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Variation in the composition of microorganisms in the rumen (the rumen microbiome) of dairy cattle (Bos taurus) is of great interest because of possible links to methane emission levels. Feed additives are one method being investigated to reduce enteric methane production by dairy cattle. Here we report the effect of 2 methanemitigating feed additives (grapemarc and a combination of lipids and tannin) on rumen microbiome profiles of Holstein dairy cattle. We used untargeted (shotgun) massively parallel sequencing of microbes present in rumen fluid to generate quantitative rumen microbiome profiles. We observed large effects of the feed additives on the rumen microbiome profiles using multiple approaches, including linear mixed modeling, hierarchical clustering, and metagenomic predictions. The effect on the fecal microbiome profiles was not detectable using hierarchical clustering, but was significant in the linear mixed model and when metagenomic predictions were used, suggesting a more subtle effect of the diets on the lower gastrointestinal microbiome. A differential representation analysis (analogous to differential expression in RNA sequencing) showed significant overlap in the contigs (which are genome fragments representing different microorganism species) that were differentially represented between experiments. These similarities suggest that, despite the different additives used, the 2 diets assessed in this investigation altered the microbiomes of the samples in similar ways. Contigs that were differentially represented in both experiments were tested for associations with methane production in an independent set of animals. These animals were not treated with a methane-mitigating diet, but did show substantial natural variation in methane emission levels. The contigs that were significantly differentially represented in response to both dietary additives showed a significant enrichment for associations with methane production. This suggests that these methane-mitigating diets have altered the rumen microbiome toward naturally low methane-emitting microbial profiles. The contig sequences are predominantly new and include Faecalibacterium spp. The contigs we have identified here are potential biomarkers for low-methane-emitting cattle. [ABSTRACT FROM AUTHOR]

Looks at who is responsible for the administration of medications in schools. Reference to the changing nature of childhood illness; Expectations of parents from teachers, relating to the treatment of their child's illness; Details on the role of the school health service. INSETS: Summary points;Summary of recommended core activities for school nurses.

Background: Genomic prediction describes the use of SNP genotypes to predict complex traits and has been widely applied in humans and agricultural species. Genotyping-by-sequencing, a method which uses low-coverage sequence data paired with genotype imputation, is becoming an increasingly popular SNP genotyping method for genomic prediction. The development of Oxford Nanopore Technologies' (ONT) MinION sequencer has now made genotyping-by-sequencing portable and rapid. Here we evaluate the speed and accuracy of genomic predictions using low-coverage ONT sequence data in a population of cattle using four imputation approaches. We also investigate the effect of SNP reference panel size on imputation performance. Results: SNP array genotypes and ONT sequence data for 62 beef heifers were used to calculate genomic estimated breeding values (GEBVs) from 641 k SNP for four traits. GEBV accuracy was much higher when genome-wide flanking SNP from sequence data were used to help impute the 641 k panel used for genomic predictions. Using the imputation package QUILT, correlations between ONT and low-density SNP array genomic breeding values were greater than 0.91 and up to 0.97 for sequencing coverages as low as 0.1 × using a reference panel of 48 million SNP. Imputation time was significantly reduced by decreasing the number of flanking sequence SNP used in imputation for all methods. When compared to high-density SNP arrays, genotyping accuracy and genomic breeding value correlations at 0.5 × coverage were also found to be higher than those imputed from low-density arrays. Conclusions: Here we demonstrated accurate genomic prediction is possible with ONT sequence data from sequencing coverages as low as 0.1 × , and imputation time can be as short as 10 min per sample. We also demonstrate that in this population, genotyping-by-sequencing at 0.1 × coverage can be more accurate than imputation from low-density SNP arrays. [ABSTRACT FROM AUTHOR]

Context: Genotyping-by-sequencing, the use of sequence reads to genotype single-nucleotide polymorphisms (SNPs), has seen an increase in popularity as a tool for genomic prediction. Oxford Nanopore Technologies (Nanopore) sequencing is an emerging technology that produces long sequence reads in real-time. Recent studies have established the ability for low-coverage Nanopore sequence data to be used for genomic prediction. However, the value proposition of Nanopore sequencing for individuals could be improved if both genotyping and disease diagnosis are achieved from a single sample. Aims: This study aimed to demonstrate that Nanopore sequencing can be used for both rapid genotyping and as a disease diagnostic tool using the same sample in livestock. Methods: Total DNA extracts from nasal swabs collected from 48 feedlot cattle presenting with clinical signs of bovine respiratory disease (BRD) were sequenced using the Nanopore PromethION sequencer. After 24 h of sequencing, genotypes were imputed and genomic estimated breeding values (GEBVs) for four traits were derived using 641 163 SNPs and corresponding SNP effects. These GEBVs were compared with GEBVs derived from SNP array genotypes and calculated using the same SNP effects. Unmapped sequence reads were classified into taxa using Kraken2 and compared with quantitative real-time polymerase chain reaction (qPCR) results for five BRD-associated pathogens of interest. Key results: Sequence-derived genotypes for 46 of the 48 animals were produced in 24 h and GEBV correlations ranged between 0.92 and 0.94 for the four traits. Eleven different BRD-associated pathogens (two viruses and nine bacterial species) were detected in the samples using Nanopore sequence data. A significant (P < 0.001) relationship between Nanopore and qPCR results was observed for five overlapping species when a maximum threshold cycle was used. Conclusions: The results of this study indicated that 46 cattle genomes can be multiplexed and accurately genotyped for downstream genomic prediction by using a single PromethION flow cell (ver. R9.4) in 24 h. This equates to a cost of AUD35.82 per sample for consumables. The concordance between qPCR results and pathogen proportion estimates also indicated that some pathogenic species, in particular bacterial species, can be accurately identified from the same test. Implications: Using Nanopore sequencing, routine genotyping and disease detection in livestock could be combined into one cost-competitive test with a rapid turnaround time. Genotyping, to test an animal or herd genetic merit, has become a routine part of most livestock production systems. New genotyping methods offer the potential to significantly decrease the turnaround time of genotyping and also incorporate new genetic information into the analysis. In this study, we have demonstrated that one such genotyping method can be used to genotype cattle and detect bacterial bovine respiratory pathogens in 24 h at a cost similar to that of existing methods. [ABSTRACT FROM AUTHOR]

Physicians are accustomed to making decisions based on information regarding the prevalence of disease, symptoms, physical signs, laboratory test results, and the risks and benefits of alternative treatments. If nutritional assessment and therapeutics are to become more common components of medical practice, significant barriers in each of these areas must be overcome. Even rudimentary dietary assessment is often missing from physician education. Dietary assessment tools that are readily available and that have demonstrated usefulness are largely unknown. In addition, many nutritional interventions have not been formally investigated in randomized, controlled trials, and thus their cost-effectiveness remains unknown. We present one approach to these issues by discussing the construction of a decision model examining strategies for vitamin D and calcium screening. The application of medical decision making techniques to problems in clinical nutrition illustrates how findings from research studies may be used to determine the risks, benefits and costs of alternative population based health related nutrition policies which can then be applied by physicians in their daily interactions with patients. [ABSTRACT FROM AUTHOR]

The rumen of the dairy cow contains a rich and diverse collection of microbes that during feed digestion produce significant quantities of methane gas and ammonia, both of which contribute to greenhouse gas emissions. Strategies to redirect rumen carbon and nitrogen metabolism away from these products provide opportunities for significant productivity improvements in livestock systems not only by improving nutrient retention, but also by reducing greenhouse gas emissions. In order to develop these strategies, a greater knowledge of the diversity of the microbes within their rumen and their genomic capability is required. Many have used several techniques to study the rumen microbes, and the technology continues to improve. Among them include researchers at the Department of Primary Industries Victoria (DPI Vic) and the Dairy Futures Cooperative Research Centre (CRC) who are addressing the issue of regulation of methane emissions in dairy cattle, while scientists in Queensland and New South Wales, as part of the most recent Beef CRC program, focus on beef cattle. In this brief review, we examine how the techniques used in rumen microbial ecology have changed, and how technology improvements continue to allow us to examine the rumen microbiota of cattle and other ruminants, so as to better understand and possibly select animals with superior traits, leading to improvements in feed efficiency, methane emissions and nitrogen retention. The rumen microorganisms provide energy for the ruminant animal but also influence productivity, methane emissions and nitrogen retention. This review focuses on technology changes within rumen ecology, with emphasis on our research toward increased productivity of cattle. Exploring the symbiotic relationships of the rumen through (meta)genomics may hold the key to a better understanding, and subsequent improvements in productivity, with less environmental impacts. [ABSTRACT FROM AUTHOR]

Background: Primary human herpesvirus-6 and -7 (HHV-6/-7) infections cause febrile illness sometimes complicated by convulsions and rarely encephalopathy. Aims: To explore the extent of such HHV-6 and -7 induced disease in young children. Methods: In a three year prospective study in Britain and Ireland, 205 children (2-35 months old) hospitalized with suspected encephalitis and/or severe illness with fever and convulsions were reported via he British Paediatric Surveillance Unit network. Blood samples were tested for primary HHV-6 and -7 infections. Results: 26/156 (17%) of children aged 2-23 months had primary infection (11 HHV-6; 13 HHV-7; two with both viruses) coinciding with the acute illness; this was much higher than the about three cases expected by chance. All 26 were pyrexical; 25 had convulsions (18 status epileptic's), 11 requiring ventilation. Median hospital stay was 7.5 days. For HI-JV-6 primary infection the median age was 53 weeks (range 42-94) and the distribution differed from that of uninfected children; for HI-IV-7, the median was 60 weeks (range 17-102) and the distribution did not differ for the uninfected. Fewer (5/15) children with primary HHV-7 infection had previously been infected with HHV-6 than expected. Conclusions: Primary HHV-6 and HHV-7 infections accounted for a significant proportion of cases in those 2 years old of severe illness with fever and convulsions requiring hospital admission; each virus contributed equally. Predisposing factors are age for HHV-6 and no previous infection with I-II-IV-6 for HHV-7. Children with such neurological disease should be investigated for primary I-IHV-6/-7 infections, especially in rare cases coinciding by chance with immunisation to exclude misdiagnosis as vaccine reactions. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the review of the article "Human Herpesviruses-6 and -7 and Neurological Morbidity in Britain and Ireland," by K. N. Ward, N. J. Andrews and C. M. Verity in the June 2005 issue.