Progress and opportunities through use of genomics in animal production.

The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.

SARS-CoV-2 Infection in Beaver Farm, Mongolia, 2021.

We report an outbreak of COVID-19 in a beaver farm in Mongolia in 2021. Genomic characterization revealed a unique combination of mutations in the SARS-CoV-2 of the infected beavers. Based on these findings, increased surveillance of farmed beavers should be encouraged.

FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.

The Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. A key goal of the initiative is to ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays. By defining rich sample and experimental metadata standards and promoting best practices in data descriptions, deposition and openness, FAANG champions higher quality and reusability of published datasets. FAANG has established a Data Coordination Centre, which sits at the heart of the Metadata and Data Sharing Committee. It continues to evolve the metadata standards, support submissions and, crucially, create powerful and accessible tools to support deposition and validation of metadata. FAANG conforms to the findable, accessible, interoperable, and reusable (FAIR) data principles, with high quality, open access and functionally interlinked data. In addition to data generated by FAANG members and specific FAANG projects, existing datasets that meet the main-or more permissive legacy-standards are incorporated into a central, focused, functional data resource portal for the entire farmed and companion animal community. Through clear and effective metadata standards, validation and conversion software, combined with promotion of best practices in metadata implementation, FAANG aims to maximise effectiveness and inter-comparability of assay data. This supports the community to create a rich genome-to-phenotype resource and promotes continuing improvements in animal data standards as a whole.

Microplastics contamination in commercial fish meal and feed: a major concern in the cultured organisms.

The growing scale of plastic pollution causes a devastating impact on the aquatic ecosystem. The people largely depend on animal-based food for their protein requirements. In this study, we analysed 10 different fish meal samples and 20 feed samples used in farming to understand the level of microplastic (MPs) contamination and estimate the amount of MPs ingested by farmed fish, shrimp, and chicken through feed. The abundance of MPs in fish meal samples ranges from 210 ± 98.21 to 1154 ± 235.55 items/kg. The fish meal produced from dried fish is more prone to MPs contamination than that produced from fresh fish. In the case of fish feed, MP abundances range from 50 ± 22.36 to 160 ± 36.57 items/kg in shrimp feeds, 60 ± 26.74 to 230 ± 52.32 items/kg in fish feeds and 90 ± 25.11 to 330 ± 36.12 items/kg in chicken feeds. The exposure rate of MPs is higher in the grower- and finisher-stage feeds than in the starter feed. Fiber-shaped MPs of size 100-500 µm with PE and PP polymers were predominantly found in fish meal and feed samples. EDAX analysis showed the presence of Cr, Cd, Ti, Ni, Cu, As, Al, Pb, Hg, Cd, Ti, Fe, Ca, K, and Si in fish meal samples and Ca, Na, Zn, Cu, Ni, Cl, Al, Si, S, Pb, Cd, Ti, Cr, Mg and Fe in feed samples. The possible level of exposure of microplastic particles was calculated based on MP contamination in feed, feed consumption rate, and body weight. We estimated an MP exposure level of 531-1434 items/kg feed for farmed shrimp, 234-4480 items/kg feed for fishes, and 3519-434,280 items/kg feed for chicken. This study concludes that fish meal and feed are one of the important exposure routes of MPs to the farmed animals.

A novel p.127Val>Ile SNP in the MTNR1A gene and its relation to litter size in Thin-tailed Indonesian ewes.

Objective: The primary objective is to identify and characterize the Single Nucleotide Polymorphisms (SNPs) within the MTNR1A gene sequence in thin-tailed Indonesian ewes to assess the possible association of MTNR1A gene polymorphism with litter size trait. Methods: Forty-seven thin-tailed Indonesian sheep were selected for the study. Genotyping involved collecting blood samples, and sequencing exon 2 of the MTNR1A gene. Results: The study identified 19 novel SNPs, with 10 being non-synonymous variations, in the MTNR1A gene of Thin-tailed Indonesian ewes. One non-synonymous SNP (rs1087815963) showed a significant association with litter size, with the GC genotype exhibiting a higher average litter size than the GG genotype. The deleterious impact of p.Val127Ile SNP was predicted by various in silico tools that predicted a highly damaging effect of p.Val127Ile SNP on the structure, function, and stability of MTNR1A. Docking reactions showed a critical involvement of this locus with the binding with melatonin. Conclusion: In conclusion, the results of our study suggest that rs1087815963 has a remarkable negative impact on the MTNR1A with a putative alteration in the binding with melatonin. Therefore, it can be stated that the implementation of the novel p.Val127Ile could be a useful marker in marker-assisted selection.

Bibliometric analysis of veterinary medicine on embryo of animals in textbook in conceptualizing disease and health.

In veterinary medicine, the concept of disease is critical because it related to the survivability rate of the veterinary, especially livestock. Chicken was the most popular livestock that was observed in veterinary medicine. However, veterinary books were less popular compared to article and conference paper in global academic. This study's goal was to look how was the depiction of topic disease was used in veterinary textbooks that were related to the embryo of chicken as well as the trend of that topic. This study gathered 90 books meta-data donwloaded from Scopus website in form of CSV file. The data were analyzed using Vosviewer and biblioshiny of R Studio software to see the topic trend, citation, and number of book pages. Literature review also used to see the depiction of disease inside samples. Result showed that authors' keywords, heart and disease were closely related with a keyword chicken embryo. Moreover, each book get at least 10-11 citations globally. Moreover, repetitive keywords used in abstract of samples of this study were cells/cell, gene, and human. Those repetitive words were closely related to a word disease. It could be means that cell of the embryo of chicken also played the important role in determining its resistance against disease.

Approximating the global economic (market) value of farmed animals.

Understanding the global economic importance of farmed animals to society is essential as a baseline for decision making about future food systems. We estimated the annual global economic (market) value of live animals and primary production outputs, e.g., meat, eggs, milk, from terrestrial and aquatic farmed animal systems. The results suggest that the total global market value of farmed animals ranges between 1.61 and 3.3 trillion USD (2018) and is expected to be similar in absolute terms to the market value of crop outputs (2.57 trillion USD). The cattle sector dominates the market value of farmed animals. The study highlights the need to consider other values of farmed animals to society, e.g., finance/insurance value and cultural value, in decisions about the sector's future.

Evaluating the contribution of antimicrobial use in farmed animals to global antimicrobial resistance in humans.

Antimicrobial resistance (AMR) is currently regarded by the World Health Organization (WHO) as one of the most significant risks to global public health. The most critical causes of AMR infections in humans are the misuse and overuse of antimicrobials in humans and farmed animals. The rising global demand for food of animal origin encourages the increase of animal production worldwide, especially in developing countries. Simultaneously, current farming practices often extensively use antimicrobials on animals, influencing bacterial AMR incidence. This study aims to evaluate the correlation between antimicrobial use (AMU) in farmed animals and the detection of AMR infections in humans, the effects of enforcing laws in animal farming in a country on AMR situation in the neighbors, and the potential of AMR to spread from one country to another. Using data from 30 largest animal-producing countries in different regions of the world, between 2010 and 2020, and a Spatial Durbin Model (SDM), we found that AMU in farmed animals increases AMR in humans and there is a spatial dependence between countries regarding AMR spreading. Such findings indicate that a globally coordinated strategy regulating AMU on farmed animals may reduce AMR emergence and worldwide spreading.

Object Play as a Positive Emotional State Indicator for Farmed Spotted Paca (Cuniculus paca).

We aimed to assess whether object play can be used as a positive emotional state indicator for farmed spotted pacas (Cuniculus paca) by examining its association with other positive welfare markers including affiliative behavior and low-amplitude vocalizations. We submitted six groups of spotted pacas (one male/two females per group) (N = 18) to an ABA experimental design (A1/A2: without ball; B: with three boomer balls). Object play behavior occurred only during phase B (mean = 35.5 s, SE = 6.4). The spotted pacas spent more time in affiliative and exploratory behaviors and less time engaging in agonistic interactions during phase B than in both control phases (A1 and A2) (p < 0.05). Moreover, the spotted pacas emitted more low-amplitude bark vocalizations during phase B than during either control phase (p < 0.05), and such vocalizations have previously been shown to indicate a positive affective state and low arousal level. Because the expression of object play was associated with a decrease in aggression, an increase in affiliative behavior, and an increase in low-amplitude barking, we suggest that object play can be used as a non-invasive indicator of positive emotional state in this species.

Interactions between commensal bacteria and viral infection: insights for viral disease control in farmed animals.

Viral diseases cause serious economic loss in farmed animals industry. However, the efficacy of remedies for viral infection in farmed animals is limited, and treatment strategies are generally lacking for aquatic animals. Interactions of commensal microbiota and viral infection have been studied in recent years, demonstrating a third player in the interaction between hosts and viruses. Here, we discuss recent developments in the research of interactions between commensal bacteria and viral infection, including both promotion and inhibition effect of commensal bacteria on viral pathogenesis, as well as the impact of viral infection on commensal microbiota. The antiviral effect of commensal bacteria is mostly achieved through priming or regulation of the host immune responses, involving differential microbial components and host signaling pathways, and gives rise to various antiviral probiotics. Moreover, we summarize studies related to the interaction between commensal bacteria and viral infection in farmed animals, including pigs, chickens, fish and invertebrate species. Further studies in this area will deepen our understanding of antiviral immunity of farmed animals in the context of commensal microbiota, and promote the development of novel strategies for treatment of viral diseases in farmed animals.

Accessing Livestock Resources in Ensembl.

Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl's goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.

Consumer Acceptance of Meat from Animals Reared on Insect Meal as Feed.

Insect protein production requires much less land, feed, and water, and thus has a much smaller ecological footprint than animal protein production, which is important for reducing global warming. Poultry, pigs, and fish consume insects in nature, so insect meal could be a good substitute for soybean and fishmeal as a protein source in diets. The aim of this study was to examine consumer opinion on meat that originated from animals whose diet contained insect meal. The study was conducted in Hungary in 2020 (N = 414). On a scale of 1-7, respondents gave much lower scores (3.96) to this product than that which originated from a free-range system (5.11; p < 0.001). Male, more highly educated, and 30-39 year-old respondents gave significantly higher scores than other groups. The most important factor in accepting insect meal in animal feed was "no risk", while the least important factor was "replacement of Genetically Modified (GM) soybeans". Since free-range animals also consume insects, the difference in the attitude of respondents was based on their aversion to insects, while accepting free-range as the best animal welfare system. Thus, more emphasis should be placed on the benefits of insect meal in animal feed in order to bring about awareness and acceptance.

A Christian Case for Farmed Animal Welfare.

It is now common to blame Christianity for broader society's general inattention to the needs and comfort of animals in general, and farmed animals in particular. This critique of Christianity claims that certain biblical themes and particular biblical passages form the foundation for an anti-animal position that Christianity has imposed on Christians and on wider Western society. This article concedes that Christianity has often been used to justify exploitation of animals, but argues that it is a mistake to consider Christianity inevitably opposed to concern for animals. After reviewing the views of critics such as Lynn White Jr., Peter Singer, and Tom Regan, the article demonstrates the complexity of interpreting biblical passages and the possibility of readings that affirm the importance of treating animals well. It shows that Christians have indeed been advocates for animals, notably in relation to the first legislation against animal cruelty in the early nineteenth century and the formation of the RSPCA. Finally, it proposes a constructive framework for a Christian ethics of farmed animal welfare that could provide the basis for Christian action to reduce consumption of animals and shift to higher welfare sources of animal products.