Comparative physiology applies methods established in domestic animal science to a wider variety of species. This can lead to improved insight into evolutionary adaptations of domestic animals, by putting domestic species into a broader context. Examples include the variety of responses to seasonally fluctuating environments, different adaptations to heat and drought, and in particular adaptations to herbivory and various herbivore niches. Herbivores generally face the challenge that a high food intake compromises digestive efficiency (by reducing ingesta retention time and time available for selective feeding and for food comminution), and a variety of digestive strategies have evolved in response. Ruminants are very successful herbivores. They benefit from potential advantages of a forestomach without being constrained in their food intake as much as other foregut fermenters, because of their peculiar reticuloruminal sorting mechanism that retains food requiring further digestion but clears the forestomach of already digested material; the same mechanism also optimises food comminution. Wild ruminants vary widely in the degree to which their rumen contents ‘stratify’, with little stratification in ‘moose-type’ ruminants (which are mostly restricted to a browse niche) and a high degree of stratification into gas, particle and fluid layers in ‘cattle-type’ ruminants (which are more flexible as intermediate feeders and grazers). Yet all ruminants uniformly achieve efficient selective particle retention, suggesting that functions other than particle retention played an important role in the evolution of stratification-enhancing adaptations. One interesting emerging hypothesis is that the high fluid turnover observed in ‘cattle-type’ ruminants – which is a prerequisite for stratification – is an adaptation that not only leads to a shift of the sorting mechanism from the reticulum to the whole reticulo-rumen, but also optimises the harvest of microbial protein from the forestomach. Although potential benefits of this adaptation have not been quantified, the evidence for convergent evolution toward stratification suggests that they must be substantial. In modern production systems, the main way in which humans influence the efficiency of energy uptake is by manipulating diet quality. Selective breeding for conversion efficiency has resulted in notable differences between wild and domestic animals. With increased knowledge on the relevance of individual factors, that is fluid throughput through the reticulo-rumen, more specific selection parameters for breeding could be defined to increase productivity of domestic ruminants by continuing certain evolutionary trajectories.

The gastrointestinal tract (GIT) has multiple functions including digestion, nutrient absorption, secretion of hormones and excretion of wastes. In the ruminant animal, development of this organ system is more complex than that of the monogastric animal due to the necessity to establish a fully functional and differentiated rumen, in which a diverse microbial population of bacteria, fungi and protozoa support fermentation and digestion of dietary fiber. Central to the goal of animal scientists to enhance nutrient uptake and production efficiency of ruminants is the need for a comprehensive understanding of GIT development, as well as conditions that alter the digestion process. The relatively recent availability of genome sequence information has permitted physiological investigations related to the process of digestion for many agriculturally important species at the gene transcript level. For instance, numerous studies have evaluated the expression of ruminant GIT genes to gain insight into mechanisms involved in normal function, physiology and development, such as nutrient uptake and transport across the epithelial cell barrier throughout the alimentary canal, maintenance of rumen pH, and regulation of GIT motility and cell proliferation. Further, multiple studies have examined the effects of dietary modification, including feeding of supplemental fat, starch and protein, or a forage- v. concentrate-based diet on expression of critical gene pathways in the gut. In addition, the expression of genes in the GIT in response to disease, such as infection with gastrointestinal parasites, has been investigated. This review will summarize some of the recent scientific literature related to the gene expression in the GIT of ruminants, primarily cattle, sheep and goats, as it pertains to normal physiology, and dietary, developmental, and disease effects to provide an overview of critical proteins participating in the overall digestive processes, and their physiological functions. Recent findings from our laboratory will be highlighted also related to expression of the glucagon-like peptide two-hormone pathway in the GIT of dairy cattle during in various stages of the development and lactation, alterations in gene pathways associated with the rumen development and differentiation in the weaning calf, and genes of the GIT responding to Ostertagia, a common nematode infection of the cattle. Finally, prospective areas of investigation will be highlighted.

Despite the fact that the ruminant diet is rich in polyunsaturated fatty acids (PUFA), ruminant products – meat, milk and dairy – contain mainly saturated fatty acids (SFA) because of bacterial lipolysis and subsequent biohydrogenation of ingested PUFA in the rumen. The link between SFA consumption by man and coronary heart disease is well established. In contrast, ruminant products also contain fatty acids that are known to be beneficial to human health, namely conjugated linoleic acids (CLAs). The aims of research in this field have been to understand the microbial ecology of lipolysis and biohydrogenation and to find ways of manipulating ruminal microbes to increase the flow of PUFA and CLA from the rumen into meat and milk. This review describes our present understanding of the microbial ecology of ruminal lipid metabolism, including some apparently anomalous and paradoxical observations, and the status of how the metabolism may be manipulated and the possible consequential effects on other aspects of ruminal digestion. Intuitively, it may appear that inhibiting the ruminal lipase would cause more dietary PUFA to reach the mammary gland. However, lipolysis releases the non-esterified fatty acids that form the substrates for biohydrogenation, but which can, if they accumulate, inhibit the whole process. Thus, increasing lipase activity could be beneficial if the increased release of non-esterified PUFA inhibited the metabolism of CLA. Rumen ciliate protozoa do not carry out biohydrogenation, yet protozoal lipids are much more highly enriched in CLA than bacterial lipids. How could this happen if protozoa do not metabolise PUFA? The answer seems to lie in the ingestion of plant organelles, particularly chloroplasts, and the partial metabolism of the fatty acids by contaminating bacteria. Bacteria related to Butyrivibrio fibrisolvens are by far the most active and numerous biohydrogenating bacteria isolated from the rumen. But do we misunderstand the role of different bacterial species in biohydrogenation because there are uncultivated species that we need to understand and include in the analysis? Manipulation methods include dietary vegetable and fish oils and plant-derived chemicals. Their usefulness, efficacy and possible effects on fatty acid metabolism and on ruminal microorganisms and other areas of their metabolism are described, and areas of opportunity identified.

Ruminant production is under increased public scrutiny in terms of the importance of cattle and other ruminants as major producers of the greenhouse gas methane. Methanogenesis is performed by methanogenic archaea, a specialised group of microbes present in several anaerobic environments including the rumen. In the rumen, methanogens utilise predominantly H2 and CO2 as substrates to produce methane, filling an important functional niche in the ecosystem. However, in addition to methanogens, other microbes also have an influence on methane production either because they are involved in hydrogen (H2) metabolism or because they affect the numbers of methanogens or other members of the microbiota. This study explores the relationship between some of these microbes and methanogenesis and highlights some functional groups that could play a role in decreasing methane emissions. Dihydrogen (‘H2’ from this point on) is the key element that drives methane production in the rumen. Among H2 producers, protozoa have a prominent position, which is strengthened by their close physical association with methanogens, which favours H2 transfer from one to the other. A strong positive interaction was found between protozoal numbers and methane emissions, and because this group is possibly not essential for rumen function, protozoa might be a target for methane mitigation. An important function that is associated with production of H2 is the degradation of fibrous plant material. However, not all members of the rumen fibrolytic community produce H2. Increasing the proportion of non-H2 producing fibrolytic microorganisms might decrease methane production without affecting forage degradability. Alternative pathways that use electron acceptors other than CO2 to oxidise H2 also exist in the rumen. Bacteria with this type of metabolism normally occupy a distinct ecological niche and are not dominant members of the microbiota; however, their numbers can increase if the right potential electron acceptor is present in the diet. Nitrate is an alternative electron sinks that can promote the growth of particular bacteria able to compete with methanogens. Because of the toxicity of the intermediate product, nitrite, the use of nitrate has not been fully explored, but in adapted animals, nitrite does not accumulate and nitrate supplementation may be an alternative under some dietary conditions that deserves to be further studied. In conclusion, methanogens in the rumen co-exist with other microbes, which have contrasting activities. A better understanding of these populations and the pathways that compete with methanogenesis may provide novel targets for emissions abatement in ruminant production.

Secretion of saliva as well as absorptive and secretory processes across forestomach epithelia ensures an optimal environment for microbial digestion in the forestomachs. Daily salivary secretion of sodium (Na+) exceeds the amount found in plasma by a factor of 2 to 3, while the secretion of bicarbonate (HCO3−) is 6 to 8 times higher than the amount of HCO3− in the total extracellular space. This implies a need for efficient absorptive mechanisms across forestomach epithelia to allow for an early recycling. While Na+ is absorbed from all forestomachs via Na+/H+ exchange and a non-selective cation channel that shows increased conductance at low concentrations of Mg2+, Ca2+ or H+ in the luminal microclima and at low intracellular Mg2+, HCO3− is secreted by the rumen for the buffering of ingesta but absorbed by the omasum to prevent liberation of CO2 in the abomasum. Fermentation provides short chain fatty acids and ammonia (NH3) that have to be absorbed both to meet nutrient requirements and maintain ruminal homeostasis of pH and osmolarity. The rumen is an important location for the absorption of essential minerals such as Mg2+ from the diet. Other ions can be absorbed, if delivered in sufficient amounts (Ca2+, Pi, K+, Cl− and NH4+). Although the presence of transport mechanisms for these electrolytes has been described earlier, our knowledge about their nature, regulation and crosstalk has increased greatly in the last years. New transport pathways have recently been added to our picture of epithelial transport across rumen and omasum, including an apical non-selective cation conductance, a basolateral anion conductance, an apical H+-ATPase, differently expressed anion exchangers and monocarboxylate transporters.

Carbohydrates are the main source of energy in ruminants. Their site, extent and kinetics of digestion highly impact the amount and profile of nutrients delivered to peripheral tissues, and the responses of the animal, i.e. ingestion, efficiency of production, N and methane excretion, quality of products and welfare. Development of multi-objective feed evaluation systems thus requires a more integrated quantitative knowledge on carbohydrate digestion and yield of terminal products, as well as on their metabolism by splanchnic tissues. The objective of this paper is to review (i) quantitative knowledge on fibre, starch and sugar digestion, volatile fatty acids (VFA) and glucose production and splanchnic metabolism and (ii) modelling approaches which aim at representing and/or predicting nutrient fluxes in the digestive tract, portal and hepatic drainage. It shows that the representation of carbohydrate digestion and VFA yield is relatively homogeneous among models. Although published quantitative comparisons of these models are scarce, they stress that prediction of fibre digestion and VFA yield and composition is still not good enough for use in feed formulation, whereas prediction of microbial N yield and ruminal starch digestion seems to be more satisfactory. Uncertainties on VFA stoichiometric coefficients and absorption rates may partly explain the poor predictions of VFA. Hardly any mechanistic models have been developed on portal-drained viscera (PDV) metabolism whereas a few exist for liver metabolism. A qualitative comparison of these models is presented. Most are focused on dairy cows and their level of aggregation in the representation of nutrient fluxes and metabolism highly differs depending on their objectives. Quantitative comparison of these models is still lacking. However, recent advances have been achieved with the empirical prediction of VFA and glucose production and fluxes through PDV and liver based on the current INRA feed evaluation system. These advances are presented. They illustrate that empirical prediction of ruminal VFA and intestinal glucose production can be evaluated by comparison with measured net portal net fluxes. We also illustrate the potential synergy between empirical and mechanistic modelling. It is concluded that concomitant empirical and mechanistic approach may likely help to progress towards development of multi-objective feed evaluation systems based on nutrient fluxes.

The maternal nutritional and metabolic environment is critical in determining not only the reproductive success but also the long-term health and viability of the offspring. Changes in maternal diet at defined stages of gestation coincident with different stages of development can have pronounced effects on organ and tissue function in later life. This includes adipose tissue for which differential effects are observed between brown and white adipose tissues. One early, critical window of organ development in the ruminant relates to the period covering uterine attachment, or implantation, and rapid placental growth. During this period, there is pronounced cell division within developing organelles in many fetal tissues, leading to their structural development. In sheep, a 50% global reduction in caloric intake over this specific period profoundly affects placental growth and morphology, resulting in reduced placentome weight. This occurs in conjunction with a lower capacity to inactivate maternal cortisol through the enzyme 11β-hydroxysteroid dehydrogenase type 2 in response to a decrease in maternal plasma cortisol in early gestation. The birth weight of the offspring is, however, unaffected by this dietary manipulation and, although they possess more fat, this adaptation does not persist into adulthood when they become equally obese as those born to control fed mothers. Subsequently, after birth, further changes in fat development occur which impact on both glucocorticoid action and inflammatory responses. These adaptations can include changes in the relative populations of both brown and white adipocytes for which prolactin acting through its receptor appears to have a prominent role. Earlier when in utero nutrient restricted (i.e. between early-to-mid gestation) offspring are exposed to an obesogenic postnatal environment; they exhibit an exaggerated insulin response, which is accompanied by a range of amplified and thus, adverse, physiological or metabolic responses to obesity. These types of adaptations are in marked contrast to the effect of late gestational nutrient restriction, which results in reduced fat mass at birth. As young adults, however, fat mass is increased and, although basal insulin is unaffected, these offspring are insulin resistant. In conclusion, changes in nutrient supply to either the mother and/or her fetus can have profound effects on a range of metabolically important tissues. These have the potential to either exacerbate, or protect from, the adverse effects of later obesity and accompanying complications in the resulting offspring.

Energy requirements of animals are most readily expressed in terms of net energy (NE), while the energy yield of feed is, at least initially, expressed in terms of metabolisable energy (ME). Energy evaluation systems ‘translate’ NE requirements into ME requirements (ME systems) or assign NE values to feeds (NE systems). Efficiency of ME utilisation is higher for maintenance than for production and the NE yield of a feed varies, therefore, with ME intake. In addition, energetic efficiency for maintenance and production is thought to be different for lactating and non-lactating animals and to be affected by diet quality. As a result, there are currently many national energy evaluation systems that are complex, differ in their approach and are, as a result, difficult to compare. As ruminants in most production systems are fed ad libitum, this is also the most appropriate intake level at which to estimate energetic efficiency. Analyses of older as well as more recent data suggest that ad libitum feeding (i) abolishes the effects of diet quality on energetic efficiency (almost) completely, (ii) abolishes the differences between lactating and non-lactating animals (almost) entirely and (iii) results in overall energetic efficiencies that are always close to 0.6. The paper argues that there is now sufficient information to develop an international energy evaluation system for ad libitum fed ruminants. Such a system should (i) unify ME and NE systems, (ii) avoid the systematic bias and large errors that can be associated with current systems (iii) be simpler than current systems and (iv) have as a starting point a constant efficiency of ME utilisation, with a value of around 0.6. The remarkably constant efficiency of ME utilisation in ad libitum fed ruminants could be the result of energetic efficiency as well as feed intake regulation being affected by the same variables or of a direct role of energetic efficiency in feed intake regulation. Models to predict intake on the basis of the latter hypothesis are already available for non-reproducing ruminants but remain to be developed for reproducing animals.

The lean-to-fat ratio, that is, the relative masses of muscle and adipose tissue, is a criterion for the yield and quality of bovine carcasses and meat. This review describes the interactions between muscle and adipose tissue (AT) that may regulate the dynamic balance between the number and size of muscle v. adipose cells. Muscle and adipose tissue in cattle grow by an increase in the number of cells (hyperplasia), mainly during foetal life. The total number of muscle fibres is set by the end of the second trimester of gestation. By contrast, the number of adipocytes is never set. Number of adipocytes increases mainly before birth until 1 year of age, depending on the anatomical location of the adipose tissue. Hyperplasia concerns brown pre-adipocytes during foetal life and white pre-adipocytes from a few weeks after birth. A decrease in the number of secondary myofibres and an increase in adiposity in lambs born from mothers severely underfed during early pregnancy suggest a balance in the commitment of a common progenitor into the myogenic or adipogenic lineages, or a reciprocal regulation of the commitment of two distinct progenitors. The developmental origin of white adipocytes is a subject of debate. Molecular and histological data suggested a possible transdifferentiation of brown into white adipocytes, but this hypothesis has now been challenged by the characterization of distinct precursor cells for brown and white adipocytes in mice. Increased nutrient storage in fully differentiated muscle fibres and adipocytes, resulting in cell enlargement (hypertrophy), is thought to be the main mechanism, whereby muscle and fat masses increase in growing cattle. Competition or prioritization between adipose and muscle cells for the uptake and metabolism of nutrients is suggested, besides the successive waves of growth of muscle v. adipose tissue, by the inhibited or delayed adipose tissue growth in bovine genotypes exhibiting strong muscular development. This competition or prioritization occurs through cellular signalling pathways and the secretion of proteins by adipose tissue (adipokines) and muscle (myokines), putatively regulating their hypertrophy in a reciprocal manner. Further work on the mechanisms underlying cross-talk between brown or white adipocytes and muscle fibres will help to achieve better understanding as a prerequisite to improving the control of body growth and composition in cattle.

The peripartal period is characterized by dramatic alterations in metabolism and function of key tissues such as liver, adipose and mammary. Metabolic regulation relies partly on transcriptional control of gene networks, a collection of DNA segments, which interact with a transcription factor or nuclear receptor, as a mechanism controlling the concentration of key enzymes in cells. These ‘global’ interactions can govern the rates at which genes in the network are transcribed into mRNA. The study of the entire genome, sub-networks or candidate genes at the mRNA level encompasses the broad field of genomics. Genomics of peripartal metabolic adaptations has traditionally been focused on candidate genes and more recently, using microarrays, on the broader transcriptome landscape. The candidate gene approach has expanded our knowledge on the functional adaptations of ureagenesis, fatty acid oxidation, gluconeogenesis, inflammation and growth hormone signaling in liver. More recent work with peripartal mammary tissue has used a gene network approach to study milk fat synthesis regulation as well as a candidate gene approach to study lipid transport, glucose uptake and inflammatory response. Network and pathway analysis of microarray data from cows fed different levels of dietary energy pre partum has revealed unique clusters encompassing functional categories including signal transduction, endoplasmic reticulum stress, peroxisome proliferator-activated receptors (PPARγ) signaling, PPARα signaling, immune or inflammatory processes and cell death in subcutaneous adipose tissue as well as liver. Of interest from a nutritional perspective is the potential to alter PPARγ signaling in adipose and PPARα signaling in liver as a means to enhance insulin sensitivity as well as fatty acid oxidation post partum. Major advances in understanding the metabolic adaptations of peripartal cows will come from using a systems biology approach to integrate data generated at the mRNA, protein, metabolite and tissue level across different nutritional management approaches and with cows of different genetic merit. This will allow the assembly of the important components needed to improve existing metabolic models of the peripartal cow and provide the tools to manipulate complex processes that could have significant long-term economic impact including lactation persistency, fertility and efficiency. An important goal of the future will be to apply additional experimental tools (e.g. gene silencing) and bioinformatics (e.g. transcription factor binding site identification) to studies focused on peripartal cows.

Fat is an important constituent contributing to the organoleptic, processing and physical properties of ruminant milk. Understanding the regulation of milk fat synthesis is central to the development of nutritional strategies to enhance the nutritional value of milk, decrease milk energy secretion and improve the energy balance of lactating ruminants. Nutrition is the major environmental factor regulating the concentration and composition of fat in ruminant milk. Feeding low-fibre/high-starch diets and/or lipid supplements rich in polyunsaturated fatty acids induce milk fat depression (MFD) in the bovine, typically increase milk fat secretion in the caprine, whereas limited data in sheep suggest that the responses are more similar to the goat than the cow. Following the observation that reductions in milk fat synthesis during diet-induced MFD are associated with increases in the concentration of specific trans fatty acids in milk, the biohydrogenation theory of MFD was proposed, which attributes the causal mechanism to altered ruminal lipid metabolism leading to increased formation of specific biohydrogenation intermediates that exert anti-lipogenic effects. Trans-10, cis-12 conjugated linoleic acid (CLA) is the only biohydrogenation intermediate to have been infused at the abomasum over a range of experimental doses (1.25 to 14.0 g/day) and shown unequivocally to inhibit milk fat synthesis in ruminants. However, increases in ruminal trans-10, cis-12 CLA formation do not explain entirely diet-induced MFD, suggesting that other biohydrogenation intermediates and/or other mechanisms may also be involved. Experiments involving abomasal infusions (g/day) in lactating cows have provided evidence that cis-10, trans-12 CLA (1.2), trans-9, cis-11 CLA (5.0) and trans-10 18:1 (92.1) may also exert anti-lipogenic effects. Use of molecular-based approaches have demonstrated that mammary abundance of transcripts encoding for key lipogenic genes are reduced during MFD in the bovine, changes that are accompanied by decrease in sterol response element binding protein 1 (SREBP1) and alterations in the expression of genes related to the SREBP1 pathway. Recent studies indicate that transcription of one or more adipogenic genes is increased in subcutaneous adipose tissue in cows during acute or chronic MFD. Feeding diets of similar composition do not induce MFD or substantially alter mammary lipogenic gene expression in the goat. The available data suggests that variation in mammary fatty acid secretion and lipogenic responses to changes in diet composition between ruminants reflect inherent interspecies differences in ruminal lipid metabolism and mammary specific regulation of cellular processes and key lipogenic enzymes involved in the synthesis of milk fat triacylglycerides.

Environmentally induced periods of heat stress decrease productivity with devastating economic consequences to global animal agriculture. Heat stress can be defined as a physiological condition when the core body temperature of a given species exceeds its range specified for normal activity, which results from a total heat load (internal production and environment) exceeding the capacity for heat dissipation and this prompts physiological and behavioral responses to reduce the strain. The ability of ruminants to regulate body temperature is species- and breed-dependent. Dairy breeds are typically more sensitive to heat stress than meat breeds, and higher-producing animals are more susceptible to heat stress because they generate more metabolic heat. During heat stress, ruminants, like other homeothermic animals, increase avenues of heat loss and reduce heat production in an attempt to maintain euthermia. The immediate responses to heat load are increased respiration rates, decreased feed intake and increased water intake. Acclimatization is a process by which animals adapt to environmental conditions and engage behavioral, hormonal and metabolic changes that are characteristics of either acclimatory homeostasis or homeorhetic mechanisms used by the animals to survive in a new ‘physiological state’. For example, alterations in the hormonal profile are mainly characterized by a decline and increase in anabolic and catabolic hormones, respectively. The response to heat load and the heat-induced change in homeorhetic modifiers alters post-absorptive energy, lipid and protein metabolism, impairs liver function, causes oxidative stress, jeopardizes the immune response and decreases reproductive performance. These physiological modifications alter nutrient partitioning and may prevent heat-stressed lactating cows from recruiting glucose-sparing mechanisms (despite the reduced nutrient intake). This might explain, in large part, why decreased feed intake only accounts for a minor portion of the reduced milk yield from environmentally induced hyperthermic cows. How these metabolic changes are initiated and regulated is not known. It also remains unclear how these changes differ between short-term v. long-term heat acclimation to impact animal productivity and well-being. A better understanding of the adaptations enlisted by ruminants during heat stress is necessary to enhance the likelihood of developing strategies to simultaneously improve heat tolerance and increase productivity.

The efficiency of N utilization in ruminants is typically low (around 25%) and highly variable (10% to 40%) compared with the higher efficiency of other production animals. The low efficiency has implications for the production performance and environment. Many efforts have been devoted to improving the efficiency of N utilization in ruminants, and while major improvements in our understanding of N requirements and metabolism have been achieved, the overall efficiency remains low. In general, maximal efficiency of N utilization will only occur at the expense of some losses in production performance. However, optimal production and N utilization may be achieved through the understanding of the key mechanisms involved in the control of N metabolism. Key factors in the rumen include the efficiency of N capture in the rumen (grams of bacterial N per grams of rumen available N) and the modification of protein degradation. Traditionally, protein degradation has been modulated by modifying the feed (physical and chemical treatments). Modifying the rumen microflora involved in peptide degradation and amino acid deamination offers an alternative approach that needs to be addressed. Current evidence indicates that in typical feeding conditions there is limited net recycling of N into the rumen (blood urea-N uptake minus ammonia-N absorption), but understanding the factors controlling urea transport across the rumen wall may reverse the balance to take advantage of the recycling capabilities of ruminants. Finally, there is considerable metabolism of amino acids (AA) in the portal-drained viscera (PDV) and liver. However, most of this process occurs through the uptake of AA from the arterial blood and not during the ‘absorptive’ process. Therefore, AA are available to the peripheral circulation and to the mammary gland before being used by PDV and the liver. In these conditions, the mammary gland plays a key role in determining the efficiency of N utilization because the PDV and liver will use AA in excess of those required by the mammary gland. Protein synthesis in the mammary gland appears to be tightly regulated by local and systemic signals. The understanding of factors regulating AA supply and absorption in the mammary gland, and the synthesis of milk protein should allow the formulation of diets that increase total AA uptake by the mammary gland and thus reduce AA utilization by PDV and the liver. A better understanding of these key processes should allow the development of strategies to improve the efficiency of N utilization in ruminants.

There has been a significant decline in the reproductive performance of dairy cattle in recent decades. Cows, take longer time to return to the oestrus after calving, have poorer conception rates, and show fewer signs of oestrus. Achieving good reproductive performance is an increasing challenge for the dairy producer. In this study we focus on understanding the overall biological phenomena associated with nutritional sub-fertility rather than the underlying multiplicity of physiological interactions (already described in a number of recent studies). These phenomena are important because they represent the natural adaptations of the animal for dealing with variations in the nutritional environment. They can also be used to monitor and modulate reproductive performance on-farm. There is an underlying trade-off between two aspects of reproduction: investment in the viability of the current calf and investment in future offspring. As the investment in, and viability of, the current calf is related to maternal milk production, we can expect that level of milk production per se has effects on subsequent reproductive performance (investment in future offspring). Lactating cows have a lower proportion of viable embryos, which are of poorer quality, than do non-lactating cows. The same applies to high- compared to medium-genetic merit cows. Another important biological property is the adaptive use of body reserves in support of reproduction. Orchestrated endocrine changes in pregnancy and lactation facilitate the deposition of body lipid during pregnancy and mobilisation in early lactation. When the cow fails to accumulate the reserves she needs to safeguard reproduction she delays committing to further reproductive investment. But how does the cow ‘know’ that she is failing in energy terms? We argue that the cow does this by ‘monitoring’ both the body fat mobilisation and body fatness. Excessive body fat mobilisation indicates that current conditions are worse than expected. Body fatness indicates the future ability of the cow to safeguard her reproductive investment is compromised. Both delay further reproductive commitment. The relationship between reproductive performance and; milk production as an index of maternal investment, body fatness as an index of ability to safeguard reproductive investment, and body fat mobilisation as an index of the current nutritional environment – are examined. Nutritional strategies that seek to modulate body mobilisation and the endocrine environment by use of glucogenic and lipogenic diets, and the use of in-line progesterone profiles to monitor reproductive status are then discussed in this biological context.

In mature male sheep and goats, changes in feed intake seem to have little effect on gonadal endocrine function but induce profound changes on sperm production. These outcomes are due to changes in size of the seminiferous tubules and in spermatogenic efficiency. Except with severe underfeeding, there are only minor changes in the endocrine function of the testis (testosterone production) unless season-long treatments are imposed. For cattle, nutrition clearly affects testicular development and the production of spermatozoa in young bulls, as it does in other species but, after the period of rapid growth has ended, there appears to be little or no response to nutrition. We are developing a clear picture of the metabolic signals, neuroendocrine processes and hormonal control systems that are involved, particularly for the mature male sheep. The energetic components of the diet, rather than protein, seem to be responsible, so we have envisaged a model of the relationship between energy balance and reproduction that has 4 ‘dimensions’: genotype, structure (organs), communication (chemical and neural signals, nutrient sensing) and time (dynamics, metabolic memory, programming). We have linked these perspectives to ‘resource allocation theory’ and incorporated them into strategies for ‘clean, green and ethical animal production’. In contrast to the clear outcomes with respect to spermatogenesis, the effects of nutrition on sexual behaviour are more difficult to define, perhaps because the behaviour is affected by a complex mix of physiological factors and because of flawed methods for quantifying male behaviour. For example, sexual behaviour is compromised by severe feed restriction, but male sexual behaviour requires intensive motor activity so a decline in libido could be caused by general weakness rather than specific nutritional limitations. The interaction between sexual activity and feeding behaviour also complicates the issue under field conditions. At the other end of the scale, overweight males can show reduced sexual success because they have difficulty courting and mounting. For this reason, exercise can enhance the fertilising capacity of rams. This will be important in extensive mating systems where males need to assemble and guard a harem and then mate many times for several weeks. For artificial insemination centres, there seems to be very few data on the nutritional management of males, but problems with overfed animals appear to be a risk. Future research should concentrate on the intra-testicular systems mediating the effects of nutrition on the production of spermatozoa.

Anthropogenic pollutants comprise a wide range of synthetic organic compounds and heavy metals, which are dispersed throughout the environment, usually at low concentrations. Exposure of ruminants, as for all other animals, is unavoidable and while the levels of exposure to most chemicals are usually too low to induce any physiological effects, combinations of pollutants can act additively or synergistically to perturb multiple physiological systems at all ages but particularly in the developing foetus. In sheep, organs affected by pollutant exposure include the ovary, testis, hypothalamus and pituitary gland and bone. Reported effects of exposure include changes in organ weight and gross structure, histology and gene and protein expression but these changes are not reflected in changes in reproductive performance under the conditions tested. These results illustrate the complexity of the effects of endocrine disrupting compounds on the reproductive axis, which make it difficult to extrapolate between, or even within, species. Effects of pollutant exposure on the thyroid gland, immune, cardiovascular and obesogenic systems have not been shown explicitly, in ruminants, but work on other species suggests that these systems can also be perturbed. It is concluded that exposure to a mixture of anthropogenic pollutants has significant effects on a wide variety of physiological systems, including the reproductive system. Although this physiological insult has not yet been shown to lead to a reduction in ruminant gross performance, there are already reports indicating that anthropogenic pollutant exposure can compromise several physiological systems and may pose a significant threat to both reproductive performance and welfare in the longer term. At present, many potential mechanisms of action for individual chemicals have been identified but knowledge of factors affecting the rate of tissue exposure and of the effects of combinations of chemicals on physiological systems is poor. Nevertheless, both are vital for the identification of risks to animal productivity and welfare.

Nutrition is an important aspect of welfare, and in most recommendations for the welfare of animals adequate nutrition is a primary requirement. However, in intensive livestock production systems the decision for adequate nutrition is made based on traditional paradigms of feeding monotonous rations or plant monocultures, frequently with excesses or imbalances of nutrients relative to the individuals’ physiology, which can compromise welfare. Individual ruminants can better meet their needs for nutrients and regulate their intake of secondary compounds when offered a variety of foods than when constrained to a single food, even if the food is nutritionally balanced. The concept of food variety is central because monotonous flavors and feeds and excess nutrients all cause animals to satiate, which in turn causes animals to eat a variety of foods. When offered a variety of foods, satiety for single foods stimulates the selection of a diverse diet and thus food intake, but when restricted to a monotonous diet satiety is aversive and limits food intake. Moreover, if a monotonous diet is aversive to animals then this could be stressful, even if monotony implies consuming a balanced diet. A diverse diet may also increase resistance to disease in ruminants, by allowing consumption of small amounts of compounds with antimicrobial/antiparasitic effects and immunity-enhancing properties. Herbivores also experience the benefits of ingesting compounds with medicinal (i.e. antiparasitic) benefits and they learn to prefer foods containing such compounds as their preferences are associatively conditioned by the food’s homeostatic utility to the body. Such learned patterns of behavior begin in utero and feeding experiences early in life cause changes – neurological, morphological and physiological – in animals, which influence on their subsequent behavior and welfare. Such experiences with the environment enable animals to adapt to local diets and stressors and reduce the levels of fear. Finally, feeding behavior in farm animals could be an aid in the early detection and mitigation of pain or sickness, and as such become an important tool in the identification of welfare and health of animals before the appearance of clinical signs. Management strategies in ruminant production systems could benefit by allowing animals to manifest their feeding preferences, thereby acknowledging the animals’ role as active players in feeding systems, instead of regarding them as passive entities that just respond to prescriptions and formulations.

The feed efficiency of ruminant meat and dairy livestock can be significantly influenced by factors within their living environments. In particular, events perceived by the animals as stressful (such as parturition, transport or handling) have been found to affect susceptibility to infection. It has been well documented that even minor stress such as weighing can result in an increase in colonisation and faecal shedding of enteric pathogens such as Salmonella enterica and Escherichia coli O157:H7. Such infections affect both ruminant overall health and therefore performance, and are a particular problem for the meat production industries. Prior explanations for stress enhancing the likelihood of infection is that activation of the sympathetic nervous system under stress leads to the release of neuroendocrine mediators such as the catecholamine stress hormones noradrenaline and adrenaline, which may impair innate and adaptive immunity. More recently, however, another equally compelling explanation, viewed through the lens of the newly recognised microbiological discipline of microbial endocrinology is that the myriad of bacteria within the ruminant digestive tract are as responsive to the hormonal output of stress as the cells of their host. Work from our laboratories has shown that enteric pathogens have evolved systems for directly sensing stress hormones. We have demonstrated that even brief exposure of enteric pathogens to physiological concentrations of stress hormones can result in massive increases in growth and marked changes in expression of virulence factors such as adhesins and toxins. Happy, less stressed ruminants may therefore be better-nourished animals and safer sources of meat. This article reviews evidence that stress, as well as affecting nutrition, in ruminants is correlated with increased risk of enteric bacterial infections, and examines the molecular mechanisms that may be at work in both processes.

There are numerous recent studies highlighting sustainability problems for the development of ruminant production systems (RPS) while facing increasing human food necessities and global climate change. Despite the complexity of the context, in our view the main objectives of the ruminants’ physiologist should be convergent for both industrialized (IC) and developing countries (DC) in a common and global strategy of advancing knowledge. In DC, this means improving the efficiency of RPS, taking into account the unique possibility of using rangelands. For IC settings, RPS should be revisited in terms of autonomy and environment- friendly feeding and managing practices. Assuming that competition for feed/food use is still a crucial criterion, future ruminant feeding systems (FeSyst) should preferably focus on lignocellulosic sources. According to biome distributions, and the recent increases in volumes of crop residues and their by-products, the annually renewed volumes of these biomasses are considerable. Therefore, we need to redesign our strategies for their efficient utilization at the local level. For this purpose, digestion processes and rumen functioning need to be better understood. The renewed vision of ruminal digestion through the reduction of greenhouse gas emissions is also a key aspect as it is an environmental demand that cannot be ignored. With regard to other ruminants’ physiological functions, accumulated knowledge could be mobilized into an integrative approach that puts forward the adaptive capacities of animals to face variability in quantity and quality of supplied feeds. Basically, the reduction of inputs that were traditionally used to ensure FeSyst will need more flexible animals. In that sense, the concepts of homeostasis and teleophorhesis need to be updated and adapted to domestic species and breeds that were until now largely excluded from the dominant productive systems. In conclusion, a more holistic approach of research targets is required in which physiological functions and farmers’ practices must converge and respond to each particular situation in an integral, dynamic and flexible conceptual perspective. From a scientific point of view, both for ICs and DCs, a broader range of experimental scenarios should be explored in order to arrive at innovative practices and solutions that respect environmental, ethical and economical issues. The clear challenge is to in evaluate the sustainability of RPSs. This includes, in our opinion, a strong interaction with other disciplines (multi- and trans-disciplinary conception), thus structuring new relevant indicators for the evaluation sustainability.