Livestock play a significant role in rural livelihoods and the economies of developing countries. They are providers of income and employment for producers and others working in, sometimes complex, value chains. They are a crucial asset and safety net for the poor, especially for women and pastoralist groups, and they provide an important source of nourishment for billions of rural and urban households. These socio-economic roles and others are increasing in importance as the sector grows because of increasing human populations, incomes and urbanisation rates. To provide these benefits, the sector uses a significant amount of land, water, biomass and other resources and emits a considerable quantity of greenhouse gases. There is concern on how to manage the sector's growth, so that these benefits can be attained at a lower environmental cost. Livestock and environment interactions in developing countries can be both positive and negative. On the one hand, manures from ruminant systems can be a valuable source of nutrients for smallholder crops, whereas in more industrial systems, or where there are large concentrations of animals, they can pollute water sources. On the other hand, ruminant systems in developing countries can be considered relatively resource-use inefficient. Because of the high yield gaps in most of these production systems, increasing the efficiency of the livestock sector through sustainable intensification practices presents a real opportunity where research and development can contribute to provide more sustainable solutions. In order to achieve this, it is necessary that production systems become market-orientated, better regulated in cases, and socially acceptable so that the right mix of incentives exists for the systems to intensify. Managing the required intensification and the shifts to new value chains is also essential to avoid a potential increase in zoonotic, food-borne and other diseases. New diversification options and improved safety nets will also be essential when intensification is not the primary avenue for developing the livestock sector. These processes will need to be supported by agile and effective public and private institutions.

The expected higher global demand for animal proteins and the competition for starch and sugars between food, fuel and feed seem to favour herbivores that convert solar energy captured in fibrous plants into animal products. However, the required higher production level of herbivores questions the sustainability of this conversion. An increase in herbivore production can be achieved by increasing the number of animals associated with the increasing demand of plant biomass or by improving the efficiency with which plant biomass is converted into meat and milk. The potential to increase food production by cattle, the main food-producing herbivore in the temperate zones outside China, was considered in three production systems: grassland-based, mixed rain-fed and mixed irrigated systems. The potential to increase plant biomass production in grassland-based systems seems limited, unless fertiliser is imported in large quantities and crop production is increased, sacrificing valuable, high-quality grasslands, which often conflicts with sustainable production methods. Also, in mixed systems with high inputs of fertiliser or water, improvements in plant biomass production seem marginal and the main challenges for these systems are in breeding high-quality plant biomass at lower levels of fertiliser and the use of new co-products from food processing and bio-based economies. Consequently, the main challenge in herbivore nutrition management is to improve the efficiency of plant biomass utilisation. Stocking rate management along with seasonal variation in the grazing capacity of grasslands and moderate use of fertiliser may increase meat production in grassland-based systems by 400%. Improving plant biomass utilisation in the more industrialised mixed rain-fed systems seems possible by better feed storage technologies and for dairy cattle by improving animal health and lifetime production level. Managing the transition period seems crucial to achieve more sustainable mixed rain-fed and mixed irrigated dairy production systems. Whether sustainable production methods will be implemented also depends on macro-economic conditions and awareness of regional and global environmental concerns.

Herbivores are a significant source of nitrous oxide (N2O) emissions. They account for a large share of manure-related N2O emissions, as well as soil-related N2O emissions through the use of grazing land, and land for feed and forage production. It is widely acknowledged that mitigation measures are necessary to avoid an increase in N2O emissions while meeting the growing global food demand. The production and emissions of N2O are closely linked to the efficiency of nitrogen (N) transfer between the major components of a livestock system, that is, animal, manure, soil and crop. Therefore, mitigation options in this paper have been structured along these N pathways. Mitigation technologies involving diet-based intervention include lowering the CP content or increasing the condensed tannin content of the diet. Animal-related mitigation options also include breeding for improved N conversion and high animal productivity. The main soil-based mitigation measures include efficient use of fertilizer and manure, including the use of nitrification inhibitors. In pasture-based systems with animal housing facilities, reducing grazing time is an effective option to reduce N2O losses. Crop-based options comprise breeding efforts for increased N-use efficiency and the use of pastures with N2-fixing clover. It is important to recognize that all N2O mitigation options affect the N and carbon cycles of livestock systems. Therefore, care should be taken that reductions in N2O emissions are not offset by unwanted increases in ammonia, methane or carbon dioxide emissions. Despite the abundant availability of mitigation options, implementation in practice is still lagging. Actual implementation will only follow after increased awareness among farmers and greenhouse gases targeted policies. So far, reductions in N2O emissions that have been achieved are mostly a positive side effect of other N-targeted policies.

Concentrations of methane (CH4) in the atmosphere have almost doubled since the mid 1700s, and it is estimated that ∼30% of the global warming experienced by the planet in the last century and a half can be attributed to CH4. Between 25% and 40% of anthropogenic CH4, emissions are estimated to arise from livestock farming. Mitigating absolute emissions from livestock is extremely challenging technically and is made more difficult because of the need to increase food production to meet the demands of a burgeoning world population. Opportunities for manipulating the diet of intensively managed ruminant to reduce absolute CH4 exist, but in grazing livestock the opportunities are constrained practically and economically. Mitigating emissions per unit of product is more tractable, especially in the short term. Although the formation of CH4 is an anaerobic microbiological process, the host animal does seem to exert an influence, as animals differ in the quantity of CH4 they emit when fed the same diet. The reasons for this are not yet clear, but evidence is accumulating that these differences are consistent and have a genetic basis. Exploiting these between animal differences by animal breeding is an attractive mitigation option as it is potentially applicable to all animals and is open to continuous improvement. However, identifying the desired phenotype poses severe practical constraints. Vaccinating the host animal to produce antibodies that can modulate the activities of the organisms responsible for CH4 formation also presents a novel mitigation option.

The digestion of plant biomass by symbiotic microbial communities in the gut of herbivore hosts also results in the production of methane, a greenhouse gas that is released into the environment where it contributes to climate change. As methane is exclusively produced by methanogenic archaea, various research groups have devoted their efforts to investigate the population structure of symbiotic methanogens in the gut of herbivores. In this review, we summarized and compared currently available results from 16S rRNA gene clone library studies, which cover a broad range of hosts from ruminant livestock species to wild ruminants, camelids, marsupials, primates, birds and reptiles. Although gut methanogens are very diverse, they tend to be limited to specific phylogenetic groups. Overall, methanogens related to species of the genus Methanobrevibacter are the most highly represented archaea in the gut of herbivores. However, under certain conditions, archaea from more phylogenetically distant groups are the most prevalent, such as methanogens belonging to either the genus Methanosphaera, the order Methanomicrobiales or the Thermoplasmatales-Affiliated Lineage C Comparisons not only highlight the strong influence of host species and diet in the determination of the population structure of symbiotic methanogens, but also reveal other complex relationships, such as wide differences between breeds, as well as unexpected similarities between unrelated species. These observations strongly support the need for high throughput sequencing and metagenomic studies to gain further insight.

Grazed pasture, which is the cheapest source of nutrients for dairy cows, should form the basis of profitable and low-input animal production systems. Management of high-producing dairy cows at pasture is thus a major challenge in most countries. The objective of the present paper is to review the factors that can affect nutrient supply for grazing dairy cows in order to point out areas with scope for improvement on managing variations in nutrient supply to achieve high animal performance while maintaining efficient pasture utilisation per hectare (ha). Reviewing the range in animal requirements, intake capacity and pasture nutritive values shows that high-producing cows cannot satisfy their energy requirements from grazing alone and favourable to unfavourable situations for grazing dairy cows may be classified according to pasture quality and availability. Predictive models also enable calculation of supplementation levels required to meet energy requirements in all situations. Solutions to maintain acceptable level of production per cow and high output per ha are discussed. Strategies of concentrate supplementation and increasing use of legumes in mixed swards are the most promising. It is concluded that although high-producing cow cannot express their potential milk production at grazing, there is scope to improve animal performance at grazing given recent developments in our understanding of factors influencing forage intake and digestion of grazed forages.

Inter-annual rainfall variability is a major challenge to sustainable and productive grazing management on rangelands. In Australia, rainfall variability is particularly pronounced and failure to manage appropriately leads to major economic loss and environmental degradation. Recommended strategies to manage sustainably include stocking at long-term carrying capacity (LTCC) or varying stock numbers with forage availability. These strategies are conceptually simple but difficult to implement, given the scale and spatial heterogeneity of grazing properties and the uncertainty of the climate. This paper presents learnings and insights from northern Australia gained from research and modelling on managing for rainfall variability. A method to objectively estimate LTCC in large, heterogeneous paddocks is discussed, and guidelines and tools to tactically adjust stocking rates are presented. The possible use of seasonal climate forecasts (SCF) in management is also considered. Results from a 13-year grazing trial in Queensland show that constant stocking at LTCC was far more profitable and largely maintained land condition compared with heavy stocking (HSR). Variable stocking (VAR) with or without the use of SCF was marginally more profitable, but income variability was greater and land condition poorer than constant stocking at LTCC. Two commercial scale trials in the Northern Territory with breeder cows highlighted the practical difficulties of variable stocking and provided evidence that heavier pasture utilisation rates depress reproductive performance. Simulation modelling across a range of regions in northern Australia also showed a decline in resource condition and profitability under heavy stocking rates. Modelling further suggested that the relative value of variable v. constant stocking depends on stocking rate and land condition. Importantly, variable stocking may possibly allow slightly higher stocking rates without pasture degradation. Enterprise-level simulations run for breeder herds nevertheless show that poor economic performance can occur under constant stocking and even under variable stocking in some circumstances. Modelling and research results both suggest that a form of constrained flexible stocking should be applied to manage for climate variability. Active adaptive management and research will be required as future climate changes make managing for rainfall variability increasingly challenging.

Animal production is a fundamental component of the food supply chain, and with an increasing global population production levels are set to increase. Ruminant animals in particular are valuable in their ability to convert a fibre-rich forage diet into a high-quality protein product for human consumption, although this benefit is offset by inefficiencies in rumen fermentation that contribute to emission of significant quantities of methane and nitrogenous waste. Through co-operation between plant and animal sciences, we can identify how the nutritional requirements of ruminants can be satisfied by high-quality forages for the future. Selective forage plant breeding has supported crop improvement for nearly a century. Early plant breeding programmes were successful in terms of yield gains (4% to 5% per decade), with quality traits becoming increasingly important breeding targets (e.g. enhanced disease resistance and digestibility). Recently, demands for more sustainable production systems have required high yielding, high-quality forages that enable efficient animal production with minimal environmental impact. Achieving this involves considering the entire farm system and identifying opportunities for maximising nutrient use efficiency in both forage and animal components. Forage crops of the future must be able to utilise limited resources (water and nutrients) to maximise production on a limited land area and this may require us to consider alternative plant species to those currently in use. Furthermore, new breeding targets will be identified as the interactions between plants and the animals that consume them become better understood. This will ensure that available resources are targeted at delivering maximum benefits to the animal through enhanced transformation efficiency.

In recent years, it has become increasingly clear that understanding nutrient partitioning is central to a much broader range of issues than just being able to predict productive outputs. The extent to which nutrients are partitioned to other functions such as health and reproduction is clearly important, as are the efficiency consequences of nutrient partitioning. Further, with increasing environmental variability, there is a greater need to be able to predict the ability of an animal to respond to the nutritional limitations that arise from the environment in which it is placed. How the animal partitions its nutrients when resources are limited, or imbalanced, is a major component of its ability to cope, that is, its robustness. There is mounting evidence that reliance on body reserves is increased and that robustness of dairy cows is reduced by selection for increased milk production. A key element for predicting the partition of nutrients in this wider context is to incorporate the priorities of the animal, that is, an explicit recognition of the role of both the cow's genotype (genetic make-up), and the expression of this genotype through time on nutrient partitioning. Accordingly, there has been a growing recognition of the need to incorporate in nutritional models these innate driving forces that alter nutrient partitioning according to physiological state, the genetically driven trajectories. This paper summarizes some of the work carried out to extend nutritional models to incorporate these trajectories, the genetic effects on them, as well as how these factors affect the homeostatic capacity of the animal. At present, there are models capable of predicting the partition of nutrients throughout lactation for cows of differing milk production potentials. Information concerning genotype and stage of lactation effects on homeostatic capacity has not yet been explicitly included in metabolic models that predict nutrient partition, although recent results suggest that this is achievable. These developments have greatly extended the generality of nutrient partitioning models with respect to the type of animal and its physiological state. However, these models remain very largely focussed on predicting partition between productive outputs and body reserves and, for the most part, remain research models, although substantial progress has been made towards developing models that can be applied in the field. The challenge of linking prediction of nutrient partitioning to its consequences on health, reproduction and longevity, although widely recognized, is only now beginning to be addressed. This is an important perspective for future work on nutrient partitioning.

The present work summarizes research related to the definition of nutrient recommendations for feeds used in the intensive production of rabbit's meat. Fibre is the main chemical constituent of rabbit diets that typically contain 320 to 360 and 50 to 90 g/kg of insoluble and soluble fibre, respectively. Instead, the dietary contents of cereal grains (∼120 to 160 g/kg), fat (15 to 25 g/kg) and protein concentrates (150 to 180 g/kg) are usually low with respect to other intensively reared monogastric animals. Cell wall constituents are not well digested in rabbits, but this effect is compensated by its stimulus of gut motility, which leads to an increasing rate of passage of digesta, and allows achieving an elevated dry matter intake. A high feed consumption and an adequate balance in essential nutrients are required to sustain the elevated needs of high-productive rabbits measured either as reproductive yield, milk production or growth rate in the fattening period. Around weaning, pathologies occur in a context of incomplete development of the digestive physiology of young rabbits. The supply of balanced diets has also been related to the prevention of disorders by means of three mechanisms: (i) promoting a lower retention time of the digesta in the digestive tract through feeding fibre sources with optimal chemical and physical characteristics, (ii) restricting feed intake after weaning or (iii) causing a lower flow of easily available substrates into the fermentative area by modifying feed composition (e.g. by lowering protein and starch contents, increasing its digestibility or partially substituting insoluble with soluble fibre), or by delaying age at weaning. The alteration in the gut microbiota composition has been postulated as the possible primary cause of these pathologies.

The large increase in milk yield and the structural changes in the dairy industry have caused major changes in the housing, feeding and management of the dairy cow. However, while large improvements have occurred in production and efficiency, the disease incidence, based on veterinary records, does not seem to be improved. Earlier reviews have covered critical periods such as the transition period in the cow and its influence on health and immune function, the interplay between the endocrine system and the immune system and nutrition and immune function. Knowledge on these topics is crucial for our understanding of disease risk and our effort to develop health and welfare improving strategies, including proactive management for preventing diseases and reducing the severity of diseases. To build onto this the main purpose of this review will therefore be on the effect of physiological imbalance (PI) on immune function, and to give perspectives for prevention of diseases in the dairy cow through nutrition. To a large extent, the health problems during the periparturient period relate to cows having difficulty in adapting to the nutrient needs for lactation. This may result in PI, a situation where the regulatory mechanisms are insufficient for the animals to function optimally leading to a high risk of a complex of digestive, metabolic and infectious problems. The risk of infectious diseases will be increased if the immune competence is reduced. Nutrition plays a pivotal role in the immune response and the effect of nutrition may be directly through nutrients or indirectly by metabolites, for example, in situations with PI. This review discusses the complex relationships between metabolic status and immune function and how these complex interactions increase the risk of disease during early lactation. A special focus will be placed on the major energetic fuels currently known to be used by immune cells (i.e. glucose, non-esterified fatty acids, beta-hydroxybutyrate and glutamine) and how certain metabolic states, such as degree of negative energy balance and risk of PI, contribute to immunosuppression during the periparturient period. Finally, we will address some issues on disease prevention through nutrition.

The principles of domestic herbivore nutrition are well understood and have been developed through detailed physiological studies, although methods to accurately measure field-based intake still challenge herbivore nutrition research. Nutritional ecology considers an animal's interaction with the environment based on its nutritional demands. Although there are a number of theoretical frameworks that can be used to explore nutritional ecology, optimal foraging provides a suitable starting point. Optimal foraging models have progressed from deterministic techniques to spatially explicit agent-based simulation methods. The development of optimal foraging modelling points towards opportunities for field-based research to explore behavioural preferences within studies that have an array of nutritional choices that vary both spatially and temporally. A number of techniques including weighing animals, weighing herbage, using markers (both natural and artificial) and sampling forage, using oesophageal-fistulated animals, have been used to determine intake in the field. These intake measurement techniques are generally most suited to studies that occur over a few days and with relatively small (often less than 10) groups of animals. Over the last 10 years, there have been a number of advances in automated behavioural monitoring technology (e.g. global positioning systems) to track animal movement. A number of recent studies have integrated detailed spatial assessments of vegetation using on-ground sampling and satellite remote sensing; these data have been linked to behavioural preferences of herbivores. Although the recent studies still do not address nutritional interactions over months or years, they do point to methods that could be used to address landscape scale nutritional interactions. Emerging telemetry techniques used to monitor herbivore behavioural preferences and also to determine detailed landscape vegetation mapping provide the opportunity for future herbivore nutritional ecology studies.

There is increasing evidence to indicate that nutrition is an important factor involved in the onset and development of several chronic human diseases including cancer, cardiovascular disease (CVD), type II diabetes and obesity. Clinical studies implicate excessive consumption of medium-chain saturated fatty acids (SFA) and trans-fatty acids (TFA) as risk factors for CVD, and in the aetiology of other chronic conditions. Ruminant-derived foods are significant sources of medium-chain SFA and TFA in the human diet, but also provide high-quality protein, essential micronutrients and several bioactive lipids. Altering the fatty acid composition of ruminant-derived foods offers the opportunity to align the consumption of fatty acids in human populations with public health policies without the need for substantial changes in eating habits. Replacing conserved forages with fresh grass or dietary plant oil and oilseed supplements can be used to lower medium-chain and total SFA content and increase cis-9 18:1, total conjugated linoleic acid (CLA), n-3 and n-6 polyunsaturated fatty acids (PUFA) to a variable extent in ruminant milk. However, inclusion of fish oil or marine algae in the ruminant diet results in marginal enrichment of 20- or 22-carbon PUFA in milk. Studies in growing ruminants have confirmed that the same nutritional strategies improve the balance of n-6/n-3 PUFA, and increase CLA and long-chain n-3 PUFA in ruminant meat, but the potential to lower medium-chain and total SFA is limited. Attempts to alter meat and milk fatty acid composition through changes in the diet fed to ruminants are often accompanied by several-fold increases in TFA concentrations. In extreme cases, the distribution of trans 18:1 and 18:2 isomers in ruminant foods may resemble that of partially hydrogenated plant oils. Changes in milk fat or muscle lipid composition in response to diet are now known to be accompanied by tissue-specific alterations in the expression of one or more lipogenic genes. Breed influences both milk and muscle fat content, although recent studies have confirmed the occurrence of genetic variability in transcript abundance and activity of enzymes involved in lipid synthesis and identified polymorphisms for several key lipogenic genes in lactating and growing cattle. Although nutrition is the major factor influencing the fatty acid composition of ruminant-derived foods, further progress can be expected through the use of genomic or marker-assisted selection to increase the frequency of favourable genotypes and the formulation of diets to exploit this genetic potential.

In 1991, the Committee on Medical Aspects of Food Policy produced a report on the dietary reference values for food energy and nutrients for groups of people in the United Kingdom. The resulting recommendations, which included specific limits for intakes of total, saturated, trans- and cis-polyunsaturated fatty acids (PUFA) have remained a cornerstone of public health policy ever since, and similar recommendations have been adopted by the World Health Organization. These recommendations were made largely on the basis of specific effects of these fatty acids on the risk of developing atherosclerotic cardiovascular disease (CVD). The intervening years have seen a plethora of human epidemiological and intervention trials to further elucidate the specific relationship between dietary fatty acid intake, plasma lipids and lipoproteins and cardiovascular morbidity and mortality. A number of recent meta-analyses and systematic reviews have revisited the role of specific dietary fatty acid classes and CVD risk. In general, these continue to support a link between saturated fatty acids (SFA) and CVD morbidity/mortality. They also highlight the potent adverse effects of trans fatty acids derived from partially hydrogenated vegetable oil. The most recent data suggest that replacing SFA with cis-PUFA (primarily linoleic acid) has the greatest impact on reducing CVD risk. Evidence of specific beneficial effects of n-3 PUFA is generally stronger for secondary, rather than primary, CVD risk, and it is restricted to very long chain fatty acids of marine origin as opposed to alpha-linolenic acid. Taken together, these data suggest that recent focus on dietary n-6-to-n-3 PUFA ratios may have been misguided, and that future strategies should focus on replacing dietary SFA with total PUFA, rather than concentrating on n-6 : n-3 PUFA ratio.

The recently sequenced cattle (Bos taurus) genome unraveled the unique genomic features of the species and provided the molecular basis for applying a systemic approach to systematically link genomic information to metabolic traits. Comparative analysis has identified a variety of evolutionary adaptive features in the cattle genome, such as an expansion of the gene families related to the rumen function, large number of chromosomal rearrangements affecting regulation of genes for lactation, and chromosomal rearrangements that are associated with segmental duplications and copy number variations. Metabolic reconstruction of the cattle genome has revealed that core metabolic pathways are highly conserved among mammals although five metabolic genes are deleted or highly diverged and seven metabolic genes are present in duplicate in the cattle genome compared to their human counter parts. The evolutionary loss and gain of metabolic genes in the cattle genome may reflect metabolic adaptations of cattle. Metabolic reconstruction also provides a platform for better understanding of metabolic regulation in cattle and ruminants. A substantial body of transcriptomics data from dairy and beef cattle under different nutritional management and across different stages of growth and lactation are already available and will aid in linking the genome with metabolism and nutritional physiology of cattle. Application of cattle genomics has great potential for future development of nutritional strategies to improve efficiency and sustainability of beef and milk production. One of the biggest challenges is to integrate genomic and phenotypic data and interpret them in a biological and practical platform. Systems biology, a holistic and systemic approach, will be very useful in overcoming this challenge.

Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.