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.

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.

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.

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.

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.

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

Simple Summary

Poultry, pigs, and fish consume insects in nature and therefore insect meal could be considered to be an acceptable substitute for soybean and fishmeal as a protein source in the diets of these animals. Hungarian respondents were asked about their opinion on consuming meat obtained from animals under free-range conditions or from animals that had received insect meal in their diet. On a scale of 1–7, the respondents gave 5.11 points for the meat of free-range animals, but significantly less points (3.69) for the meat of animals that had consumed insect meal. However, free-ranging animals also consume insects and other small animals, of which the origin is not known, while the insects used as feed are produced under controlled conditions. The consumers’ decisions are affected by their attitudes: free-range is associated with animal welfare, but mentioning insects creates feelings of aversion and antipathies. In conclusion, to increase the consumers’ acceptance of meat products from animals reared on insect meal, consumers need to be made aware of the various benefits of insect meal in animal feed.

Abstract

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

Simple Summary

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. Critics claim that certain biblical themes and biblical passages form the foundation for an anti-animal position that has influenced Christians and 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. It shows that Christians have 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 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.

Abstract

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.

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.