National Capability Grant - Edinburgh Genomics

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

The ARK Genomics Centre for Comparative and Functional Genomics (ARK Genomics) is an established high throughput research and technology facility which utilises the  latest genomics technologies for research into genome structure, genetic variation, gene expression and gene function with a focus on systems of relevance to animal health and food security. The laboratory employs a range of technologies, including DNA Sequencing (Illumina GAII, HiSeq2000 wef Q2 2011, Sanger ABI3730), microarrays (Agilent, Affymetrix, Illumina, Nimblegen), genotyping (Goldengate, Infinium, Affymetrix) and bioinformatics, as well as managing and distributing an extensive and unique clone/vector library. ARK-Genomics combines the latest technologies with bioinformatics research to provide a complete genomics solution from concept to conclusion. Global demand for food is rising, both as a result of population growth and due to dietary changes in developing countries. A UN FAO report on this issue forecasts that food production will need to increase by over 40% by 2030 and by over 70% by 2050. In order to address the Grand Challenge on Food Security there is a need to increase yield, diseases resistance, food production, food safety and quality and to decrease infections, water use, energy use, the environmental impact and the chance of zoonoses. Genomics technologies are critical to the strategic research programmes at the BBSRC National Institutes of Bioscience (including Roslin, IAH, IBERS) and elsewhere which are being conducted to address these challenges. Similarly, these technologies are also essential for research that addresses the BBSRC Core Priority on Basic Bioscience Underlying Health. Thus, a key strategic role for ARK-Genomics is to provide access to the latest advances in technology that are essential to researchers in animal science and to the bioinformatics skills with which to analyse the resulting large datasets. ARK-Genomics focuses on the quantitative biology, genetics and genomics of food-producing animals, their model systems and their pathogens. This focus covers the BBSRC priority areas of “Food Security” and “Basic Bioscience underpinning Health”. The objectives are to investigate the genetic factors that influence yield, animal production, food safety, resistance to pathogens, and the immune response, as well as basic science underpinning the search for drug targets and vaccine development. The outputs feed directly into the breeding and other translational programmes of industrial and academic partners. With a track record in animal sciences and the close integration with The Roslin Institute, ARK-Genomics addresses the challenges of food production and animal disease, and the increasing global demand for food production and security.

Publications

10 25 50

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Adkar-Purushothama CR (2015) Analysis and application of viroid-specific small RNAs generated by viroid-inducing RNA silencing. in Methods in molecular biology (Clifton, N.J.)

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Adkar-Purushothama CR (2015) Analysis and application of viroid-specific small RNAs generated by viroid-inducing RNA silencing. in Methods in molecular biology (Clifton, N.J.)

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Amin SA (2012) Iron transport in the genus Marinobacter. in Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine

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Andermatt I (2014) RNAi-based gene silencing in chicken brain development. in Methods in molecular biology (Clifton, N.J.)

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Andermatt I (2014) RNAi-based gene silencing in chicken brain development. in Methods in molecular biology (Clifton, N.J.)

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Anderson CJ (2013) Life-history effects of arsenic toxicity in clades of the earthworm Lumbricus rubellus. in Environmental pollution (Barking, Essex : 1987)

 
Description The ARK-Genomics centre for comparative and functional genomics has been a successful, multi-user national capability since 2002, providing collaborative access to the latest genomics technologies to the farm animal community and interacting with 1000s of researchers from every continent (we have engaged in projects with researchers from 45 different countries).

In the period Apr 2012 to date, we have delivered data to several thousand separate projects, processing 8000-10,000 samples per year, including high-throughput sequencing, SNP array, gene expression microarray, microsatellite and bioinformatics projects. We engaged in over 1000 detailed consultations with our users every year that result in a written quotations, which includes full project design and specification. Quotes represent knowledge transfer from ourselves to our users as we help them to design optimal experiments and to understand the technologies we use. Whilst we do not explicitly track internal or external projects, we estimate that approximately 50% of our projects are with researchers outside of the University of Edinburgh.

To ensure we remain internationally competitive, we have adopted the latest sequencing technologies: the HiSeq 4000 and the MinION. The HiSeq 4000 is the latest general-purpose sequencer from Illumina which has approximately 1.5X the run throughput of the HiSeq 2500 and 3X the throughput when decreased run-time is taken into account. The adoption of this technology will ensure that we are internationally competitive, will maintain our position as a provider of access to the latest technologies, and will ensure that BBSRC gets maximum value for investment. The MinION is a new, single-molecule sequencer capable of producing many thousands of long reads (approx. 6Kb in length). The facility has been at the forefront of MinION research, publishing one of the first papers ever published for MinION data (http://tinyurl.com/WATSONPORE) and developing strategies for the finishing of bacterial genomes (http://tinyurl.com/WATSONBFRAG). The MinION and the PromethION (capable of sequencing large numbers of eukaryotic genomes) represent an exciting future for large scale genomics, allowing us to access parts of the genome that short-read sequencers cannot. In 2015/16 ARK-Genomics merged with The GenePool to form Edinburgh Genomics. Since then we have tried to track ARK-Genomics outputs (i.e. BBBSRC investment) separately to those of the wider Edinburgh Genomics. We currently track some 387 research outputs, primarily peer reviewed papers, which resulted directly from the BBSRC investment. Not all are import-able into ResearchFish, and most can be found here: https://www.research.ed.ac.uk/portal/en/projects/ncg-ark-genomics(be0b26a2-7e54-42bf-a753-93dc36735cfe).html. This number is just over half of the total number of outputs from Edinburgh Genomics (which has also had/has NERC and MRC funding) which currently stands at 733, tracked here: https://www.research.ed.ac.uk/portal/en/organisations/work-enabled-by-edinburgh-genomics(771a1b4d-e9e5-4a42-9378-bf3f9741cb12)/publications.html
Exploitation Route As a national capability, we provide access to technologies that allow researchers to carry out cutting-edge work across the biomedical sciences. By working with both industry and academia, in over 45 different countries, we have enabled huge impact across the life sciences and internationally. The data we produce are used by breeding companies in breeding decisions, by health practitioners, by environmentalists and many researchers and professionals across the life sciences
Sectors Agriculture, Food and Drink,Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://www.ark-genomics.org
 
Description KEC activity with industry continues to grow, with ongoing collaborations with Ingenza, Genus, Aviagen, Cobb-Vantress, Illumina, Roche Nimblegen and Oxford Nanopore. Our publication of the pig exome (now available from the Roche Nimblegen website) is an example of the benefits of such collaborations to the farm animal community (DOI: doi:10.1186/1471-2164-15-550). We have also previously contributed to the development of chicken (DOI: 10.1186/1471-2164-14-59), cattle and salmon (DOI: 10.1186/1471-2164-15-90) SNP chips. In collaboration with Dr John Hickey and the breeding companies Genus (pigs) and Aviagen (poultry), we are enabling advances in genotyping-by-sequencing with the potential to transform genomic selection. Funded by InnovateUK and the industry partners, these projects aim to develop whole-genome genotyping technologies that can scale to thousands of animals at low cost. Within ARK-Genomics, our contribution has been to develop automated, ultra-low-cost library preparation and multiplexing techniques. The resulting low-cost, low-coverage whole-genome sequences will be used as input to the AlphaGenes resource at RI to impute haplotypes and enable genome selection. Overall, the impact of this BBSRC investment cannot be overstated, having worked with researchers from over 45 countries worldwide, providing expertise, knowledge and the latest genomics technologies to researchers, industry, professionals and educators.
First Year Of Impact 2002
Sector Agriculture, Food and Drink,Education,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description PoreCamp Texas
Geographic Reach North America 
Policy Influence Type Influenced training of practitioners or researchers
URL http://porecamp.github.io/texas/
 
Description Training in genomics
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Our genomics training activity is open to all, including academia, industry, professionals and the public. We train people in software development and data analysis as pertains to the analysis of genomic data. Our training programme has so far consisted of 37 workshops in the last 2 years (each consisting of between 1 and 5 days hands-on training), and has provided advanced training in bioinformatics to 483 unique individuals, 47% of whom come from outside of the University of Edinburgh, spanning 15 countries including The Netherlands, India, Denmark, Belgium, Germany, Ireland, Luxembourg, Finland, Northern Ireland, Spain, Sweden, France, South Africa and Norway. Whilst the majority of our trainees are academics, we have also trained individuals from private companies and the NHS. At present we do not collect detailed statistics about training level, though we are certain that the vast majority of our trainees are post-docs and PhD students in need of vital expertise to complete their training/projects. The data underlying this report are available upon request, but should not be shared widely as they contain sensitive information.
URL http://genomics.ed.ac.uk/services/training
 
Description A global shared data biological sample resource to support productivity improvement for tropical livestock
Amount £5,000,000 (GBP)
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 10/2015 
End 09/2020
 
Description Adapted yeast for superior carbon conversion
Amount £573,511 (GBP)
Funding ID 100962 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2011 
End 07/2014
 
Description Comparison between maize-based and wheat-based diets on intestinal microbiome and intestinal gene expression after anticoccidial vaccine administration in broiler chickens
Amount £302,278 (GBP)
Organisation Industry Partners 
Sector Private
Country United States
Start 09/2016 
End 09/2019
 
Description Comprehensive training in computational biology techniques for analyzing second and third generation sequencing data
Amount £28,000 (GBP)
Funding ID BB/N019636/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2015 
End 05/2018
 
Description Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development
Amount £384,966 (GBP)
Funding ID BB/R007632/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development
Amount £312,917 (GBP)
Funding ID BB/R007632/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2018 
End 05/2021
 
Description EBI Metagenomics - enabling the reconstruction of microbial populations
Amount £112,997 (GBP)
Funding ID BB/R015023/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2021
 
Description GCRF Data and Resources round 1
Amount £946,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 07/2017
 
Description GCRF Data and Resources round 2
Amount £220,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 07/2018
 
Description GCRF Impact Accelerator
Amount £300,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 07/2018
 
Description Microbiome and metagenomic study of the rumen microbial population and their microbial enzyme genes
Amount £90,000 (GBP)
Organisation Government of Scotland 
Sector Public
Country United Kingdom
Start 09/2016 
End 09/2019
 
Description Mining new enzymes in the rumen for biomass processing and chiral synthesis
Amount £356,941 (GBP)
Funding ID 100970 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2011 
End 01/2014
 
Title Custom sheep SNP chip for genes involved in one-carbon metabolism 
Description This DNA chip allows the simultaneous genotyping of ca. 4,000 independent single nucleotide polymorphism (SNP) loci in the sheep genome with an emphasis on SNP loci within or close to genes involved in one-carbon metabolism. This custom sheep SNP chip exploited knowledge of SNP loci in public databases (e.g. dbSNP, EVA) as well as new SNP variants discovered by re-sequencing DNA from Texel sheep. The bioinformatics analyses and SNP selection was undertaken by the University of Nottingham partner. The SNP chip was commissioned from Illumina Inc. The resulting custom sheep SNP chips were used by Edinburgh Genomics to genotype several hundred sheep DNA samples. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact The use of the custom sheep SNP chip was essential for genotyping sheep in order to identify putative associations between genetic variation in the target genes and variation in one-carbon metabolites. 
 
Title Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen 
Description This dataset represents 913 draft bacterial and archaeal genomes assembled from over 800 gigabases of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 1.2 million predicted protein sequences, and 69,000 proteins predicted to be involved in carbohydrate metabolism. ## Relation to earlier versions ## This data is referenced by Watson et al. (In Submission). A previous paper, in bioRXiv, referenced the earlier dataset "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2772. This in turn was superseded by the more recent version Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2911. The paper underwent many rounds of review, the first-round revised paper referenced the second (Hi-C) dataset and the final, accepted version will reference the DOI of this dataset. The datasets changed in nature and in name during this process. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The dataset is expected to underpin global rumen microbiome research in the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Title Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism 
Description The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This dataset is expected to underpin research in rumen microbiomes over the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/2772
 
Title PRJEB10338 
Description This collection of data represents whole metagenome sequence data for 8 cattle chosen for low and high methane emissions after matching for breed and diet 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This is a critically important dataset for linking genotype to phenotype (methane) in the cattle rumen microbiome. Since its release, the papers based on these data have been cited over 100 times 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB10338
 
Title PRJEB14552 
Description The MHC region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Currently our knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. Construction protocol: Total RNAs were extracted from white blood cell pellets prepared form blood obtained by venepuncture using Tri-reagent (Sigma-Aldrich, Dorset) and cDNA prepared using the Reverse Transcription Kit (Promega, WI); both according to the manufacturer's protocols. PCR amplification was performed with the Phusion HF PCR kit (NEB, Herts.) using bovine MHCI primers that included Illumina sequencing primer annealing sites, multiple sample identifier tags (D501-508 and D701-712) and Illumina ligation adaptors. PCR products from ~96 animals were pooled to form a library which was then sequenced on the Illumina Miseq platform. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact These data represent a reference dataset of novel MHC alleles in cattle and may underpin research into cattle immunogenetic diversity for many years in the future 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB14552
 
Title PRJEB14979 
Description Marek's Disease Virus (MDV) is a widespread alphaherpesvirus of poultry that causes Marek's disease (MD) characterised by fatal visceral CD4+ TCRaß+ T cell tumours at high incidence in susceptible hosts. As is the case with many virus-induced tumours, immortal cell lines harbouring viral genome have been generated from ex vivo cultures of MD tumours. As readily-available sources of large numbers of cells of a uniform type, MDV-transformed lymphoblastoid cell lines (LCL) have proved extremely valuable in studying virus-host interaction. While the viral genome is held in a latent state in most of the cells, a minor population of cells display spontaneous reactivation identifiable by the expression of lytic viral genes such as pp38. The process of spontaneous reactivation in these cell populations offers the opportunity for investigating the biological processes involved in the reactivation events. For this, we used two lymphoblastoid cell lines derived from lymphomas induced by pRB1B-UL47eGFP, a recombinant MDV engineered to express EGFP fused with the UL47. We used Fluorescence-activated cell sorting (FACS) to purify the rare EGFP-positive cell population with spontaneously activating viral genome from the majority EGFP-negative cells and analysed their gene expression profiles by RNA-sequencing using Illumina HiSeq2500. The reads generated were mapped using TopHat and gene expression levels were analysed by edgeR. Ingenuity pathway analysis software on more than 2000 differentially-expressed genes between the lytically infected (EGFP-positive) and latently infected (EGFP-negative) cell populations was used identify major biological pathways involved in the reactivation. These studies revealed that amongst others, transcripts directly involved in T activation such as CD3 complex, CD28, ICOS, phospholipase C, CD3 complex were down-regulated following reactivation of the virus in the LCL. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact These data detail the gene expression changes during spontaneous activation of MDV and will be useful to researchers investigating the mechanism of action of this important virus, as well as in vaccine design 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB14979
 
Title PRJEB21624 
Description This is one of the largest rumen metagenomics datasets ever released and represents 43 Scottish cattle from diverse breeds, different in methane emissions and feed conversion ratio. These data were used to assemble over 913 novel rumen microbial genomes. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact These data were used to assemble over 913 novel rumen microbial genomes, which are expected to impact global rumen microbiome research over the next 5-10 years 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB21624
 
Title PRJEB23119 - RNA-Seq data from pig macrophages 
Description We have uploaded to the ENA raw data in the form of .fastq files from macrophages (+/-) LPS from 3 pigs, 6 RNA-Seq libraries in total, with corresponding metadata. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact No impact yet. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB23119
 
Title PRJEB23196 - 54 RNA-Seq libraries from goat 
Description We have uploaded to the European Nucleotide Archive under accession number PRJEB23196 the raw data in the form of .fastq files from 54 RNA-Seq libraries from tissues and cell types from domestic goats. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact No impact yet. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB23196
 
Title PRJEB24920 - RNA-Seq data from horse macrophages 
Description We have uploaded raw read data in the form of .fastq files from macrophages (+/-) stimulation with LPS from 3 horses, 6 RNA-Seq libraries in total, with corresponding experimental metadata to the ENA. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact No impact yet. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB24920
 
Title Pig reference genome sequence Sscrofa11 
Description This pig genome sequence (Sscrofa11) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). The Consortium is coordinating genome-wide analysis, annotation and publication. The sequence data from which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact The Sscrofa11 assembly has been updated recently to Sscrofa11.1 by the addition of the SSCY sequence data from Skinner et al. 2016 (Genome Res 26:130-9). The BAC and fosmid clone resource from Duroc 2-14 will facilitate further targeted sequence closure. These improved genome assemblies will be a key resource for research in pigs and will enable applications in agriculture and biomedicine. The SScrofa11.1 assembly is currently being analysed and annotated. 
URL https://www.ncbi.nlm.nih.gov/assembly/GCA_000003025.5/
 
Title Sheep mini tissue gene expression atlas 
Description Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode. These RNA-seq data were generated from 83 different adult and embryonic tissue / cell samples. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact These RNA-seq data were a key resource for the annotation of the draft sheep reference genome sequence (Oar_v3.1) and the associated genome paper (Jiang et al. 2014. Science 344:1168-73) and a subsequent paper by Xiang et al. 2016. PeerJ 4:e1762. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJEB6169
 
Title Sheep reference genome sequence Oar_v3.1 
Description A single Texel ewe and a single Texel ram were sequenced and the 75-fold coverage by Illumina reads of the Texel ewe were assembled de novo into contigs and scaffolds with SOAPdenovo. Then 120-fold coverage Illumina sequences from both the ewe and the ram were used for a round of gap-filling. At this point, the N50 length of contigs was 18 kb, and the N50 length of the assembled scaffolds was 1.1Mb, achieving a total length of 2.64 Gb and leaving 6.9% gaps. This assembly was the previous Oar v2.0. The current assembly, Oar_v3.1, was created with another round of gap-filling by adding 21-fold coverage of GC content unbiased Illumina sequencing data from the male and 3 Gb MeDIP-seq for high GC content sequence from the female to the original datasets. Approximately 200,000 gaps were filled, including about 5000 that were filled using CHORI-243 BAC library sequences and 454 reads generated for the Oar v1.0 assembly (ACIV000000000, BioProject PRJNA33937). Segmental duplicates were identified by Whole Genome Assembly Comparison (WAGC), and their read coverage checked by GC content adjustment. Probable artificial tandem duplicates were identified using the larger insert 454 and BAC libraries and comparison to the UMD3 bovine genome assembly, and one copy of the tandem pairs was removed. The assembly of 775 overlapping scaffold ends were revised and these adjacent scaffold pairs were linked together. Artificial duplicated copies that had been generated by multiple gap-filling steps using gapcloser were removed, and erroneously assembled scaffolds identified during the error checking were manually split. A high-density RH map with 39,042 SNP markers and Ovine SNP50 genotyping linkage data were used to check scaffold integrity and to anchor scaffolds and super-scaffolds to chromosomes, leaving roughly 5700 unplaced scaffolds. Of the data cited above, the Illumina sequence data generated from the Texel ram were produced by the ARK-Genomics Centre for Comparative and Functional Genomics, The Roslin Institute, University of Edinburgh (now part of Edinburgh Genomics). 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact The generation, analysis and annotation of this draft sheep reference genome sequence was described in the sheep genome paper (Jiang et al. 2014. Science 344:1168-1173. As at 13 March 2017, this sheep genome paper has been cited 74 times. 
URL https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.1/
 
Title Whole genome sequence data from Texel ram 20118011 
Description The DNA of a male Texel sheep (20118011) was sequenced to great depth using a combination of different insert size libraries. Insert sizes of approximately 400 bp, and 700 bp were used for the bulk of the sequencing. An additional library of Illumina Mate paired inserts with an average insert size of 3.2kbp is included in the data set. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact These data contributed to the draft reference sheep genome sequence Oar_v3.1 (Jiang et al. 2014. Science 344:1168-73) and the sheep genome paper describing the analysis and annotation of the draft genome sequence. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJEB6251
 
Description Charoen Pokphand (CP) group 
Organisation Charoen Pokphand Group
Country Thailand 
Sector Private 
PI Contribution Charoen Pokphand (CP) group are a large Asian conglomerate with an interest in farming, food production and feed additives. They have placed one of their staff members with me for PhD training, fully funded by them. We are training the staff member in laboratory and bioinformatics techniques related to microbiome research in chickens.
Collaborator Contribution CP provide access to large chicken flocks both in at their farms and in their production facility. This enables us to study chicken breeds in the actual environments in which they live throughout Asia.
Impact This is a multi-disciplinary project involving both laboratory and computational techniques. The major outcome so far include a review paper (http://aem.asm.org/content/early/2018/01/29/AEM.02627-17.abstract) and the technology transfer from our group into the commercial partner.
Start Year 2017
 
Description David Griffiths, Moredun 
Organisation Moredun Research Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have been working with David Griffiths at The Moredun Research Institute since 2011 in the study of ovine pulmonary adenocarcinoma
Collaborator Contribution David Griffiths is an expert in the study of ovine pulmondary adenocarcinoma, how the virus functions and how we might design intervention strategies such as vaccines. My group is expert in the use of genomics and bioinformatics and together we are using sequencing to understand how the virus interacts with its host
Impact NA
Start Year 2011
 
Description ILRI 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training.
Collaborator Contribution We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training.
Impact So far we have sequenced the genomes of approx 800 African farm animals from diverse breeds and ecotypes
Start Year 2016
 
Description Ingenza 
Organisation Ingenza Ltd
Country United Kingdom 
Sector Private 
PI Contribution Ingenza are a local biofuels and biotechnology company who are interested in novel enzymes of industrial value from metagenomic sequence data.
Collaborator Contribution My group can provide 1000s of potential leads from metagenomic sequencing data - proteins of potential industrial value that are novel and of interest. Ingenza can then test the functionality of those proteins in E coli and yeast expression systems
Impact We have provided 1000s of leads to Ingenza that we hope will eventually be used in their core biofuels business. In addition, one of our students, Deppie Roumpeka, has spent 6 months in the lab at Ingenza purifying some of the proteins that we identified using metagenomics. These proteins show potential activity related to the degradation of cellulose, specifically they are novel beta-glucosidases that break down comples carbohydrates into sugar that can be subsequently used by yeast in ethanol production.
Start Year 2011
 
Description PoreCamp 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution PoreCamp is a training programme in nanopore sequencing run via a collaboration between Universities of Edinburgh, Birmingham and Nottingham
Collaborator Contribution The first PoreCamp was a training course run for users of the Oxford Nanopore MinION, taking place over 5 days in December 2015. Users were trained in library preparation, sequencing and bioinformatics. A second PoreCamp occurred in Exeter in 2016. A third PoreCamp occured in Texas in 2017.
Impact Well over 200 students trained to date
Start Year 2015
 
Description PoreCamp 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution PoreCamp is a training programme in nanopore sequencing run via a collaboration between Universities of Edinburgh, Birmingham and Nottingham
Collaborator Contribution The first PoreCamp was a training course run for users of the Oxford Nanopore MinION, taking place over 5 days in December 2015. Users were trained in library preparation, sequencing and bioinformatics. A second PoreCamp occurred in Exeter in 2016. A third PoreCamp occured in Texas in 2017.
Impact Well over 200 students trained to date
Start Year 2015
 
Description SRUC - Rainer Roehe 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collaborated with Rainer Roehe at SRUC since 2011, and we provide expertise in genomics, DNA sequencing, metagenomics and bioinformatics. We use this to investigate the role of the microbiome in methane emissions and feed conversion ratio.
Collaborator Contribution The SRUC partners provide expertise in rumen biology and function, alongside samples collected and measured for methane emissions and feed conversion ratio
Impact • Rumen metagenomics: we have sequenced the rumen metagenome of 8 cattle selected for high- and low- methane emissions, matched for breed and diet; and we have demonstrated that high methane emitters are enriched for (i) methanogenic Archaea and (ii) enzymes involved in the methane production pathway. Of the latter, we show that there exists over 5000 novel versions of known enzymes involved in methane production. We have made available a database of over 1.9 million proteins, the majority of them novel, as part of this study (10.1186/s12864-015-2032-0) • Host control of the microbiome: using the same dataset, we demonstrate that largely speaking the rumen microbiome structure and function if under genetic control; and can be significantly associated with both methane emissions and feed-conversion-ratio (FCR) (journal.pgen.1005846) • We have subsequently sequenced over 300 Scottish cattle rumens as part of a project funded by BBSRC. These ruminant metagenomes have resulted in the assembly and publication of several hundred novel rumen microbial genomes (10.1101/162578), publication of a novel pipeline for annotating such genomes (10.1101/233544), publication of robust methane markers in across multiple breeds (10.3389/fmicb.2017.02642) and associations between diet, rumen microbes and anti-microbial resistance (10.1186/s40168-017-0378-z)
Start Year 2011
 
Description The University of Aberdeen 
Organisation University of Aberdeen
Department Institute of Medical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been working with Alan Walker and Tim Snelling in the field of rumen metagenomic profiling
Collaborator Contribution Alan and Tim are experts in rumen microbiology and 16S sequencing, whereas my group is expert in whole-genome-shotgun metagenomics and bioinformatics
Impact As part of a Scottish government project, we have sequenced 90 rumen metagenomes using whole genome sequencing, and almost 300 using 16S profiling. Data analysis is ongoing, but my team have assembled hundreds of microbial genomes from the rumen (10.1101/162578) and written a pipeline for analysiing such data(10.1101/233544)
Start Year 2016
 
Description Venu Nair, The Pirbright Institute 
Organisation The Pirbright Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been working with Venu Nair at The Pirbright Institute for over 10 years, broadly in the area of avian oncogenic viruses such as Marek's disease and ALV.
Collaborator Contribution Venu's group are expert in virology and virus research whereas my group is expert in genomics and bioinformatics. Together we use genomics to explore virus-host interactions.
Impact 28113043 24155381 23967013 22492913 19403687 19297609 18256158
Start Year 2006
 
Title Discovery of biomass degrading enzymes 
Description We work with a local biofuels company to discover novel enzymes involved in the degradation of complex carbohydrates into glucose, which may then be used by yeast for conversion to bioethanol. We have discovered several thousand of these, and the local company have assayed the activity of 5 of them 
IP Reference  
Protection Protection not required
Year Protection Granted 2016
Licensed No
Impact Our collaborators have assayed the activity of 5 enzymes of potential interest and have demonstrated that 3 of them have activity as good as or better than commercially available alternatives
 
Title Pig exome sequencing 
Description We have exome sequenced 96 pigs for a large pig breeding company and have provided these data to said company 
IP Reference  
Protection Protection not required
Year Protection Granted 2014
Licensed No
Impact The exome variants are being used by the company internally for R&D and breeding decisions
 
Title MAGpy 
Description Recent advances in bioinformatics have enabled the rapid assembly of genomes from metagenomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously. Here we present MAGpy, a Snakemake pipeline that takes FASTA input and compares MAGs to several public databases, checks quality, assigns a taxonomy and draws a phylogenetic tree. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software was used to annotate 913 metagenome assembled genomes from the cattle rumen, a dataset which is expected to underpin rumen metagenomics research for the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Title Meta4: a web application for sharing and annotating metagenomic gene predictions using web services 
Description Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website1, code is available on Github2, a cloud image is available, and an example implementation can be seen at http://www.ark-genomics.org/tools/meta4 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact NA 
URL http://www.ark-genomics.org/tools/meta4
 
Title PULpy 
Description Polysaccharide utilisation loci (PUL) are regions within bacterial genomes that encode all the necessary machinery for the cleavage of particular carbohydrates. For the Bacteroidetes phylum, prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact We use this software in our metagenomics and microbiome research 
URL https://github.com/WatsonLab/PULpy
 
Title poRe: an R package for the visualization and analysis of nanopore sequencing data 
Description Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data. Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device. Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/ 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact NA 
URL http://sourceforge.net/projects/rpore/
 
Title viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. 
Description SUMMARY: RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports. AVAILABILITY AND IMPLEMENTATION: viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome. 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact NA 
URL http://www.ark-genomics.org/bioinformatics/virome
 
Description A presentation on "Phylogenomics of Suina Species" at the 2018 Livestock Genomics workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The biennial Livestock Genomics workshop is a small international meeting held close to the larger Genome Informatics conference that alternates between EMBL-EBI and Cold Spring Harbor Laboratory. This talk was an opportunity to present progress on characterising the genomes of three African Suina species - common warthog, red river hog and bushpig.
Year(s) Of Engagement Activity 2018
 
Description Animal Microbiome Congress London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented his work on functional microbiome analysis at the Animal Microbiome Congress London. Attendees included industry/business, farmers, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description Aviagen / CP workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I presented our work on functional microbiome analysis during a one-day workshop which I set up and organised at The Roslin Institute. In attendance were employees of CP (a large Asian conglomerate) and Aviagen (one of the world's largest chicken breeding companies). The focus of the workshop was animal genetics and microbiome.
Year(s) Of Engagement Activity 2010,2017
 
Description EASTBIO genomics masterclass 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Mick Watson organised a day-long genomics masterclass for the EASTBIO postgraduate students
Year(s) Of Engagement Activity 2017
 
Description Ethics of DNA sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Mick Watson gave a presentation on the ethics of DNA sequencing to post-graduate students at the University of Edinburgh
Year(s) Of Engagement Activity 2017
 
Description Evonik research day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I presented my work on precision analysis of microbiomes to Evonik, an international company with over 13000 employees and with interests in chemical and food production. This was part of a one day workshop with Evonik, hosted by Roslin and focused on microbiomes
Year(s) Of Engagement Activity 2018
 
Description Fetival of Genomics 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented at a workshop, hosted by Edinburgh Genomics, on software for the handling and analysis of MinION sequencing data
Year(s) Of Engagement Activity 2016
 
Description ISAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented work on cutting edge techniques that can be used to analyse metagenomics sequence data. ISAG is the international society for animal genetics and this was the very first microbiome session. In attendance were industry practitioners and academics
Year(s) Of Engagement Activity 2017
URL http://www.isag.us/2017/
 
Description MIck Watson comments on Genia 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson published a blog post on the patent dispute between Genia and the Unioversity of California, which was subsequently picked up by GenomeWeb, a website and news outlet followed by genomics investors, scientists and industry professionals
Year(s) Of Engagement Activity 2016
URL https://www.genomeweb.com/sequencing/university-california-files-suit-against-genia-cofounder
 
Description Mick Watson Roslin Industry Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Mick Watson presented on how genomic technologies are transforming biological research, to an audience of industry and professional practitioners invited to The Roslin Institute to discuss science and policy
Year(s) Of Engagement Activity 2016
 
Description Mick Watson comments on MinION 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Mick Watson was interviewed by the local press in Texas and this was then covered by multiple international news outlets. The focus was the MinION, a handheld sequencer capable of producing large amounts of DNA sequence data quickly and cheaply, and on which Mick Watson is considered an expert.
Year(s) Of Engagement Activity 2017
URL https://www.research.ed.ac.uk/portal/en/clippings/mick-watson-helps-to-develop-minion-a-handheld-dev...
 
Description Mick Watson comments on MinION sequencing of human genome 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson provided quotes and comments to a STAT news article on the recent MinION sequencing of a whole human genome
Year(s) Of Engagement Activity 2018
URL https://www.statnews.com/2018/01/29/hand-held-dna-sequencer-minion/
 
Description Mick Watson comments on NGS market 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson comments on the NGS market and the future of technologies such as the PacBio Sequel, Illumina and the Oxford Nanopore MinION
Year(s) Of Engagement Activity 2015
URL https://www.genomeweb.com/sequencing-technology/technology-improvements-long-reads-lead-ngs-market-a...
 
Description Mick Watson comments on PacBio Sequel 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact MIck Watson provided comments to an article on the PacBio Sequel, a (at the time) new sequencer from Pacific Biosciences
Year(s) Of Engagement Activity 2015
URL https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule...
 
Description PAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson gave a talk at PAG 2017 on Comparison of Methods for Functional and Phylogenetic Characterisation of Rumen Metagenomic Data. Attendees include industry, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description PAG 2018 microbiome talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk on microbiome bioinformatics at PAG 2018 in San Diego in the microbiome session. PAG includes attendees from industry, farming and academia.
Year(s) Of Engagement Activity 2018
 
Description PoreCamp 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact PoreCamp was a training course run for users of the Oxford Nanopore MinION, taking place over 5 days in December 2015. Users were trained in library preparation, sequencing and bioinformatics. A second PoreCamp occurred in Exeter in 2016
Year(s) Of Engagement Activity 2015
URL https://porecamp.github.io/
 
Description Presentation to Gates Foundation and DfID 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Mick Watson presented work on African farm animal genomics and data science to attendees from the Bill and Melinda Gates Foundation (BMGF) and the department for international development (DfID)
Year(s) Of Engagement Activity 2017
 
Description Rumen microbiome article in Farmer's Weekly 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Mick Watson was personally interviewed for an article in Farmer's weekly on the potential impact of our rumen microbiome work (doi:10.1038/s41467-018-03317-6) on breeding for production traits in beef and dairy cattle.
Year(s) Of Engagement Activity 2018
URL http://www.fwi.co.uk/livestock/rumen-genotyping-advances-enhance-cattle-breeding.htm
 
Description Rumen microbiome work in the national press (print editions) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Various articles about our rumen microbiome work appeared in the national press, including: Scottish Daily Express, Scottish Sun, The Scotsman and the Press and Journal
Year(s) Of Engagement Activity 2018
URL https://www.pressandjournal.co.uk/fp/business/farming/1427948/cow-digestion-discovery-could-boost-pr...
 
Description Rumen microbiome work on National Public Radio (NPR) in the USA 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our rumen microbiome work was featured on NPR.org, (National Public Radio), a US news network that has over 7 million followers on Twitter and reaches millions of people online and via radio. The article was immediately syndicated across an additional ~40 NPR-associated websites
Year(s) Of Engagement Activity 2018
URL https://www.npr.org/sections/thesalt/2018/03/06/589997622/mysteries-of-the-moo-crobiome-could-tweaki...
 
Description The National 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Our work was featured in The National

https://www.thenational.scot/news/17377150.scottish-team-warns-of-false-data-from-dna-reading/
Year(s) Of Engagement Activity 2019
URL https://www.thenational.scot/news/17377150.scottish-team-warns-of-false-data-from-dna-reading/
 
Description Various articles on rumen microbiome work 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Various online websites picked up our press release on our rumen microbiome work (doi:10.1038/s41467-018-03317-6) including:
https://phys.org/news/2018-02-dna-cow-stomachs-aid-meat.html
https://www.sciencedaily.com/releases/2018/02/180228085347.htm
http://www.labmanager.com/news/2018/02/dna-study-of-cow-stomachs-could-aid-meat-and-dairy-production#.WpwhWOjFLZs
https://www.technologynetworks.com/genomics/news/cows-guts-could-hold-secrets-to-more-meat-and-milk-298080
http://www.sciencenewsline.com/news/2018030111510072.html
https://www.eurekalert.org/pub_releases/2018-02/uoe-dso022718.php
http://biofuelsdigest.com/nuudigest/2018/02/28/cow-stomach-microbes-could-hold-key-for-increased-food-and-biofuel-production/
Year(s) Of Engagement Activity 2018
URL https://www.sciencedaily.com/releases/2018/02/180228085347.htm