SciCombinator

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Concept: Cattle

370

The growing popularity of unpasteurized milk in the United States raises public health concerns. We estimated outbreak-related illnesses and hospitalizations caused by the consumption of cow’s milk and cheese contaminated with Shiga toxin-producing Escherichia coli, Salmonella spp., Listeria monocytogenes, and Campylobacter spp. using a model relying on publicly available outbreak data. In the United States, outbreaks associated with dairy consumption cause, on average, 760 illnesses/year and 22 hospitalizations/year, mostly from Salmonella spp. and Campylobacter spp. Unpasteurized milk, consumed by only 3.2% of the population, and cheese, consumed by only 1.6% of the population, caused 96% of illnesses caused by contaminated dairy products. Unpasteurized dairy products thus cause 840 (95% CrI 611-1,158) times more illnesses and 45 (95% CrI 34-59) times more hospitalizations than pasteurized products. As consumption of unpasteurized dairy products grows, illnesses will increase steadily; a doubling in the consumption of unpasteurized milk or cheese could increase outbreak-related illnesses by 96%.

Concepts: United States, Milk, Butter, Cattle, Pasteurization, Dairy product, Cheese, Raw milk

256

A quarter of all anthropogenic methane emissions in the United States are from enteric fermentation, primarily from ruminant livestock. This study was undertaken to test the effect of a methane inhibitor, 3-nitrooxypropanol (3NOP), on enteric methane emission in lactating Holstein cows. An experiment was conducted using 48 cows in a randomized block design with a 2-wk covariate period and a 12-wk data collection period. Feed intake, milk production, and fiber digestibility were not affected by the inhibitor. Milk protein and lactose yields were increased by 3NOP. Rumen methane emission was linearly decreased by 3NOP, averaging about 30% lower than the control. Methane emission per unit of feed dry matter intake or per unit of energy-corrected milk were also about 30% less for the 3NOP-treated cows. On average, the body weight gain of 3NOP-treated cows was 80% greater than control cows during the 12-wk experiment. The experiment demonstrated that the methane inhibitor 3NOP, applied at 40 to 80 mg/kg feed dry matter, decreased methane emissions from high-producing dairy cows by 30% and increased body weight gain without negatively affecting feed intake or milk production and composition. The inhibitory effect persisted over 12 wk of treatment, thus offering an effective methane mitigation practice for the livestock industries.

Concepts: United States, Milk, Affect, Cattle, Dairy farming, Dairy cattle, Dairy, Methane

217

Mammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daughters, however few studies have addressed sex-biased milk synthesis. Here we leverage the dairy cow model to investigate such phenomena. Using 2.39 million lactation records from 1.49 million dairy cows, we demonstrate that the sex of the fetus influences the capacity of the mammary gland to synthesize milk during lactation. Cows favor daughters, producing significantly more milk for daughters than for sons across lactation. Using a sub-sample of this dataset (N = 113,750 subjects) we further demonstrate that the effects of fetal sex interact dynamically across parities, whereby the sex of the fetus being gestated can enhance or diminish the production of milk during an established lactation. Moreover the sex of the fetus gestated on the first parity has persistent consequences for milk synthesis on the subsequent parity. Specifically, gestation of a daughter on the first parity increases milk production by ∼445 kg over the first two lactations. Our results identify a dramatic and sustained programming of mammary function by offspring in utero. Nutritional and endocrine conditions in utero are known to have pronounced and long-term effects on progeny, but the ways in which the progeny has sustained physiological effects on the dam have received little attention to date.

Concepts: Pregnancy, Female, Milk, Lactation, Mammal, Cattle, Dairy farming, Dairy cattle

204

Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.

Concepts: DNA, Gene, Genetics, Evolution, Molecular biology, Cattle, Bos, Aurochs

180

Livestock play an important role in carbon cycling through consumption of biomass and emissions of methane. Recent research suggests that existing bottom-up inventories of livestock methane emissions in the US, such as those made using 2006 IPCC Tier 1 livestock emissions factors, are too low. This may be due to outdated information used to develop these emissions factors. In this study, we update information for cattle and swine by region, based on reported recent changes in animal body mass, feed quality and quantity, milk productivity, and management of animals and manure. We then use this updated information to calculate new livestock methane emissions factors for enteric fermentation in cattle, and for manure management in cattle and swine.

Concepts: Carbon dioxide, Milk, Carbon, Mammal, Cattle, Meat, Methane, Enteric fermentation

169

Badgers are involved in the transmission to cattle of bovine tuberculosis (TB), a serious problem for the UK farming industry. Cross-sectional studies have shown an association between bite wounds and TB infection in badgers which may have implications for M. bovis transmission and control, although the sequence of these two events is unclear. Transmission during aggressive encounters could potentially reduce the effectiveness of policies which increase the average range of a badger and thus its opportunities for interaction with other social groups.

Concepts: Tuberculosis, Mycobacterium, Cattle, Mycobacterium bovis, Bacillus Calmette-Guérin, Tuberculosis treatment, Badger

168

BACKGROUND: Hitherto, methicillin-resistant Staphylococcus aureus (MRSA) has not been detected in Swedish cattle. However, due to the report of mecC, a novel homologue to the mecA gene, there was reason to re-evaluate susceptibility results from strain collections of Staphylococcus aureus and test suspected isolates for the presence of mecC. FINDINGS: Bovine isolates of S. aureus with elevated minimum inhibitory concentrations of beta-lactams were retrospectively tested for presence of mecC. In four of the isolates mecC was detected. CONCLUSION: In Sweden, this is the first finding of MRSA in cattle and the first detection of MRSA harbouring mecC of domestic animal origin. MRSA in animal populations has implications as a potential reservoir with risk for spread to humans. Occurrence of MRSA among Swedish cattle appears still very limited.

Concepts: Staphylococcus aureus, Antibiotic resistance, Milk, Methicillin-resistant Staphylococcus aureus, Vancomycin, Panton-Valentine leukocidin, Cattle, Oxacillin

168

The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54% of the Bowtie SNPs and 57-58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.

Concepts: DNA, Gene, Genetics, Infectious disease, Biology, Cattle, Bovinae, African Buffalo

165

The main purpose of this study is to evaluate whether the population structure in Danish Jersey (DJ) known from the history of the breed also is reflected in its genomic structure. This is done by comparing the linkage disequilibrium and persistence of phase for subgroups of Jersey animals with high proportions of Danish (DNK) or US (USJ) origin. Furthermore, it is investigated whether a model explicitly incorporating breed origin of animals, inferred either through the known pedigree or from SNP marker data, leads to improved genomic predictions compared to a model ignoring breed origin. The study of the population structure incorporated 1,730 genotyped Jersey animals. In total 39,542 SNP markers were included in the analysis. The 1,079 genotyped bulls with de-regressed proof for udder health were used in the analysis for the predictions of the genomic breeding values. A range of random regressions models that included the breed origin were analyzed and compared to a basic genomic model that assumes a homogeneous breed structure. The main finding in this study is that the importation of germplasm from the USJ population is readily reflected in the genomes of modern DJ animals. First, linkage disequilibrium in the group of admixed DJ animals is lower compared to the groups of the original DNK and USJ animals. Second, persistence of linkage disequilibrium phase is not conserved for longer marker distances between animals with mainly Danish or US origin. Third, the STRUCTURE analysis could retrieve genomic based breed proportions in alignment to the pedigree based breed proportions. However, including this population structure in a random regression prediction model, did not clearly improve the reliabilities of the genomic predictions compared to a basic genomic model.

Concepts: Scientific method, Regression analysis, Gene, Sociology, Cattle, Logic, Linkage disequilibrium, Jersey cattle

147

Although papillomaviruses (PVs) have been widely reported in vertebrates, there have been only a few PV reports in yaks (Bos grunniens). In 2012, Bam et al. reported bovine papillomavirus type 1 (BPV-1) and BPV-2 associated with cutaneous papillomatosis in yaks, which provided genomic and pathology information for yak PVs. However, nucleotide identity and phylogenic analyses revealed that there are two isolates with a high possibility of belonging to a novel type that is not BPV-1. The argument was thought to be caused by type-specific primers. Our analysis showed that BPV-1 type-specific primers can detect not only BPV-1 but also other PVs. It suggests that identification results using type-specific primers should be confirmed with more robust methods in molecular epidemiological studies.

Concepts: Papillomavirus, Cattle, Bovine papillomavirus, Papillomaviridae, Bovines, Bos, Yak, Gaur