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Scientific Publications on Next Generation Sequencing Applications in Animal Genetics and Food Safety

This page introduces a selection of scientific publications of NGS applications in animal genetics including the major topics of animal breeding and diagnostics of infectious diseases.

Scientific Publications on NGS application in Animal Health and Animal Genetics

A Metagenomics and Case-Control Study To Identify Viruses Associated with Bovine Respiratory Disease

In order to identify viruses associated with bovine respiratory disease (BRD), a metagenome sequencing study was performed on samples from 50 young dairy cattle with BRD symptoms. The results showed that a large number of different viruses were detected using metagenome analysis in the BRD-positive samples compared to samples from healthy control animals. In the control samples also different BRD-associated viruses were detected, but the levels of coinfections were significant higher in samples from the BRD-positive animals. The set of severe BRD symptoms were mainly associated with three viruses (BAdV3, BRAV, and bovine influenza D virus). Remarkably, some of the viruses routinely tested for in BRD (BHV-1, PI3V, BVDV, BoCV, and BRSV) were not detected in this study.
Fei Fan NG et al. 2015

Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencingtechnologies

This paper discusses the application of NGS technology in order to study the phylogeny of PRRSV. The author introduces current protocols for PRRSV NGS workflow including data analysis, and gives an overview of NGS application to PRRSV sequencing. The main focus of this study is the quasispecies analysis of PRRSV samples through the application of NGS technology in order to better understand PRRSV phylogeny and evolution.
Lu et al 2014

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Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle

In this publication, the influences of host genes on disease resistance and vaccine response are investigated, with a focus on bovine respiratory disease (BRD) and FMDV. Relevant viruses and bacteria and corresponding treatment and vaccination strategies related to BRD are introduced, and the immunologic background related to infection and vaccination is explained. Different host genome regions are investigated, including potential SNPs and QTL that can be related to the immune response following infection or vaccination.
Glass et al. 2012

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Microbial Diversity of Bovine Mastitic Milk as Decribed by Pyrosequencing of Metagenomic 16s rDNA

In this paper, more than 150 milk samples were sequenced using Roche 454 NGS technology in order to identify bacteria related to bovine mastitis, based on the 16s rDNA. The NGS results were compared with traditional bacterial cultivation methods, with the NGS-based diagnosis shown to be significantly more sensitive and capable of detecting all samples positive for mastitis. Furthermore, DNA from different bacteria was detected in the mastitis-negative samples, leading to the proposal that differentiation between mastitis-infected and healthy animals by analysing differences in microorganisms found in milk was possible. The presence of bacterial DNA, however, cannot prove the pathogenicity of the bacteria. Furthermore, possible contamination arising during sample transport and handling might lead to misinterpretation of the results.
Oikonomou et al. 2012

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New viruses in veterinary medicine, detected by metagenomic approaches

In this paper, the author describes the methods, technologies and bioinformatics workflow used for the development of the World Organisation for Animal Health (OIE) state of the art platform for the metagenomic analysis of animal samples. In addition to known pathogens, the workflow could detect new variants of astroviruses, porcine bocavirus, and NDV.
Belak et al. 2013


Sequencing approach to analyze the role of quasispecies for classical swine fever

This paper addressed two topics. Firstly, whether the quasispecies composition influences the virulence of different CSFV strains, and secondly, different software packages for quasispecies analysis were compared in order to evaluate differences in the resulting output. Viral RNA was extracted from animal samples infected with different virulent CSFV strains in order to evaluate if the quasispecies determines or correlates to the virulence of these strains. The main limitation of this study was the potential bias introduced during animal infection, sample collection, RNA extraction, amplification, and library preparation. In order to facilitate a more reliable conclusion with statistical significance, a higher number of samples is required for comparison.
Töpfer et al. 2013

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The Fecal Virome of Pigs on a High-Density Farm

In this publication, whole genome sequencing data from the faeces of healthy and diarrheic piglets at a single high-density pig farm were investigated. Different enteric pig viruses were identified in both healthy and diarrheic pigs. All samples contained mammalian viruses. Additionally, various unknown or partially characterised viral genomes were identified.
Shan et al. 2011

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Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection?

This paper describes the background of zoonoses and their routes of transmission, such as domestic animals, wildlife (including bats, rodents, and arthropods), or transmission by human to human.
The author described a number of viruses with zoonotic potential that are insect specific or occur in wildlife along with future perspectives of meta genome analysis for surveillance programs and how the NGS technology will help to detect new viruses.
Temmam et al 2014

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Within- and across-breed genomic prediction using whole-genome sequence and single nucleotidepolymorphism panels

19. February 2016, Genetics Selection Evolution published the study from Iheshiulor et al. "Within- and across-breed genomic prediction using whole-genome sequence and single nucleotidepolymorphism panels."

Currently, genetic breeding in cattle is largely based on the application of specific SNP panels for within breed investigations. The progress in NGS and the rising number of whole-genome sequence (WGS) data are the bases for cross breed studies. As WGS data are not restricted to SNP detection they can lead to a more accurate genetic prediction in breeding.
This study examined the accuracy of genomic prediction for within-population, across-population, and multi-breed reference populations in cattle breeds based on whole genome sequence data, various SNP densities, QTL densities, trait heritabilities, and GEBV estimation methods. For genomic prediction the SNP-based best linear unbiased prediction (SNP-BLUP) and a variable selection (MixP) methods were used.
Furthermore, the assumptions and implications of using WGS in genomic predictions are described.
In summary, the use of WGS data can increase accuracy of genomic prediction for low to moderately heritable traits in small populations and WGS data are especially beneficial for multi breed predictions and when a variable selection method was used.

The publication is free available an Springer Link

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

In this publication, M. bovis whole genome sequencing data were investigated epidemiologically in order to trace infection mechanisms and the relationship of M. bovis within different herds and its potential reservoir, the badger population. Various options for re-introduction and persistence of M. bovis were discussed.
Biek et al 2012

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Scientific Publications on Next Generation Sequencing applications in Food Safety

Current and New Approaches in GMO Detection: Challenges and Solutions

This review introduces different methods that currently used for the detection of GMO in food. These are qPCR, digital PCR, LAMP, Microarray , Luminex and NGS. The advantages and disadvantages of the different methods are discussed.
This review briefly introduces target specific sequencing and WGS and its potential application of NGS in GMO detection.
In summary, qPCR is still the method of choice for GMO routine analysis. Promising alternatives are LAMP, microarrays or Luminex technology. Applying of NGS in routine GMO detection is currently difficult due to the relative high costs and technical and personal requirements.
Fraiture et al. 2015

Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems

An overview of the usage of advanced genomic technologies such as NGS in the characterisation of bacterial pathogens, with a focus on Shiga toxin-producing E. coli (STEC), is given in this review. Following a brief introduction to NGS, the workflow and data analysis, as well as the applications of NGS in evolution and virulence are discussed. A number of databases for bacterial genomic studies are introduced, and the role of phage in STEC evolution is discussed. NGS applications, such as diagnostics for clinical decision-making, outbreak detection, identification of infection source, antibiotic resistance testing, detection of asymptomatic carriers, and food safety testing are introduced.
In summary, this paper shows how the application of NGS enables a higher phylogenetic accuracy and resolution compared to traditional typing methods. Some recommendations of the authors for future NGS application in food safety include validation and standardisation of methods and databases, routine sequencing for database generation, standardised open source software, and the development of training programs, are given.

Franz et al 2014


Impact of next generation sequencing techniques in food microbiology

This review gives a short introduction to the most commonly-used NGS technologies, Roche 454, Illumina, SOLiD™, Ion Torrent and PacBio, and different steps of the NGS workflow, applicable to food safety and food control applications, are discussed. Furthermore, applications of NGS in food microbiota are introduced, including studies of the microbiota of milk, fermented dairy products, and plant, meat, and fermented foods. A comprehensive list of studies performed on different food samples or sources is also provided.
Mayo et al 2014

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Isolation and genomic sequence of hepatitis A virus from mixed frozen berries in Italy

This publication is included in order to demonstrate the various applications of NGS and its subsequent benefits.
This short communication, describes the detection of hepatitis A virus in frozen berries in Italy. The entire viral genome sequence was assembled from one sample after cultivation, and from another sample directly sequenced from total RNA extraction of a frozen berry sample. The sequences obtained were classified into the corresponding subtypes.
F Chiapponi et al 2014

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Next-generation sequencing: The future of molecular genetics in poultry production and food safety

An overview of sequencing in general, and different next generation sequencing technologies (Roche454, SOLiD™, Ion Torrent and Illumina) are presented in this review, along with so-called third generation NGS technologies. Different fields of NGS application in animal science, food safety, and poultry production are discussed. Additionally, the paper summarises how the applications of NGS in the poultry industry and in food safety could enhance the development of vaccines and thus reduce the requirements for antibiotic treatment.
Diaz-Sanchez et al 2013

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