Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR

Pollution of the environment by human and animal faecal pollution affects the safety of shellfish, drinking water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative PCR (qPCR) assays was therefore developed and applied to compare the composition of intestinal microbiota of these two groups. Primers were designed to quantify the 16S rRNA gene from dominant and subdominant bacterial groups. TaqMan^® probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits, goats, horses, pigs, sheep and cows. Three dominant bacterial groups ( Bacteroides/Prevotella, Clostridium coccoides and Bifidobacterium ) of the human microbiota showed differential population levels in animal species. The Clostridium leptum group showed the lowest differences among human and farm animal species. Human subdominant bacterial groups were highly variable in animal species. Partial least squares regression indicated that the human microbiota could be distinguished from all farm animals studied. This culture-independent comparative assessment of the faecal microbiota between humans and farm animals will prove useful in identifying biomarkers of human and animal faecal contaminations that can be applied to microbial source tracking methods.     

Use and non-use values as motivational construct dimensions for farm animal welfare: impacts on the economic outcome for the farm

This study explored how farmers’ motivation in terms of use values and/or non-use values to work with farm animal welfare are associated with the economic outcome for the farm. Use values in farm animal welfare refer to economic value derived from productivity and profitability considerations. Non-use values in farm animal welfare refer to economic value derived from good animal welfare, irrespective of the use the farmer derives from the animal, currently or in the future. The analysis was based on detailed information about the income statements of a sample of Swedish dairy farmers, obtained from the Swedish Farm Economic Survey, complemented with survey information about their perceived use and non-use values in farm animal welfare. The findings suggest that farm economic outcome is significantly associated with motivation in terms of use values, but not so much with motivation in terms of non-use values. This is interesting from a policy point of view, because it indicates that farmers with different approaches to farm animal welfare may experience different economic outcomes for their farms. Findings can, for instance, be used to strengthen farmers’ engagement in various private quality assurance standards, which generally focus on values of non-use type, by pointing to that realisation of such values will not impair the economic outcome of the farms. Moreover, findings also suggest that farmers’ economic incentives for engagement in such standards may need to be further strengthened in order to become more attractive, as findings point to that a focus on non-use values generally is not associated with more favourable economic outcomes.     

Mass spectrometry and animal science: protein identification strategies and particularities of farm animal species

Proteomic approaches are gaining increasing importance in the context of all fields of animal and veterinary sciences, including physiology, productive characterization, and disease/parasite tolerance, among others. Proteomic studies mainly aim the proteome characterization of a certain organ, tissue, cell type or organism, either in a specific condition or comparing protein differential expression within two or more selected situations. Due to the high complexity of samples, usually total protein extracts, proteomics relies heavily on separation procedures, being 2D-electrophoresis and HPLC the most common, as well as on protein identification using mass spectrometry (MS) based methodologies. Despite the increasing importance of MS in the context of animal and veterinary science studies, the usefulness of such tools is still poorly perceived by the animal science community. This is primarily due to the limited knowledge on mass spectrometry by animal scientists. Additionally, confidence and success in protein identification is hindered by the lack of information in public databases for most of farm animal species and their pathogens, with the exception of cattle (Bos taurus), pig (Sus scrofa) and chicken (Gallus gallus). In this article, we will briefly summarize the main methodologies available for protein identification using mass spectrometry providing a case study of specific applications in the field of animal science. We will also address the difficulties inherent to protein identification using MS, with particular reference to experiments using animal species poorly described in public databases. Additionally, we will suggest strategies to increase the rate of successful identifications when working with farm animal species.     

Farm animal genomics and informatics: an update

Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects.     

Comparative mapping in farm animals.

This paper summarises the current status of comparative mapping in farm animals. For most of the major farm animal species, a wide range of genomic tools are now available to create high-resolution genetic and physical maps of the genome. For many farm animals, the use of radiation hybrid panels and sequence data from expressed sequence tag (EST) projects has accelerated the development of high-resolution comparative maps, with human--the model species for farm animals. These tools and comparative maps are being used to map and identify the genes at the loci for simple and complex traits. The development of detailed physical maps in farm animals based on radiation hybrid panels and bacterial artificial chromosome (BAC) contigs provides a direct link between the 'information-poor' maps of farm animals and the 'information-rich' genomes of human and other model organisms.     

Complete genome sequence of bluetongue virus serotype 16 of goat origin from India

In this article, we document the first complete genome sequence of an isolate of bluetongue virus serotype 16 (BTV16) from a goat in India. The virus was isolated from an in-contact goat from an animal farm in Chennai where clinical disease occurs in sheep. The total size of the genome is 19,185 bp. The information provided for full-length sequences of all 10 segments will help in understanding the geographical origin and transmission of the Indian isolate of BTV16 as well as its comparison with global isolates of BTV16 of sheep, cattle, and other host species origins.     

Antibiotic resistance in bacterial isolates from laboratory animal colonies naive to antibiotic treatment

Antiobiogrammes were made of a number of isolates of Staphylococcus aureus, Escherichia coli and Pasteurella pneumotropica derived from rodent, rabbit or minipig colonies never treated with antibiotics. For S. aureus no differences between rats and mice were found in the percentage of resistant isolates. Gentamicin and erythromycin were found to be the most efficient, while the highest percentages of resistance were found to be against penicillins and sulphonamides. In general, the results from antibiogrammes on E. coli were rather uniform, with only slight differences between isolates from different species, except that more vancomycin and tetracycline-resistant minipig isolates were found. In almost all isolates of E. coli, resistance was shown against penicillin, fucidin, macrolides, lincosamides and tiamulin. For a number of antibiotics, mouse isolates of P. pneumotropica were more frequently found to be sensitive than rat isolates. The resistance patterns of E. coli from the minipigs were quite similar to resistance patterns found in farm pigs, but apart from this, the resistance patterns of the bacterial species tested did not resemble human or farm animal patterns in any of the animal species, and, therefore, these studies do not support the theory that S. aureus and E. coli in laboratory animal colonies derive from the normal flora of the human caretakers. The fact that rodent species of E. coli, in contrast to human and farm animal species, are sensitive to ampicillin, tetracyclines, and the combination of sulphonamides and trimethoprim, might be due to the fact that these antibiotics are not used in rodent populations.     

Seasonality of reproduction and production in farm fishes, birds and mammals

A very large majority of farm animals express seasonal variations in their production traits, thus inducing seasonal availability of fresh derived animal products (meat, milk, cheese and eggs). This pattern is in part the consequence of the farmer's objective to market his products in the most economically favourable period. It may also be imposed by the season-dependent access to feed resources, as in ruminants, or by the specific requirements derived from adaptation to environmental conditions such as water temperature in fish. But seasonal variations in animal products are also the consequence of constraints resulting from the occurrence of a more or less marked seasonal reproductive season in most farm animal species including fish, poultry and mammals. Like their wild counterparts, at mid and high latitudes, most farm animals normally give birth at the end of winter-early spring, the most favourable period for the progeny to survive and thus promote the next generation. As a consequence, most species show seasonal variations in their ovulation frequency (mammals and fish: presence or absence of ovulation; birds: variations or suppression of laying rates), spermatogenic activity (from moderate to complete absence of sperm production), gamete quality (variations in fertilisation rates and embryo survival), and also sexual behaviour. Among species of interest for animal production, fishes and birds are generally considered as more directly sensitive to external factors (mainly temperature in fish, photoperiod in birds). In all species, it is therefore advisable that artificial photoperiodic treatments consisting of extra-light during natural short days (in chickens, turkeys, guinea fowl, sheep and goats) or melatonin during long days (in goats, sheep) be extensively used to either adjust the breeding season to animal producer needs and/or to completely overcome seasonal variations of sperm production in artificial insemination centres (mammals) and breeder flock operations (poultry, fish farming). Pure light treatments (without melatonin), especially when applied in open barns, could be considered as non invasive ones which fully respect animal welfare.     

内蒙古典型草原优化放牧管理模拟研究——以内蒙古太仆寺旗为例

针对太仆寺旗公共草地全年连续放牧的传统放牧方式,通过控制性试验,并结合太仆寺旗多年的草地、家畜、经济和气象等数据,建立中国西部草地生态经济模型,对太仆寺旗典型草原公共放牧系统进行模拟分析。以草原生态恢复和牧民收入增加为目的,对典型草原的最适载畜率、家畜在冬春季节的合理补饲等问题进行探讨,提出了典型草原放牧管理优化模式。研究结果表明,从当年10月到翌年5月份,家畜能量需求与放牧、补饲能量供给严重不平衡,家畜体重下降;随着载畜率的增加,牧民年均净收入先增加后降低,在载畜率为2.275羊单位/hm2时,收入达到最高;太仆寺旗最适载畜率为每公顷1.55-2.275羊单位。降低载畜率、加强补饲、提高草地质量都有利于提高牧民收入。     

MicroRNAs in farm animals

MicroRNAs (miRNAs) are a class of ∼22 nucleotide-long small noncoding RNAs that target mRNAs for translational repression or degradation. miRNAs target mRNAs by base-pairing with the 3′-untranslated regions (3′-UTRs) of mRNAs. miRNAs are present in various species, from animals to plants. In this review, we summarize the identification, expression, and function of miRNAs in four important farm animal species: cattle, chicken, pig and sheep. In each of these species, hundreds of miRNAs have been identified through homology search, small RNA cloning and next generation sequencing. Real-time RT-PCR and microarray experiments reveal that many miRNAs are expressed in a tissue-specific or spatiotemporal-specific manner in farm animals. Limited functional studies suggest that miRNAs have important roles in muscle development and hypertrophy, adipose tissue growth, oocyte maturation and early embryonic development in farm animals. Increasing evidence suggests that single-nucleotide polymorphisms in miRNA target sites or miRNA gene promoters may contribute to variation in production or health traits in farm animals.     

The robustness of a network of ecological networks to habitat loss

There have been considerable advances in our understanding of the tolerance of species interaction networks to sequential extinctions of plants and animals. However, communities of species exist in a mosaic of habitats, and the vulnerability of habitats to anthropogenic change varies. Here, we model the cascading effects of habitat loss, driven by plant extinctions, on the robustness of multiple animal groups. Our network is constructed from empirical observations of 11 animal groups in 12 habitats on farmland. We simulated sequential habitat removal scenarios: randomly; according to prior information; and with a genetic algorithm to identify best‐ and worst‐case permutations of habitat loss. We identified two semi‐natural habitats (waste ground and hedgerows together comprising < 5% of the total area of the farm) as disproportionately important to the integrity of the overall network. Our approach provides a new tool for network ecologists and for directing the management and restoration of multiple‐habitat sites.     

Science and technology of farm animal cloning: state of the art

Details of the first mammal born after nuclear transfer cloning were published by Steen Malte Willadsen in 1986. In spite of its enormous scientific significance, this discovery failed to trigger much public concern, possibly because the donor cells were derived from pre-implantation stage embryos. The major breakthrough in terms of public recognition has happened when Ian Wilmut et al. [Wilmut, I., Schnieke, A.E., McWhir, J., Kind, A.J., Campbell, K.H., 1997. Viable offspring derived from fetal és adult mammalian cells. Nature 385, 810-813] described the successful application of almost exactly the same method, but using the nuclei of somatic cells from an adult mammal, to create Dolly the sheep. It has become theoretically possible to produce an unlimited number of genetic replicates from an adult animal or a post-implantation foetus. Since 1997 a number of different species including pigs, goats, horses, cats, etc. have been cloned with the somatic cell nuclear transfer technique. Although the technology still has relatively low success rates and there seems to be substantial problems with the welfare of some of the cloned animals, cloning is used both within basic research and the biomedical sector. The next step seems to be to implement cloning in the agricultural production system and several animals have been developed in this direction. This article reviews the current state of the art of farm animal cloning from a scientific and technological perspective, describes the animal welfare problems and critically assess different applications of farm animal cloning. The scope is confined to animal biotechnologies in which the use of cell nuclear transfer is an essential part and extends to both biomedical and agricultural applications of farm animal cloning. These applications include the production of genetically identical animals for research purposes, and also the creation of genetically modified animals. In the agricultural sector, cloning can be used as a tool within farm animal breeding. We do not intend to give an exhaustive review of the all the literature available; instead we pinpoint issues and events pivotal to the development of current farm animal cloning practices and their possible applications.     

Interspecies differences in the empty body chemical composition of domestic animals

Domestication of animals has resulted in phenotypic changes by means of natural and human-directed selection. Body composition is important for farm animals because it reflects the status of energy reserves. Thus, there is the possibility that farm animals as providers of food have been more affected by human-directed selection for body composition than laboratory animals. In this study, an analysis was conducted to determine what similarities and differences in body composition occur between farm and laboratory animals using literature data obtained from seven comparative slaughter studies (n = 136 observations). Farm animals from four species (cattle, goats, pigs and sheep) were all castrated males, whereas laboratory animals from three species (dogs, mice and rats) comprised males and/or females. All animals were fed ad libitum. The allometric equation, Y = aX^b, was used to determine the influence of species on the accretion rates of chemical components (Y, kg) relative to the growth of the empty body, fat-free empty body or protein weights (X, kg). There were differences between farm and laboratory animals in terms of the allometric growth coefficients for chemical components relative to the empty BW and fat-free empty BW (P < 0.01); farm animals had more rapid accretion rates of fat (P < 0.01) but laboratory animals had more rapid accretion rates of protein, water and ash (P < 0.01). In contrast, there was no difference in terms of the allometric growth coefficients for protein and water within farm animals (P > 0.2). The allometric growth coefficients for ash weight relative to protein weight for six species except sheep were not different from a value of 1 (P > 0.1), whereas that of sheep was smaller than 1 (P < 0.01). When compared at the same fat content of the empty body, the rate of change in water content (%) per unit change in fat content (%) was not different (P > 0.05) across farm animal species and similar ash-to-protein ratios were obtained except for dogs. The fraction of empty body energy gain retained as fat increased in a curvilinear manner, and there was little variation among farm animals at the same fat content of the empty body. These findings may provide the opportunity to develop a general model to predict empty body composition across farm animal species. In contrast, there were considerable differences of chemical body composition between farm and laboratory animals.     

Friends with benefits: Social support and its relevance for farm animal welfare

Despite growing interest in promoting positive welfare, rather than just alleviating poor welfare, potential measures of good welfare, and means to provide it, have remained elusive. In humans social support improves stress-coping abilities, health, and promotes positive psychological welfare. Therefore, social support may be a key approach to promote positive physical and psychological welfare in farm animals. However, the roles of positive social behaviors and social support have been overlooked in comparison to negative social behaviors such as agonistic interactions. The benefits of social partners on an animal's stress coping abilities and welfare are yet poorly understood.The purpose of this paper is to review the protective or buffering effects of social support against stressful challenges and its potential implications for farm animal welfare. The biology of social support is first presented with its behavior, endocrine, autonomic and immune components. The major factors modulating the social support process are then synthesized. Research and implications for animal welfare in different farm species are discussed. Lastly, this review identifies research areas that especially deserve further attention in our effort to understand and implement social support in farm animal welfare.Social support could constitute one of the foundations for welfare researchers to leap from the absence of negative welfare to the provision of positive welfare and emotional experiences.     

Genomics for food safety and sustainable animal production

There is a growing concern in society about the safety of animal-derived food, the health and welfare of farm animals and the sustainability of current animal production systems. Along farm animal, breeding genomics may contribute to a solution for these concerns. The use of genomic analysis tools, to achieve genetic progress in typical out-bred populations of farm animals, seems to be more difficult compared to 'model' organisms or plants. However, identification of positional candidate genes may be accelerated by linkage disequilibrium (LD) mapping. Recording of sustainable traits requires a large financial and logistic input and the economic advantages for the market are not as clear as for traditional selection traits. Examples show that the major genes causing variability for similar traits in different species are rarely the same. Therefore, for breeding purposes genomic analysis of the species of interest is needed. The fundamental knowledge obtained on the genetic architecture of complex traits will open new perspectives for the use of DNA tests in selection schemes. For food safety and traceability, DNA-based techniques evolve for monitoring and early warning systems.     

Synchronization of APIIS based farm animal biodiversity systems

One of the major problems in the management of farm animal and biodiversity information is the exchange of data and keeping it up-to-date, an issue that is very common with distributed information systems consisting of number of databases. This article describes the synchronization protocol developed in APIIS (adaptable platform independent information system) framework and reviews the basic considerations required when building distributed information system that has to exchange information in a network of APIIS based systems. The protocol is designed to synchronize a common part of different database structures. It is developed without any intended use of proprietary database engine and can work with a variety of RDBMS (relational database management system). The main targets of the protocol are animal biodiversity information systems without permanently connected nodes. The EFABIS (European farm animal biodiversity information system) is reviewed as an example of the implementation.

Availability     

Species Identification of Ten Common Farm Animals Based on Mitochondrial 12S rRNA Gene Polymorphisms

Bio-techniques such as genetic manipulation, marker-assisted selection, and identity test have largely facilitated the modern animal production practices. In the present study, we established a reliable and cost-effective molecular method of species identification for common farm animals. We first (re-)analyzed 179 mitochondrial 12S rRNA gene sequences of ten farm animal species to determine the intra-species and species-specific variations. The PCR-RFLP method was subsequently designed to identify these species by using endonucleases BshNI, ScaI, AluI, and BfaI. The poultry and livestock species were first discriminated by one double-digestion of both BshNI and ScaI, which generated different fragment patterns (325?bp and 115?bp for poultry vs. 364?bp and 76?bp for livestock). The ten species could be further discerned according to species-specific restriction pattern by subjecting to digestion of AluI and BfaI, respectively. Our approach would be more reliable by taking the intra-species variations into consideration and could be applied to species identity test, commercial fraud, and wildlife crime.     

Invited review: resource allocation mismatch as pathway to disproportionate growth in farm animals – prerequisite for a disturbed health

The availability of resources including energy, nutrients and (developmental) time has a crucial impact on productivity of farm animals. Availability of energy and nutrients depends on voluntary feed intake and intestinal digestive and absorptive capacity at optimal feeding conditions. Availability of time is provided by the management in animal production. According to the resource allocation theory, resources have to be allocated between maintenance, ontogenic growth, production and reproduction during lifetime. Priorities for these processes are mainly determined by the genetic background, the rearing system and the feeding regimen. Aim of this review was to re-discuss the impact of a proper resource allocation for a long and healthy life span in farm animals. Using the barrel model of resource allocation, resource fluxes were explained and were implemented to specific productive life conditions of different farm animal species, dairy cows, sows and poultry. Hypothetically, resource allocation mismatch neglecting maintenance is a central process, which might be associated with morphological constraints of extracellular matrix components; evidence for that was found in the literature. A potential consequence of this limitation is a phenomenon called disproportionate growth, which counteracts the genetically determined scaling rules for body and organ proportions and could have a strong impact on farm animal health and production.     

Toftanes: The Paleoecology of a Faroese <Emphasis Type="Italic">Landnám</Emphasis> Farm

For the first time in the Faroe Islands, the paleoecological content of an early Norse farm has been sampled comprehensively in an effort to understand how it functioned and its relationship to the landscape in which it was located. Organic deposits indicate an increase in species diversity at the time of settlement, including the introduction of several new species. Plant resources from various areas of the treeless landscape were exploited and farm buildings contained suites of synanthropic insects dominated by those associated with accumulations of decaying plant debris. Potential fuels included wood, peat, dung, and seaweed. Insect faunas lacked both ectoparasites and a significant foul beetle component. This may be a reflection of animal husbandry, with stock not being stalled over winter in the farm buildings examined, or an absence of wool-processing in the buildings. Results compare well with other sites in the North Atlantic and argue for the consistent nature of the Norse farming economy across the region.     

Do vitamin E supplements in diets for laboratory animals jeopardize findings in animal models of disease?

Vitamin E has been supplemented to the diets of farm animals to improve fertility, health, growth rates and quality of animal products. Because of the positive experience obtained in farm animals, vitamin E has been added in increasing amounts to the diets of laboratory animals. Today, vitamin E levels in standard rodent maintenance diets range from 30 mg/kg (France, United States), 90–120 mg/kg (Netherlands, United Kingdom) to as much as 200 mg/kg (Germany). While increasing fertility and health of laboratory animals, these vitamin E supplements affect diverse pathophysiological conditions and thus the outcome of animal models of disease. Because of the large variability of vitamin E levels between laboratories within and between different countries, results obtained in established animal models may no longer be comparable and/or reproducible. Researchers should be aware of these vitamin E supplements and carefully control for potential effects in their respective animal models that involve — or may involve — the generation of reactive oxygen species.