The rise of sequencing technologies has greatly contributed to our knowledge of the microbiota and its role in animal health and production. However, many members of the microbiota have historically been considered “unculturable.” Culturomics can be utilized to bring these fastidious microbes into cultivation and can be used in conjunction with culture-independent methods to study the microbiota in a more comprehensive manner. This review paper details culturomics’ role in revolutionizing human, swine, and bovine microbiota research and how its use has greatly increased the bacterial repertoire. Additionally, it describes how culturomics can be applied to develop microbiota-derived therapeutics, such as next-generation probiotics, and to study the role of the microbiota. Finally, this review provides potential methods and considerations for designing future culturomics studies.

Animal husbandry is increasingly under pressure to meet world food demand. Thus, strategies are sought to ensure this productivity increment. The objective of this review was to gather advances in the use of bacterial probiotics in animal production. Lactobacilli correspond to the most used bacterial group, with several beneficial effects already reported and described, as well as the Enterococcus and Pediococcus genera – being the latter expressively used in aquaculture. Research on the Bifidobacterium genus is mostly focused on human health, which demonstrates great effects on blood biochemical parameters. Such results sustain the possibility of expanding its use in veterinary medicine. Other groups commonly assessed for human medicine but with prospective expansion to animal health are the genera Leuconostoc and Streptococcus, which have been demonstrating interesting effects on the prevention of viral diseases, and in dentistry, respectively. Although bacteria from the genera Bacillus and Lactococcus also have great potential for use in animal production, a complete characterization of the candidate strain must be previously made, due to the existence of pathogenic and/or spoilage variants. It is noteworthy that a growing number of studies have investigated the genus Propionibacterium, but still in very early stages. However, the hitherto excellent results endorse its application. In this way, in addition to the fact that bacterial probiotics represent a promising approach to promote productivity increase in animal production, the application of other strains than the traditionally employed genera may allow the exploitation of novel mechanisms and enlighten unexplored possibilities.

Animal welfare encompasses all aspects of an animal's life and the interactions between animals. Consequently, welfare must be measured across a variety of factors that consider aspects such as health, behaviour and mental state. Decisions regarding housing and grazing are central to farm management. In this study, two beef cattle systems and their herds were compared from weaning to slaughter across numerous indicators. One herd (‘HH’) were continuously housed, the other (‘HG’) were housed only during winter. Inspections of animals were conducted to assess body condition, cleanliness, diarrhoea, hairlessness, nasal discharge and ocular discharge. Hair and nasal mucus samples were taken for quantification of cortisol and serotonin. Qualitative behaviour assessments (QBA) were also conducted and performance monitored. Physical health indicators were similar between herds with the exception of nasal discharge which was more prevalent in HH (P < 0.001). During winter, QBA yielded differences between herds over PC1 (arousal) (P = 0.032), but not PC2 (mood) (P = 0.139). Through summer, there was a strong difference across both PC1 (P < 0.001) and PC2 (P = 0.002), with HG exhibiting more positive behaviour. A difference was found in hair cortisol levels, with the greatest concentrations observed in HG (P = 0.011), however such a pattern was not seen for nasal mucus cortisol or for serotonin. Overall, providing summer grazing (HG) appeared to afford welfare benefits to the cattle as shown with more positive QBA assessments, but also slightly better health indicators, notwithstanding the higher levels of cortisol in that group.

Expectations of retailers and consumers regarding animal health and welfare and meat quality are particularly high for organic products. The aim of this study was therefore to provide an overview of the health and welfare of pigs on organic farms in Austria. Eighty-four organic pig farms were investigated. The farmers were interviewed using a questionnaire. In addition to clinical examination, the pigs were monitored at slaughter to determine the prevalence of organ lesions. The average herd size was 20.1 productive sows in the sow units and 84 fattening pigs in the finishing units. All farms used indoor production systems and provided straw to the pigs. Pregnant sows and finishers had access to an outdoor run in more than 90% of farms, but less than 15% of farms had outdoor runs for lactating sows and weaners. In more than 75% of the herds, endoparasites were found in faecal samples. About 50% of slaughter pigs displayed milk spots on the liver, 24% had pneumonic lesions and 18% showed mange. The results indicate that preventive measures in husbandry, management and hygiene must be intensified to improve animal health and welfare on organic pig farms and to meet the expectations of the consumers.

The Office International des Épizooties (OIE) is a Paris-based, inter-governmental organisation with 164 member countries. Since its establishment in 1924, the OIE has made a major indirect contribution to animal welfare, at a global level, via the organisation's role in epizootic disease control. The OIE animal health code includes a chapter on minimum animal welfare standards for trade and a standard-setting role has also been played in respect of animal transportation. In 1994, the publication Animal Welfare and Veterinary Services was included in the OIE Scientific and Technical Review Series, and provides a valuable State Veterinary Service perspective on animal welfare capability and specific animal welfare issues. In drawing up its strategic plan for the period 2001 to 2005, animal welfare and food safety were identified as two areas for future OIE involvement and these were formally accepted as strategic initiatives at the 2001 OIE General Assembly meeting. An international expert group was established to provide specific recommendations on the nature and scope of the OIE's animal welfare role. The expert group's recommendations were reviewed and adopted, as Resolution XIV, at the May 2002 OIE General Assembly meeting. A permanent international working group was established and met for the first time in October 2002. This paper provides a background to animal welfare as an international trade policy issue and provides an update on progress to date in developing an OIE animal welfare mission statement, supporting guiding principles and policies, and an agreed modus operandi. Priority areas for OIE involvement are identified, and emphasis is placed on the importance of making use of all available expertise and resources, including those from academia, the research community, industry, animal welfare organisations and other relevant stakeholders.

Animal-related parameters best fulfil the requirements of a valid welfare assessment, but often they are less feasible than other parameters. Therefore, this paper examines whether animal-based parameters are connected with each other and with environmental factors in order to find out if some can be discarded without loss of information.

Eighty Austrian dairy herds (21-55 Simmental cows) housed in loose-housing cubicles were visited. Housing, management and the human-animal relationship were assessed. Animal-based parameters such as lameness, skin lesions and social behaviour were recorded. For the statistical analysis, Spearman correlation coefficients and regression trees with additional cross-validations for the assessment of the predictive performance of models were calculated.

The animal-based parameters could be explained by environmental variables only around 2/3 (goodness of fit). The calculated regression trees explained 62% of the percentage of lame animals, 58% of leg injuries on the carpal joints and 69% of the agonistic interactions. Leg injuries on the tarsal joints could be explained to quite a high degree (77%). Cross-validated regression trees, however, which are more significant for prediction on farms in excess of this study, accounted for 31% of the total variance of lameness, 44% of the leg injuries on the tarsal joints, 33% on the carpal joints and 25% of the agonistic interactions.

Only a few correlations between animal-related parameters were found: lameness was correlated with leg injuries on the tarsal joints and on the carpal joints. Leg injuries were correlated with each other.

Due to the lack of interrelations between animal-related parameters and the moderate prediction by environmental factors, we do not suggest replacing the investigated animal-related parameters for on-farm welfare assessment in dairy cattle.

The aim of this study was a comparison of Animal Needs Index (ANI) data, derived from annual inspections by a control agency, with data collected from 164 selected on-farm flocks concerning feather damage, injuries, egg production, mortality, bodyweight, foot pad dermatitis, keel bone deviations and reactions towards humans (eg flock showed marked avoidance when the observer walked through the hen-house [yes/no]).

Analysis of data showed a low number of significant correlations with total ANI scores and category scores: 1) Locomotion, 2) Social interaction, 3) Flooring, 4) Light, air and noise and 5) Stockmanship. Correlations found were low and total ANI score showed only a positive correlation with egg production at week 52. Category 3 scores correlated positively with egg production at week 70 and negatively with the percentage of hens with featherless areas and total pecking injuries. Category 5 scores showed positive correlations with egg production at week 52 as well as week 70 and negative correlations with mortality at week 52, the percentage of hens with featherless areas, pecking injuries < 0.5 cm and total pecking injuries.

Flocks showing marked avoidance had a lower total ANI score and lower category 3 and category 5 scores.

In conclusion, welfare-related animal-based parameters are poorly reflected by the ANI-35-L/2001. To assess animal welfare more adequately, animal-based parameters have to be considered additionally in a welfare assessment scheme.

Health is an important aspect of animal welfare, which is difficult to assess at herd level. Clinical examination of individual animals is time-consuming, and most measures of clinical herd health depend significantly on the examiner. Acute phase proteins are produced during inflammatory processes, and could therefore be used as general markers of infection and injury. Our objective was to evaluate whether haptoglobin could be used to monitor the health status of herds at slaughter.

107 groups of 20 slaughter pigs each were examined at two large abattoirs. Clinical signs of tail biting, lameness, injuries, abscesses, pneumonia, pleurisy, hepatitis and gastritis were recorded. The association between elevated haptoglobin concentration in meat juice samples and clinical signs was assessed via multiple logistic regression.

Pigs from groups in which tail biting, lameness, othaematomas, abscesses, pneumonia, pleurisy, pericarditis or condemnations of livers, lungs or carcasses occurred, showed higher levels of haptoglobin than pigs from slaughter groups without any of these clinical signs. In the multiple regression model, only the variables of lameness and tail biting were statistically significant. The haptoglobin test classified 66% of all slaughter groups correctly according to the presence of these clinical signs. These results demonstrate the potential for haptoglobin to be used as a screening test to identify problem herds at slaughter.

Organic livestock production has been increasing in the US, although it still merely constitutes a small fraction of total production. Its success will require detailed standards supported by scientific knowledge and consistent with organic farming principles. However, such standards, mandated under the Organic Foods Production Act of 1990, are yet to be fully developed. Regulations issued by the USDA's National Organic Program identify livestock health and welfare concerns that must be addressed in a farmer's organic farm plan (eg that there be appropriate housing). However, specifics regarding achievement of these goals are not provided in the form of clear standards for organic livestock production. This paper provides a new starting point to further the development of such standards. First, we outline a rationale based upon the legal context and state of the organic livestock industry detailing the reasons why development of these standards is timely. Second, using a review of existing organic and nonorganic national and international animal health and welfare standards, a search of available scientific research, and a consensus of key stakeholders, we identify areas in which organic standards should be readily adopted. We conclude by presenting one example of a plausible organic standard for each of four major US livestock categories: minimum space for feedlot beef cattle; prohibition of routine tail-docking in dairy cows; provision of perches for laying hens and prohibition of gestation crates for sows.

Antimicrobial resistance is a major threat to both human and animal health, but reduction of use raises issues of how standards of animal health and welfare can be maintained without them. This turns the spotlight onto the role of good management and higher standards of animal welfare as drug-free ways of improving immune function and increasing resistance to infection. Research is urgently needed into the relationship between animal welfare, immunity, gut microbiota and disease and we are not yet in a position to claim that improving welfare will improve resistance to disease. ‘Boosting’ the immune system is not straightforward and an interdisciplinary approach is needed.

Inaccessibility of veterinary and livestock extension services, and shortages of labour and forage could potentially impact the welfare of yaks (Bos grunniens) in Bhutan. The objective of this study was to assess practices relating to the welfare and management of free-ranging yaks in Bhutan and explore variations between different yak-farming regions. We interviewed herders and observed the behaviour and health status of their animals, using an adaptation of the Welfare Quality® protocol, in three yak-farming regions (east, central and west) of Bhutan between October 2018 and January 2019. In total, for 567 cows and 549 calves, integumentary condition, body cleanliness, ocular and nasal discharge, diarrhoea, signs of damage, and gait were scored. In addition, we assessed 324 cows and 272 calves for avoidance distance and examined 324 cows for subclinical mastitis. The behaviour of the herds was observed in six consecutive 20-min blocks with each block divided into two stages. The first stage (5 min) consisted of counting the number of animals eating, lying down, standing idle and walking. The second stage (15 min) consisted of counting the number of events of agonistic, allogrooming, flehming, self-licking, rubbing/scratching and playing behaviour. Avoidance distance differed between regions for calves, but not for lactating cows. Integumentary lesions, dirty body areas, nasal discharge, ocular discharge, signs of diarrhoea, subclinical mastitis and lameness were virtually absent. A few instances of agonistic behaviour (6% of all counted behavioural events) and flehming behaviour (5% of all counted behavioural events) were observed. Yaks in the central and western regions exhibited more scratching and rubbing behaviour than those in the eastern region. Herders perform a variety of painful management practices (castration, ear tagging, nasal septum piercing) without analgesia, which is a prominent welfare issue. Furthermore, mortality among yaks is relatively high and water sources often dirty, creating a health risk. Nevertheless, the welfare status of yaks living in various regions of Bhutan was assessed as good at the time of visit.

Firm operators continually manage multiple sources of risk. In an application to cattle feedlot operations, our objective is to determine if producers view output price and animal health risks separately or jointly. We conduct a survey with a choice experiment placing operators in forward looking, decision-making scenarios, and capture information on past risk management approaches. Evidence regarding a relationship between animal health and output price risk mitigation is mixed and depends on the decision being made. Combined, these results provide new insight into how managers approach multiple risks when facing resource constraints.

Livestock interventions can improve nutrition, health, and economic well-being of communities. The objectives of this review were to identify and characterize livestock interventions in developing countries and to assess their effectiveness in achieving development outcomes. A scoping review, guided by a search strategy, was conducted. Papers needed to be written in English, published in peer-reviewed journals, and describe interventions in animal health and production. Out of 2739 publications systematically screened at the title, abstract, and full publication levels, 70 met our inclusion criteria and were considered in the study. Eight relatively high-quality papers were identified and added, resulting in 78 reviewed publications. Only 15 studies used randomized controlled trial designs making it possible to confidently link interventions with the resulting outcomes. Eight studies had human nutrition or health as outcomes, 11 focused on disease control, and four were on livestock production. Eight interventions were considered successful, but only four were scalable. We found good evidence that livestock-transfer programs, leveraging livestock products for nutrition, and helping farmers manage priority diseases, can improve human well-being. Our report highlights challenges in garnering evidence for livestock interventions in developing countries and provides suggestions on how to improve the quantity and quality of future evaluations.

Feeding monogastric livestock in organic agriculture is challenging due to several tradeoffs between animal welfare aspects, resource efficiency, as well as ecological and social sustainability. Organic standards may even increase such conflicts, as is currently the case with upcoming new regulations regarding restrictions of feed sources for organic pigs in Europe. In order to contribute data for balancing reasons to minimize tradeoffs, we compared four different piglet diets, each targeted to reach a high protein quality by either a high proportion of soybean cake (SOY), inclusion of milk powder (MILK), fermentatively produced lysine (LYS) or conventional potato protein (POT). All diets were designed to meet the nutritional requirements of piglets in the best possible way, however they all represented different conflicts with either organic regulations or sustainability goals. In each of five consecutive runs, respectively three litters were assigned to every dietary treatment, resulting in 15 litters per treatment in total. In each litter, seven focus animals were defined. The piglets were studied from birth until 58 days of age. They were weaned at day 46 and sold from the farm at day 58. Piglets were individually weighed at an average age of 3, 21, 43, 50 and 58 days with simultaneous assessment of body condition score (BCS) and prevalence of diarrhea. Feed intake (FI) was recorded litter wise weekly, starting from week three. Feed conversion ratio (FCR) was calculated for the period after weaning. Statistical analysis was executed using linear mixed effect models. Regarding FI, FCR and daily weight gains, no treatment effect was found. Only at day 21, BCS was lower for piglets receiving POT. Prevalence of diarrhea increased after weaning for all treatments. All four tested diets led to similar weight gains and feed conversion in the piglets. Animals fed diet POT recovered better from diarrhea compared to the other treatments. A high soybean cake content or lysine supplementation in the diet was disadvantageous with regard to the occurrence of diarrhea. LYS diet led to signs of threonine deficit, indicating that lysine addition alone may not solve the issue. The addition of milk powder provided no extra benefit. In recognition of the health benefits, the use of 5% potato protein, even if it is sourced from conventional production, must still be considered as a sustainable option for feeding organic piglets. The sustainability implications are discussed in the paper.

Automated systems for high-input data collection and data storage have led to exponential growth in the availability of information. Such datasets and the tools applied to them have been referred to as ‘big data’. Starting with a systematic review of the terms ‘informatics, bioinformatics and big data’ in animal health this special issue of AHRR illustrates some big-data applications with papers on how the use of various omics methods may be used to facilitate the development of improved diagnostics, therapeutics, and vaccines for foodborne pathogens in poultry and on how a better understanding of rumen microbiota could lead to improved feed absorption while minimizing methane production. Other papers in this issue cover the use of big data modeling in dairy cattle for more effective disease interventions and machine learning tools for livestock breeding. The final two reviews describe the use of big data in better vector-borne pathogen forecasts with canine seroprevalence maps and modeling approaches to understand the transmission of avian influenza virus. Although a lot of technical and ethical issues remain with the use of big data, these reviews illustrate the tremendous potential that big-data systems have to revolutionize animal health research.

To implement effective stewardship in food animal production, it is essential that producers and veterinarians are aware of preventive interventions to reduce illness in livestock. Systematic reviews and meta-analyses (SR/MA) provide transparent, replicable, and quality-assessed overviews. At present, it is unknown how many SR/MA evaluate preventive antibiotic use or management practices aimed at reducing disease risk in animal agriculture. Further, the quality of existing reviews is unknown. Our aim was to identify reviews investigating these topics and to provide an assessment of their quality. Thirty-eight relevant reviews were identified. Quality assessment was based on the AMSTAR 2 framework for the critical appraisal of systematic reviews. The quality of most of the reviews captured was classified as critically low (84.2%, n = 32/38), and only a small percentage of the evaluated reviews did not contain critical weaknesses (7.9%, n = 3/38). Particularly, a small number of reviews reported the development of an a priori protocol (15.8%, n = 6/38), and few reviews stated that key review steps were conducted in duplicate (study selection/screening: 26.3%, n = 10/38; data extraction: 15.8%, n = 6/38). The development of high-quality reviews summarizing evidence on approaches to antibiotic reduction is essential, and thus greater adherence to quality conduct guidelines for synthesis research is crucial.

Systematic reviews and meta-analyses are used to summarize and interpret evidence for clinical decision-making in human health. The extent of the application of these methods in veterinary medicine and animal agriculture is unknown. The goal of this scoping study was to ascertain trends in the publication of systematic reviews and meta-analyses examining animal health, animal performance, and on-farm food safety. Online databases were searched for reviews published between 1993 and 2018 that focused on relevant outcomes in domestic livestock, companion animals, or wildlife species. In total 1787 titles and abstracts underwent data characterization. Dairy cattle, fish, and pigs were the most common target commodity groups. Few articles investigated both health and performance outcomes (only health: n = 418; only performance: n = 701; both health and performance: n = 103). Most of the reviews (67.6%, n = 1208/1787) described a meta-analysis but did not state in the title or abstract that a systematic review was also conducted, which is potentially problematic. Adherence to reporting guidelines is recommended for all systematic reviews and meta-analyses. For research areas with many reviews, an evidence repository is recommended. For less well-reviewed areas, additional investigation may be necessary to identify the reasons for the lack of synthesis research.

Research in big data, informatics, and bioinformatics has grown dramatically (Andreu-Perez J, et al., 2015, IEEE Journal of Biomedical and Health Informatics 19, 1193–1208). Advances in gene sequencing technologies, surveillance systems, and electronic medical records have increased the amount of health data available. Unconventional data sources such as social media, wearable sensors, and internet search engine activity have also contributed to the influx of health data. The purpose of this study was to describe how ‘big data’, ‘informatics’, and ‘bioinformatics’ have been used in the animal health and veterinary medical literature and to map and chart publications using these terms through time. A scoping review methodology was used. A literature search of the terms ‘big data’, ‘informatics’, and ‘bioinformatics’ was conducted in the context of animal health and veterinary medicine. Relevance screening on abstract and full-text was conducted sequentially. In order for articles to be relevant, they must have used the words ‘big data’, ‘informatics’, or ‘bioinformatics’ in the title or abstract and full-text and have dealt with one of the major animal species encountered in veterinary medicine. Data items collected for all relevant articles included species, geographic region, first author affiliation, and journal of publication. The study level, study type, and data sources were collected for primary studies. After relevance screening, 1093 were classified. While there was a steady increase in ‘bioinformatics’ articles between 1995 and the end of the study period, ‘informatics’ articles reached their peak in 2012, then declined. The first ‘big data’ publication in animal health and veterinary medicine was in 2012. While few articles used the term ‘big data’ (n = 14), recent growth in ‘big data’ articles was observed. All geographic regions produced publications in ‘informatics’ and ‘bioinformatics’ while only North America, Europe, Asia, and Australia/Oceania produced publications about ‘big data’. ‘Bioinformatics’ primary studies tended to use genetic data and tended to be conducted at the genetic level. In contrast, ‘informatics’ primary studies tended to use non-genetic data sources and conducted at an organismal level. The rapidly evolving definition of ‘big data’ may lead to avoidance of the term.