The objective of this review paper is to describe the development and application of a suite of more than 40 computerized dairy farm decision support tools contained at the University of Wisconsin-Madison (UW) Dairy Management website http://DairyMGT.info. These data-driven decision support tools are aimed to help dairy farmers improve their decision-making, environmental stewardship and economic performance. Dairy farm systems are highly dynamic in which changing market conditions and prices, evolving policies and environmental restrictions together with every time more variable climate conditions determine performance. Dairy farm systems are also highly integrated with heavily interrelated components such as the dairy herd, soils, crops, weather and management. Under these premises, it is critical to evaluate a dairy farm following a dynamic integrated system approach. For this approach, it is crucial to use meaningful data records, which are every time more available. These data records should be used within decision support tools for optimal decision-making and economic performance. Decision support tools in the UW-Dairy Management website (http://DairyMGT.info) had been developed using combination and adaptation of multiple methods together with empirical techniques always with the primary goal for these tools to be: (1) highly user-friendly, (2) using the latest software and computer technologies, (3) farm and user specific, (4) grounded on the best scientific information available, (5) remaining relevant throughout time and (6) providing fast, concrete and simple answers to complex farmers’ questions. DairyMGT.info is a translational innovative research website in various areas of dairy farm management that include nutrition, reproduction, calf and heifer management, replacement, price risk and environment. This paper discusses the development and application of 20 selected (http://DairyMGT.info) decision support tools.

Knowledge of the capabilities and limitations of the reproductive capacity of bulls is vital in maximizing reproductive efficiencies. Bull semen collection guidelines established by researchers and industry personnel to maximize the sperm harvest from bulls have been evolving for more than 60 years. Today, a mature artificial insemination industry employs those strategies to meet demands. These efficient management schemes exploit the reproductive potential of each sire while minimizing the associated risk of injury to bulls and reduce associated production costs. Personnel employed by a semen producing facility must be authorized to make effective and rational decisions based on principles of bull sexual behavior and reproductive physiology. Furthermore, collection facilities must be well planned to allow for the safe presentation of novel sexual situations while affording maximum safety for employees and proper footing for bulls. Normal bulls produce and ejaculate tremendous numbers of sperm. Most bulls have a sufficient libido for routine sexual activity, but become satiated to predictable stimulus situations. Frequent changes to the novelty should allow weekly harvest of four to six ejaculates per week for most bulls. Utilizing the physiological characteristics associated with each ejaculate to establish the collection frequency of each bull, and empowering an integrated collection and laboratory staff to monitor and make adjustments to the ejaculation frequency are necessary in maximizing the sperm harvest. Young bulls can ejaculate 10 to 20 billion sperm per week, and mature bulls should ejaculate 40 to 60 billion sperm per week. Semen collection management procedures should be reviewed when bulls do not meet production goals.

Inflammatory cascades are a critical component of the immune response to infection or tissue damage, involving an array of signals, including water-soluble metabolites, lipid mediators and several classes of proteins. Early investigation of these signaling pathways focused largely on immune cells and acute disease models. However, more recent findings have highlighted critical roles of both immune cells and inflammatory mediators on tissue remodeling and metabolic homeostasis in healthy animals. In dairy cattle, inflammatory signals in various tissues and in circulation change rapidly and dramatically, starting just prior to and at the onset of lactation. Furthermore, several observations in healthy cows point to homeostatic control of inflammatory tone, which we define as a regulatory process to balance immune tolerance with activation to keep downstream effects under control. Recent evidence suggests that peripartum inflammatory changes influence whole-body nutrient flux of dairy cows over the course of days and months. Inflammatory mediators can suppress appetite, even at levels that do not induce acute responses (e.g. fever), thereby decreasing nutrient availability. On the other hand, inhibition of inflammatory signaling with non-steroidal anti-inflammatory drug (NSAID) treatment suppresses hepatic gluconeogenesis, leading to hypoglycemia in some cases. Over the long term, though, peripartum NSAID treatment substantially increases peak and whole-lactation milk synthesis by multiparous cows. Inflammatory regulation of nutrient flux may provide a homeorhetic mechanism to aid cows in adapting to rapid changes in metabolic demand at the onset of lactation, but excessive systemic inflammation has negative effects on metabolic homeostasis through inhibition of appetite and promotion of immune cell activity. Thus, in this review, we provide perspectives on the overlapping regulation of immune responses and metabolism by inflammatory mediators, which may provide a mechanistic underpinning for links between infectious and metabolic diseases in transition dairy cows. Moreover, we point to novel approaches to the management of this challenging phase of the production cycle.

Selecting bulls for reproductive soundness requires that the bull be structurally sound, free of abnormalities that impair his ability to produce adequate numbers of motile, morphologically normal spermatozoa, and be able to successfully complete coitus. This review discusses the diagnosis and etiology of abnormalities of the penis, prepuce as well as common musculoskeletal conditions that prevent normal pasture breeding soundness. A review of testicular and thermoregulation addresses the potential impact of musculoskeletal disorders on normal sperm production.

The average productive lifespan is approximately 3 to 4 years in countries with high-producing dairy cows. This is much shorter than the natural life expectancy of dairy cattle. Dairy farmers continue to cull cows primarily for reasons related to poor health, failure to conceive or conformation problems prior to culling. These reasons may indicate reduced welfare leading up to culling. Improvements in health care, housing and nutrition will reduce forced culling related to these welfare reasons. However, productive lifespan has remained similar in decades, despite large improvements in cow comfort and genetic selection for the ability to avoid culling. On the other hand, genetic progress for economically important traits is accelerating within the last decade, which should slightly shorten the average economically optimal productive lifespan. A major driver of productive lifespan is the availability of replacement heifers that force cows out when they calve. The average productive lifespan could be extended by reducing the supply of dairy heifers, which would also have benefits for environmental sustainability. Improvements in culling decision support tools would strengthen economically optimal replacement decisions. In conclusion, major factors of the relatively short productive lifespan of dairy cows are welfare-related, but other economic factors like supply of heifers, genetic progress and non-optimal decision-making also play important roles.

Efficient and economical herd management depends a great deal on maintaining a short, well-defined calving season. This requires highly fertile females and bulls. Low pregnancy rates are very noticeable, however; potentially greater economic loss may be due to delayed conception. Many studies showed that approximately one of every five bulls had inadequate semen quality, physical soundness, or both, but when evaluation of serving capacity is included about one in four bulls is unsatisfactory. Due mainly to the time and expense that the market will bear, usually only physical soundness and semen quality are evaluated. Breeding soundness evaluation is a useful, low-cost screening method for reducing the risk of using low fertility bulls. The biggest problem with breeding soundness evaluations is not our lack of knowledge or ability, but in the willingness of veterinary schools to provide adequate equipment and training in this area, a lack of diagnostic laboratories equipped to handle the more difficult cases and, most importantly, the weaknesses of human nature that result in negligent testing procedure.

The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.

The purpose of this paper is to review scientific evidence concerning pathogens that could potentially be transmitted via bovine semen. As a result of a careful analysis of the characteristics of infections that may cause transmission of disease through semen, effective control procedures can be identified that provide minimal constraint to the introduction of new bulls into herds for natural breeding and importation of valuable novel genetics through artificial insemination. The potential for transmission through bovine semen and corresponding effective control procedures are described for bovine herpesvirus 1, bovine viral diarrhea virus, bovine leukemia virus, lumpy skin disease virus, bluetongue virus, foot-and-mouth disease virus, and Schmallenberg virus. Brief consideration is also provided regarding the potential for transmission via semen of Tritrichomonas foetus, Campylobacter fetus venerealis, Brucella abortus, Leptospira spp., Histophilus somni, Ureaplasma diversum, Mycobacterium avium subsp. paratuberculosis, Chlamydiaceae, Mycobacterium bovis, Coxiella burnetii, Mycoplasma mycoides ssp. mycoides and Neospora caninum. Thoughtful and systematic control procedures can ensure the safety of introducing new bulls and cryopreserved semen into cattle production systems.

Coordinated changes in energy metabolism develop to support gestation and lactation in the periparturient dairy cow. Maternal physiology involves the partitioning of nutrients (i.e. glucose, amino acids and fatty acids (FA)) for fetal growth and milk synthesis. However, the inability of the dairy cow to successfully adapt to a productive lactation may trigger metabolic stress characterized by uncontrolled adipose tissue lipolysis and reduced insulin sensitivity. A consequence is lipotoxicity and hepatic triglyceride deposition that favors the development of fatty liver disease (FLD) and ketosis. This review describes contemporary perspectives pertaining to FA surfeit and complex lipid metabolism in the transition dairy cow. The role of saturated and unsaturated FA as bioactive signaling molecules capable of modulating insulin secretion and sensitivity is explored. Moreover, the metabolic fate of FA as influenced by mitochondrial function is considered. This includes the influence of inadequate mitochondrial oxidation on acylcarnitine status and the use of FA for lipid mediator synthesis. Lipid mediators, including the sphingolipid ceramide and diacylglycerol, are evaluated considering their established ability to inhibit insulin signaling and glucose transport in non-ruminant diabetics. The mechanisms of FLD in the transition cow are revisited with attention centered on glycerophospholipid phosphatidylcholine and triglyceride secretion. The relationship between oxidative stress and oxylipids within the context of insulin antagonism, hepatic steatosis and inflammation is also reviewed. Lastly, peripartal hormonal involvement or lack thereof of adipokines (i.e. leptin, adiponectin) and hepatokines (i.e. fibroblast growth factor-21) is described. Similarities and differences in ruminant and non-ruminant physiology are routinely showcased. Unraveling the lipidome of the dairy cow has generated breakthroughs in our understanding of periparturient lipid biology. Therapeutic approaches that target FA and complex lipid metabolism holds promise to enhance cow health, well-being and productive lifespan.

Fertility is one of the most economically important traits in both beef and dairy cattle production; however, only female fertility is typically subjected to selection. Male and female fertility have only a small positive genetic correlation which is likely due to the existence of a relatively small number of genetic variants within each breed that cause embryonic and developmental losses. Genomic tools have been developed that allow the identification of lethal recessive loci based upon marker haplotypes. Selection against haplotypes harbouring lethal alleles in conjunction with selection to improve female fertility will result in an improvement in male fertility. Genomic selection has resulted in a two to fourfold increase in the rate of genetic improvement of most dairy traits in US Holstein cattle, including female fertility. Considering the rapidly increasing rate of adoption of high-throughput single nucleotide polymorphism genotyping in both the US dairy and beef industries, genomic selection should be the most effective of all currently available approaches to improve male fertility. However, male fertility phenotypes are not routinely recorded in natural service mating systems and when artificial insemination is used, semen doses may be titrated to lower post-thaw progressively motile sperm numbers for high-merit and high-demand bulls. Standardization of sperm dosages across bull studs for semen distributed from young bulls would allow the capture of sire conception rate phenotypes for young bulls that could be used to generate predictions of genetic merit for male fertility in both males and females. These data would allow genomic selection to be implemented for male fertility in addition to female fertility within the US dairy industry. While the rate of use of artificial insemination is much lower within the US beef industry, the adoption of sexed semen in the dairy industry has allowed dairy herds to select cows from which heifer replacements are produced and cows that are used to produce terminal crossbred bull calves sired by beef breed bulls. Capture of sire conception rate phenotypes in dairy herds utilizing sexed semen will contribute data enabling genomic selection for male fertility in beef cattle breeds. As the commercial sector of the beef industry increasingly adopts fixed-time artificial insemination, sire conception rate phenotypes can be captured to facilitate the development of estimates of genetic merit for male fertility within US beef breeds.

Rumen sensors provide specific information to help understand rumen functioning in relation to health disorders and to assist in decision-making for farm management. This review focuses on the use of rumen sensors to measure ruminal pH and discusses variation in pH in both time and location, pH-associated disorders and data analysis methods to summarize and interpret rumen pH data. Discussion on the use of rumen sensors to measure redox potential as an indication of the fermentation processes is also included. Acids may accumulate and reduce ruminal pH if acid removal from the rumen and rumen buffering cannot keep pace with their production. The complexity of the factors involved, combined with the interactions between the rumen and the host that ultimately determine ruminal pH, results in large variation among animals in their pH response to dietary or other changes. Although ruminal pH and pH dynamics only partially explain the typical symptoms of acidosis, it remains a main indicator and may assist to optimize rumen function. Rumen pH sensors allow continuous monitoring of pH and of diurnal variation in pH in individual animals. Substantial drift of non-retrievable rumen pH sensors, and the difficulty to calibrate these sensors, limits their application. Significant within-day variation in ruminal pH is frequently observed, and large distinct differences in pH between locations in the rumen occur. The magnitude of pH differences between locations appears to be diet dependent. Universal application of fixed conversion factors to correct for absolute pH differences between locations should be avoided. Rumen sensors provide high-resolution kinetics of pH and a vast amount of data. Commonly reported pH characteristics include mean and minimum pH, but these do not properly reflect severity of pH depression. The area under the pH × time curve integrates both duration and extent of pH depression. The use of this characteristic, as well as summarizing parameters obtained from fitting equations to cumulative pH data, is recommended to identify pH variation in relation to acidosis. Some rumen sensors can also measure the redox potential. This measurement helps to understand rumen functioning, as the redox potential of rumen fluid directly reflects the microbial intracellular redox balance status and impacts fermentative activity of rumen microorganisms. Taken together, proper assessment and interpretation of data generated by rumen sensors requires consideration of their limitations under various conditions.

In this position paper, I shall summarise the current status of sensor technologies in ruminant livestock farming with emphasis on dairy cattle, outline the case for why I believe that sensor technologies could revolutionise global dairy farming in a positive way, describe the significant barriers that exist if that goal is to be achieved and highlight the benefits to animal wellbeing, profitability and sustainability that could result if the technologies are implemented to a significant extent. I shall not provide a comprehensive review of the sensor technology literature since that has been done before, but I intend to provide a sensible amount of background information and data that will allow the reader to obtain a picture not only of today’s sensor usage but, more importantly, the possible future direction of dairy animal-oriented sensor technologies, and I shall substantiate my claims and conclusions with relevant literature.

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.

The so-called global change refers to changes on a planetary scale. The term encompasses various issues like resource use, energy development, population growth, land use and land cover, carbon and nitrogen cycle, pollution and health, and climate change. The paper deals with challenges for dairy cattle production systems in Europe arising from climate change as one part of global changes. Global warming is increasing, and therefore ecosystems, plant and animal biodiversity, and food security and safety are at risk. It is already accepted knowledge that the direct and indirect effects of global warming in combination with an increasing frequency of weather extremes are a serious issue for livestock production, even in moderate climate zones like Central Europe. The potential and already-measurable effects of climate change (including increase in temperature, frequency of hot days and heat waves), in particular the challenges on grassland production, fodder quality, nutrition in general, cow welfare, health as well as performance of dairy production, will be reviewed. Indirect and direct effects on animals are correlated with their performance. There are clear indications that with selection for high-yielding animals the sensitivity to climate changes increases. Cumulative effects (e.g. higher temperature plus increased pathogen and their vectors loads) do strengthen these impacts. To cope with the consequences several possible adaptation and mitigation strategies must be established on different levels. This includes changes in the production systems (e.g. management, barn, feeding), breeding strategies and health management.

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.

In animal sciences, the number of published meta-analyses is increasing at a rate of 15% per year. This current review focuses on the good practices and the potential pitfalls in the conduct of meta-analyses in animal sciences, nutrition in particular. Once the study objectives have been defined, several key phases must be considered when doing a meta-analysis. First, as a principle of traceability, criteria used to select or discard publications should be clearly stated in a way that one could reproduce the final selection of data. Then, the coding phase, aiming to isolate specific experimental factors for an accurate graphical and statistical interpretation of the database, is discussed. Following this step, the study of the levels of independence of factors and of the degree of data balance of the meta-design represents an essential phase to ensure the validity of statistical processing. The consideration of the study effect as fixed or random must next be considered. It appears based on several examples that this choice does not generally have any influence on the conclusions of a meta-analysis when the number of experiments is sufficient.

Livestock farming systems provide multiple benefits to humans: protein-rich diets that contribute to food security, employment and rural economies, capital stock and draught power in many developing countries and cultural landscape all around the world. Despite these positive contributions to society, livestock is also the centre of many controversies as regards to its environmental impacts, animal welfare and health outcomes related to excessive meat consumption. Here, we review the potentials of sustainable intensification (SI) and agroecology (AE) in the design of sustainable ruminant farming systems. We analyse the two frameworks in a historical perspective and show that they are underpinned by different values and worldviews about food consumption patterns, the role of technology and our relationship with nature. Proponents of SI see the increase in animal protein demand as inevitable and therefore aim at increasing production from existing farmland to limit further encroachment into remaining natural ecosystems. Sustainable intensification can thus be seen as an efficiency-oriented framework that benefits from all forms of technological development. Proponents of AE appear more open to dietary shifts towards less animal protein consumption to rebalance the whole food system. Agroecology promotes system redesign, benefits from functional diversity and aims at providing regulating and cultural services. We analyse the main criticisms of the two frameworks: Is SI sustainable? How much can AE contribute to feeding the world? Indeed, in SI, social justice has long lacked attention notably with respect to resource allocation within and between generations. It is only recently that some of its proponents have indicated that there is room to include more diversified systems and food-system transformation perspectives and to build socially fair governance systems. As no space is available for agricultural land expansion in many areas, agroecological approaches that emphasise the importance of local production should also focus more on yield increases from agricultural land. Our view is that new technologies and strict certifications offer opportunities for scaling-up agroecological systems. We stress that the key issue for making digital science part of the agroecological transition is that it remains at a low cost and is thus accessible to smallholder farmers. We conclude that SI and AE could converge for a better future by adopting transformative approaches in the search for ecologically benign, socially fair and economically viable ruminant farming systems.

The rumen microbiome has the important task of supplying ruminants with most of their dietary requirements and is responsible for up to 90% of their metabolic needs. This tremendous feat is possible due to the large diversity of microorganisms in the rumen. The rumen is considered one of the most diverse ecosystems on the planet in terms of species diversity and functional richness. From the moment the feed is ingested, it enters a vast cascade in which specialized microorganisms degrade specific components of the feed turning them into molecules, which in turn are utilized as anabolic precursors and energy sources for the animal. The output of this degradation process not only affects the animal, but also has an extensive impact on the environment. Some of the byproducts that are emitted as waste from this process, such as methane, act as greenhouse gases which greatly contribute to global warming. Recent technological advances developed to study this community enabled a larger overview of its vast taxonomic and functional diversity, thus leading to a better understanding of its ecology and function. This deeper understanding of the forces affecting the microbiome includes the forces that shape composition, the variation among animals, the stability of its key components, the processes of succession on a short- and long-time scales such as primary colonization and diurnal oscillations. These collective understandings have helped to provide insights into the potential effects that these forces have on the outputs observed from the animal itself. Over the recent years, there has been a growing body of evidence demonstrating the link between the microbiome and its effect on productivity of the host animals and the environment, which has placed rumen microbiome studies in the forefront of animal agricultural research. In this review, we focus on the natural variations in community composition, which are not the results of different management or feed but rather intrinsic features of animals. We characterize the rumen microbiome, its potential impact on its host as well as the barriers in implementing the current knowledge to modulate the microbiome and point toward potential avenues to overcome these hurdles.

Mechanistic models (MMs) have served as causal pathway analysis and ‘decision-support’ tools within animal production systems for decades. Such models quantitatively define how a biological system works based on causal relationships and use that cumulative biological knowledge to generate predictions and recommendations (in practice) and generate/evaluate hypotheses (in research). Their limitations revolve around obtaining sufficiently accurate inputs, user training and accuracy/precision of predictions on-farm. The new wave in digitalization technologies may negate some of these challenges. New data-driven (DD) modelling methods such as machine learning (ML) and deep learning (DL) examine patterns in data to produce accurate predictions (forecasting, classification of animals, etc.). The deluge of sensor data and new self-learning modelling techniques may address some of the limitations of traditional MM approaches – access to input data (e.g. sensors) and on-farm calibration. However, most of these new methods lack transparency in the reasoning behind predictions, in contrast to MM that have historically been used to translate knowledge into wisdom. The objective of this paper is to propose means to hybridize these two seemingly divergent methodologies to advance the models we use in animal production systems and support movement towards truly knowledge-based precision agriculture. In order to identify potential niches for models in animal production of the future, a cross-species (dairy, swine and poultry) examination of the current state of the art in MM and new DD methodologies (ML, DL analytics) is undertaken. We hypothesize that there are several ways via which synergy may be achieved to advance both our predictive capabilities and system understanding, being: (1) building and utilizing data streams (e.g. intake, rumination behaviour, rumen sensors, activity sensors, environmental sensors, cameras and near IR) to apply MM in real-time and/or with new resolution and capabilities; (2) hybridization of MM and DD approaches where, for example, a ML framework is augmented by MM-generated parameters or predicted outcomes and (3) hybridization of the MM and DD approaches, where biological bounds are placed on parameters within a MM framework, and the DD system parameterizes the MM for individual animals, farms or other such clusters of data. As animal systems modellers, we should expand our toolbox to explore new DD approaches and big data to find opportunities to increase understanding of biological systems, find new patterns in data and move the field towards intelligent, knowledge-based precision agriculture systems.

Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.