faecal recovery of Cr differed (P=0.019) from 100% when the marker was dosed once daily, whereas overall daily faecal recovery was similar to 100% for both administration frequencies when Ti was used as a marker. For both markers, the coefficient of variation of the mean faecal marker recovery between horses was lower when the markers were administrated twice per day. Across treatments, cumulative DMD and OMD estimated with Ti were similar (P=0.345; P=0.418, respectively) compared with those values determined by TFC method. When Cr was used, the calculated cumulative DMD tended (P=0.097) to be greater compared with those estimated with TFC, and cumulative OMD values were overestimated (P=0.013). Orally supplemented Ti recovery in the faeces of ponies fed chopped alfalfa hay with Ti administered once or twice daily was close to 100%, making it the preferred marker for digestibility trials in equines.

The main objective of this study was to evaluate the variability in in situ CP degradation characteristics of 15 batches lupin grains from nine genotypes in a standardised approach. This study also investigated whether differences in CP degradation can be described by protein fractionation using the Cornell Net Carbohydrate and Protein System (CNCPS) and also whether thermal processing of lupins has an effect on CP degradation in the rumen and analysed protein fractions. The rising political and consumer demand for milk products from dairy production systems based on domestic protein sources and the wide range of lupin types and varieties that can be chosen as protein feed in dairy nutrition requires research to determine the variability in CP degradation characteristics in the rumen. For CP degradation measurements, ground grains were incubated in the rumen of three lactating Jersey cows fitted with a ruminal cannula for different times from 2 to 48 h, and the washing loss of non-incubated samples was also measured. Protein fractions were analysed according to CNCPS and used for the estimation of ruminally degraded protein. In situ CP degradation parameters varied widely between untreated samples. The mean value for the washout fraction was 29.3% (from 16.4% to 43.6%). The potentially degradable fraction averaged 70.5% (from 55.6% to 83.7%), hence maximal degradation of CP was close to completeness. Mean degradation rate was 16.6%/h (from 12.6 to 21.0%/h). Variation in estimated parameters led to variation in the effective degradation (ED) averaging 76.6% (from 67.3% to 83.0%) when calculated assuming a ruminal outflow of 8%/h. Thermal treatment of lupins induced changes in degradation characteristics, primarily by lowering degradation rates, and also led to a significant reduction in ED. The ED calculated from analysed protein fractions averaged 10 percentage points higher than ED calculated from in situ parameters for untreated grains. The ED based on protein fractionation was also reduced by heat treatment, but the correlation with in situ based ED was poor. It can be concluded that the variation in ED indicates a potential to increase the amount of rumen undegraded protein without additional chemical or physical treatment and the effect of genetic factors and agronomic practices on ED of lupin grains should be investigated in systematic studies in the future.

Subcutaneous fat thickness and fatty acid composition (FAC) play an important role on seasoning loss and organoleptic characteristics of seasoned hams. Dry-cured ham industry prefers meats with low contents of polyunsaturated fatty acids (PUFA) because these negatively affect fat firmness and ham quality, whereas consumers require higher contents in those fatty acids (FA) for their positive effect on human health. A population of 950 Italian Large White pigs from the Italian National Sib Test Selection Programme was investigated with the aim to estimate heritabilities, genetic and phenotypic correlations of backfat FAC, Semimembranosus muscle intramuscular fat (IMF) content and other carcass traits. The pigs were reared in controlled environmental condition at the same central testing station and were slaughtered at reaching 150 kg live weight. Backfat samples were collected to analyze FAC by gas chromatography. Carcass traits showed heritability levels from 0.087 for estimated carcass lean percentage to 0.361 for hot carcass weight. Heritability values of FA classes were low-to-moderate, all in the range 0.245 for n-3 PUFA to 0.264 for monounsaturated FA (MUFA). Polyunsaturated fatty acids showed a significant genetic correlation with loin thickness (0.128), backfat thickness (−0.124 for backfat measured by Fat-O-Meat’er and −0.175 for backfat measured by calibre) and IMF (−0.102). Obviously, C18:2(n-6) shows similar genetic correlations with the same traits (0.211 with loin thickness, −0.206 with backfat measured by Fat-O-Meat’er, −0.291 with backfat measured by calibre and −0.171 with IMF). Monounsaturated FA, except with the backfat measured by calibre (0.068; P<0.01), do not show genetic correlations with carcass characteristics, whereas a negative genetic correlation was found between MUFA and saturated FA (SFA; −0.339; P<0.001). These results suggest that MUFA/SFA ratio could be increased without interfering with carcass traits. The level of genetic correlations between FA and carcass traits should be taken into account in dealing with the development of selection schemes addressed to modify carcass composition and/or backfat FAC.

A divergent selection experiment on litter size variability (high and low lines) was performed in rabbits over seven generations. The aim of this study was to evaluate the correlated responses to selection in body condition and fat reserves mobilisation. Litter size variability was estimated as phenotypic variance of litter size within female after correcting for the year-season and the parity-lactation status effects. A total of 226 females were used in this study, of which 158 females were used to measure body condition and energy mobilisation. Body condition was measured as BW and perirenal fat thickness. Females were stimulated with the adrenergic isoproterenol. Mobilisation capacity of fat reserves was measured by the lipolytic potential, defined as the increment in non-esterified fatty acids (NEFA) levels from basal concentration until adrenergic stimulation at mating, delivery and 10 days after delivery of the second reproductive cycle. Females were classified as survivor or non-survivor when they were culled for sanitary reasons or died before the third kindling. Data were analysed using Bayesian methodology. Survivor females presented higher BW than the non-survivor females at delivery (238 g, P=1.00) and 10 days after delivery (276 g, P=1.00). They also showed higher perirenal fat thickness at 10 days after delivery (0.62 mm, P=1.00). At delivery, basal NEFA levels was lower in survivor than non-survivor females (−0.18 mmol/l, P=1.00), but their lipolytic potential (∆NEFA) was higher (0.08 mmol/l, P=0.94). Body weight was similar between lines in survivor females. Perirenal fat thickness was lower in the high line than in the low line at delivery (−0.23 mm, P=0.90) and 10 days after delivery (−0.28 mm, P=0.92). The high line exhibited higher NEFA (0.10 mmol/l, P=0.93) and lower ∆NEFA (−0.08 mmol/l, P=0.92) than the low line at delivery. The low line showed a favourable correlated response to selection on body condition and fat reserves mobilisation. In conclusion, the low line selected for litter size variability seems to adapt better to adverse conditions, as it has a greater capacity to mobilise energy reserves at delivery than the high line. Females that adequately manage their body reserves and perform energy mobilisation correctly have a lower risk of dying or being culled.

β-Casomorphin is an opioid-like bioactive peptide derived from β-casein of milk that plays a crucial role in modulating animal’s feed intake, growth, nutrient utilization and immunity. However, the effect of β-casomorphin on lipid metabolism in chickens and its mechanism remain unclear. The aim of this study was to investigate the effects of β-casomorphin on fat deposition in broiler chickens and explore its mechanism of action. A total of 120 21-day-old Arbor Acres male broilers (747.94±8.85 g) was chosen and randomly divided into four groups with six replicates of five birds per replicate. Three groups of broilers were injected with 0.1, 0.5 or 1.0 mg/kg BW of β-casomorphin in 1 ml saline for 7 days, whereas the control group received 1 ml saline only. The results showed that subcutaneous administration of β-casomorphin to broiler chickens increased average daily gain, average daily feed intake and fat deposition, and decreased feed : gain ratio (P<0.05). The activity of malate dehydrogenase in the pectoral muscle, liver and abdominal adipose tissue was also increased along with the concentrations of insulin, very-low-density lipoprotein and triglyceride in the plasma (P<0.05). The activity of hormone-sensitive lipase in the liver and abdominal adipose tissue and the concentration of glucagon in the plasma were decreased by injection with β-casomorphin (P<0.05). Affymetrix gene chip analysis revealed that administering 1.0 mg/kg BW β-casomorphin caused differential expression of 168 genes in the liver with a minimum of fourfold difference. Of those, 37 genes are directly involved in lipid metabolism with 18 up-regulated genes such as very low density lipoprotein receptor gene and fatty acid synthase gene, and 19 down-regulated genes such as lipoprotein lipase gene and low density lipoprotein receptor gene. In conclusion, β-casomorphin increased growth performance and fat deposition of broilers. Regulation of fat deposition by β-casomorphin appears to take place through changes in hormone secretion and enzyme activities by controlling the gene expression of lipid metabolism and feed intake, increasing fat synthesis and deposition.

Growth in demand for foods with potentially beneficial effects on consumer health has motivated increased interest in developing strategies for improving the nutritional quality of ruminant-derived products. Manipulation of the rumen environment offers the opportunity to modify the lipid composition of milk and meat by changing the availability of fatty acids (FA) for mammary and intramuscular lipid uptake. Dietary supplementation with marine lipids, plant secondary compounds and direct-fed microbials has shown promising results. In this review, we have compiled information about their effects on the concentration of putative desirable FA (e.g. c9t11-CLA and vaccenic, oleic, linoleic and linolenic acids) in ruminal digesta, milk and intramuscular fat. Marine lipids rich in very long-chain n-3 polyunsaturated fatty acids (PUFA) efficiently inhibit the last step of C18 FA biohydrogenation (BH) in the bovine, ovine and caprine, increasing the outflow of t11-18:1 from the rumen and improving the concentration of c9t11-CLA in the final products, but increments in t10-18:1 are also often found due to shifts toward alternative BH pathways. Direct-fed microbials appear to favourably modify rumen lipid metabolism but information is still very limited, whereas a wide variety of plant secondary compounds, including tannins, polyphenol oxidase, essential oils, oxygenated FA and saponins, has been examined with varying success. For example, the effectiveness of tannins and essential oils is as yet controversial, with some studies showing no effects and others a positive impact on inhibiting the first step of BH of PUFA or, less commonly, the final step. Further investigation is required to unravel the causes of inconsistent results, which may be due to the diversity in active components, ruminant species, dosage, basal diet composition and time on treatments. Likewise, research must continue to address ways to mitigate negative side-effects of some supplements on animal performance (particularly, milk fat depression) and product quality (e.g. altered oxidative stability and shelf-life).

On-farm nutrition and management interventions to reduce enteric CH4 (eCH4) emission, the most abundant greenhouse gas from cattle, may also affect volatile solids and N excretion. The objective was to jointly quantify eCH4 emissions, digestible volatile solids (dVS) excretion and N excretion from dairy cattle, based on dietary variables and animal characteristics, and to evaluate relationships between these emissions and excreta. Univariate and Bayesian multivariate mixed-effects models fitted to 520 individual North American dairy cow records indicated dry matter (DM) intake and dietary ADF and CP to be the main predictors for production of eCH4 emissions and dVS and N excreta (g/day). Yields (g/kg DM intake) of eCH4 emissions and dVS and N excreta were best predicted by dietary ADF, dietary CP, milk yield and milk fat content. Intensities (g/kg fat- and protein-corrected milk) of eCH4, dVS and N excreta were best predicted by dietary ADF, dietary CP, days in milk and BW. A K-fold cross-validation indicated that eCH4 and urinary N variables had larger root mean square prediction error (RMSPE; % of observed mean) than dVS, fecal N and total N production (on average 24.3% and 26.5% v. 16.7%, 15.5% and 16.2%, respectively), whereas intensity variables had larger RMSPE than production and yields (29.4%, 14.7% and 14.6%, respectively). Univariate and multivariate equations performed relatively similar (18.8% v. 19.3% RMSPE). Mutual correlations indicated a trade-off for eCH4v. dVS yield. The multivariate model indicated a trade-off between eCH4 and dVS v. total N production, yield and intensity induced by dietary CP content.

The role of herbivorous livestock in supporting the sustainability of the farming systems in which they are found is complex and sometimes conflicting. In Sub-Saharan Africa (SSA), the integration of livestock into farming systems is important for sustainable agriculture as the recycling of nutrients for crop production through returns of animal manure is a central element of the dominant mixed crop-livestock systems. Sustainable agriculture has been widely advocated as the main practical pathway to address the challenge of meeting the food needs of the rapidly growing population in SSA while safeguarding the needs of future generations. The objective of this paper is to review the state of knowledge of the role of herbivores in sustainable intensification of key farming systems in SSA. The pathways to sustainable agriculture in SSA include intensification of production and livelihood diversification. Sustainable agricultural practices in SSA have focused on intensification practices which aim to increase the output : input ratio through increasing use of inputs, introduction of new inputs or use of existing inputs in a new way. Intensification of livestock production can occur through increased and improved fodder availability, genetic production gains, improved crop residue use and better nutrient recycling of manure. Livestock deliver many ‘goods’ in smallholder farming systems in SSA including improving food and nutrition security, increased recycling of organic matter and nutrients and the associated soil fertility amendments, adding value to crop residues by turning them into nutrient-rich foods, income generation and animal traction. Narratives on livestock ‘bads’ or negative environmental consequences have been largely shaped by the production conditions in the Global North but livestock production in SSA is a different story. In SSA, livestock are an integral component of mixed farming systems and they play key roles in supporting the livelihoods of much of the rural population. None-the-less, the environmental consequences of livestock production on the continent cannot be ignored. To enhance agricultural sustainability in SSA, the challenge is to optimize livestock’s role in the farming systems by maximizing livestock ‘goods’ while minimizing the ‘bads’. This can be through better integration of livestock into the farming systems, efficient nutrient management systems, and provision of necessary policy and institutional support.

The present review will present the recent published results and discuss the main effects of nutrients, mainly fatty acids, on the expression of genes involved in lipid metabolism. In this sense, the review focuses in two phases: prenatal life and finishing phase, showing how nutrients can modulate gene expression affecting marbling and fatty acid profile in meat from ruminants. Adiposity in ruminants starts to be affected by nutrients during prenatal life when maternal nutrition affects the differentiation and proliferation of adipose cells enhancing the marbling potential. Therefore, several fetal programming studies were carried out in the last two decades in order to better understand how nutrients affect long-term expression of genes involved in adipogenesis and lipogenesis. In addition, during the finishing phase, marbling becomes largely dependent on starch digestion and glucose metabolism, being important to create alternatives to increase these metabolic processes, and modulates gene expression. Different lipid sources and their fatty acids may also influence the expression of genes responsible to encode enzymes involved in fat tissue deposition, influencing meat quality. In conclusion, the knowledge shows that gene expression is a metabolic factor affecting marbling and fatty acid profile in ruminant meat and diets and their nutrients have direct effect on how these genes are expressed.

Animal’s feed efficiency in growing cattle (i.e. the animal ability to reach a market or adult BW with the least amount of feed intake), is a key factor in the beef cattle industry. Feeding systems have made huge progress to understand dietary factors influencing the average animal feed efficiency. However, there exists a considerable amount of animal-to-animal variation around the average feed efficiency observed in beef cattle reared in similar conditions, which is still far from being understood. This review aims to identify biological determinants and molecular pathways involved in the between-animal variation in feed efficiency with particular reference to growing beef cattle phenotyped for residual feed intake (RFI). Moreover, the review attempts to distinguish true potential determinants from those revealed through simple associations or indirectly linked to RFI through their association with feed intake. Most representative and studied biological processes which seem to be connected to feed efficiency were reviewed, such as feeding behaviour, digestion and methane production, rumen microbiome structure and functioning, energy metabolism at the whole body and cellular levels, protein turnover, hormone regulation and body composition. In addition, an overall molecular network analysis was conducted for unravelling networks and their linked functions involved in between-animal variation in feed efficiency. The results from this review suggest that feeding and digestive-related mechanisms could be associated with RFI mainly because they co-vary with feed intake. Although much more research is warranted, especially with high-forage diets, the role of feeding and digestive related mechanisms as true determinants of animal variability in feed efficiency could be minor. Concerning the metabolic-related mechanisms, despite the scarcity of studies using reference methods it seems that feed efficient animals have a significantly lower energy metabolic rate independent of the associated intake reduction. This lower heat production in feed efficient animals may result from a decreased protein turnover and a higher efficiency of ATP production in mitochondria, both mechanisms also identified in the molecular network analysis. In contrast, hormones and body composition could not be conclusively related to animal-to-animal variation in feed efficiency. The analysis of potential biological networks underlying RFI variations highlighted other significant pathways such as lipid metabolism and immunity and stress response. Finally, emerging knowledge suggests that metabolic functions underlying genetic variation in feed efficiency could be associated with other important traits in animal production. This emphasizes the relevance of understanding the biological basis of relevant animal traits to better define future balanced breeding programmes.

There is growing evidence on the extent to which projected changes in climate, including increases in atmospheric levels of carbon dioxide, higher temperatures, changes in amount, seasonality and variability of precipitation and increases in extreme weather events, may affect future availability of ruminant animal products. Elements of climate change affect livestock systems through direct impacts on animal physiology, behaviour, production and welfare and indirectly through feed availability, composition and quality. These impacts may be positive or negative and will vary across geographical regions, animal species and with adaptive capacity. However, adverse impacts are likely to be greatest in tropical and sub-tropical regions including countries where both current need and future growth in demand for nutrition is greatest. The complexity of effects means that effective adaptation strategies to mitigate negative impacts on ruminant production systems to climate changes will need to be multi-dimensional. Although predictions of future climate, particularly on regional and local scales, have a degree of uncertainty, adaptation planning is starting to be informed by changes already being observed and adjustments in management being made by farmers to maintain productivity and profitability. Regional case studies illustrate the benefits and limitations of adaptive management: potential mitigation through heightened awareness of heat stress-related mortality in French cattle; evidence of a drop in milk production in south-eastern Australian dairies during a January 2014 heat wave, from the theoretical potential of 53% to only 10% across the state; and limitations in response options to climate-induced thermal, nutritional and water stress for sheep and goat farmers in northern Ethiopia. Review of research on climate change impacts on ruminant livestock and effective adaptation together with evidence of practical adaptive management provide insights into potential strategies and gaps in knowledge to address challenges and improve future decisions.

Individual animals behave differently from one another, especially when confronting challenges such as changes in diet (e.g. weaning), environment (e.g. moving from pasture to feedlot) and social grouping (e.g. movement to lactating group after parturition). Each of these challenges involves some element of novelty, impacting the welfare and productivity of the animal. Indeed, the large individual variability in the development and expression of feeding behaviour cannot be fully explained by differences in genetics, management practices, body size or growth rate. In this review we outline evidence that individual variability in feeding behaviour is associated with the personality of the individual. We focus on three key personality traits: exploration, fear or reactivity and sociability. Individuals differ in how much they explore their feeding environment, with more exploratory individuals being less reactive to novel situations. Feeding behaviour can be impaired in individuals that are especially reactive to a change in their environment, change in diet or handling or restraint by humans. The social environment is also a major factor affecting how individuals express their behaviour. Sociability of the individual, including dominant-subordinate and affiliative relationships, affects how individuals make foraging decisions, gain access to feed and adopt particular social strategies to maintain or adjust feeding patterns when the social environment changes. Personality traits such as exploration, boldness and sociability also affect the use of social information when learning where, how or what to eat. Our review highlights the implications of feeding behaviour variability for the welfare and productivity of the individual, and how an understanding of personality can help tailor management to the needs of the individual.

Due to their high energy requirements, high-yielding dairy cows receive high-grain diets. This commonly jeopardises their gastrointestinal health by causing subacute ruminal acidosis (SARA) and hindgut acidosis. These disorders can disrupt nutrient utilisations, impair the functionalities of gastrointestinal microbiota, and reduce the absorptive and barrier capacities of gastrointestinal epithelia. They can also trigger inflammatory responses. The symptoms of SARA are not only due to a depressed rumen pH. Hence, the diagnosis of this disorder based solely on reticulo-rumen pH values is inaccurate. An accurate diagnosis requires a combination of clinical examinations of cows, including blood, milk, urine and faeces parameters, as well as analyses of herd management and feed quality, including the dietary contents of NDF, starch and physical effective NDF. Grain-induced SARA increases acidity and shifts availabilities of substrates for microorganisms in the reticulo-rumen and hindgut and can result in a dysbiotic microbiota that are characterised by low richness, diversity and functionality. Also, amylolytic microorganisms become more dominant at the expense of proteolytic and fibrolytic ones. Opportunistic microorganisms can take advantage of newly available niches, which, combined with reduced functionalities of epithelia, can contribute to an overall reduction in nutrient utilisation and increasing endotoxins and pathogens in digesta and faeces. The reduced barrier function of epithelia increases translocation of these endotoxins and other immunogenic compounds out of the digestive tract, which may be the cause of inflammations. This needs to be confirmed by determining the toxicity of these compounds. Cows differ in their susceptibility to poor gastrointestinal health, due to variations in genetics, feeding history, diet adaptation, gastrointestinal microbiota, metabolic adaptation, stress and infections. These differences may also offer opportunities for the management of gastrointestinal health. Strategies to prevent SARA include balancing the diet for physical effective fibre, non-fibre carbohydrates and starch, managing the different fractions of non-fibre carbohydrates, and consideration of the type and processing of grain and forage digestibility. Gastrointestinal health disorders due to high grain feeding may be attenuated by a variety of feed supplements and additives, including buffers, antibiotics, probiotics/direct fed microbials and yeast products. However, the efficacy of strategies to prevent these disorders must be improved. This requires a better understanding of the mechanisms through which these strategies affect the functionality of gastrointestinal microbiota and epithelia, and the immunity, inflammation and ‘gastrointestinal-health robustness’ of cows. More representative models to induce SARA are also needed.