Metagenomics Approaches for Improving Food Safety

2021 ◽  
Author(s):  
Craig Billington ◽  
Joanne M. Kingsbury ◽  
Lucia Rivas
Keyword(s):  
Food Safety ◽  
Diagnostic Techniques ◽  
Microbial Pathogens ◽  
Food Ingredient ◽  
Next Generation Sequencing Technology ◽  
Long Read ◽  
Foodborne Outbreaks ◽  
The Cost ◽  
Generation Sequencing ◽  
Conventional Detection

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole-genome sequencing. This is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, this approach is still anchored in traditional laboratory practice involving the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding, shotgun and long-read metagenomics, comprise the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed, alongside current limitations and knowledge gaps, and new opportunities arising from the use of this technology.

scholarly journals Much ado about food safety regulation in Nigeria

1970 ◽  
Vol 9 (1) ◽  
pp. 109-132
Author(s):  
Jane Ezirigwe
Keyword(s):  
Food Safety ◽  
National Policy ◽  
Foodborne Illnesses ◽  
Food Regulation ◽  
Safety Regulations ◽  
Foodborne Outbreaks ◽  
Legislative Reforms ◽  
Definition Of ◽  
The Cost ◽  
Regulatory Challenges

About 1 in 10 people in the world fall sick after eating food contaminated through improper farming, processing, preservation and services. In Nigeria, more than 200,000 persons die of food poison annually, caused by contaminated foods. The cost of illnesses associated with foodborne diseases in Nigeria is estimated at US$ 3.6 billion per annum. Though there is poor data collection on foodborne outbreaks, evidence exists to show that these contribute to ill health and death in the country as well as reduce productivity and economic growth. Studies and existing facts reveal that law makers, enforcement officers, regulators, food handlers and even the consuming public do not take food safety very seriously. This article examines the varied cases of foodborne outbreaks in Nigeria with the aim to assess the role and ambit of food safety regulations in Nigeria. It seeks to determine whether the present regulatory framework permits adequate regulation of the informal sector that serves the majority of the Nigerian consumers. While observing various challenges that may be encountered by the regulators, it offers recommendations on issues that require legislative reforms and pragmatic approaches in tackling the regulatory challenges. It concludes that the intergovernmental and the multi-agency cooperation envisaged by the National Policy on Food Safety and its Implementation Strategy, 2014, will be better achieved if the definition of “food” in the food laws are extended, in line with best practices and current realities, to allow for comprehensive regulation and coordination of the food chain system.Keywords: Food Safety, Foodborne Illnesses, Food Regulation, Food Security.

scholarly journals Beginner’s guide to next-generation sequencing

2021 ◽  
Author(s):  
Louise Aigrain
Keyword(s):  
Next Generation Sequencing ◽  
Sample Preparation ◽  
Third Generation ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Long Read ◽  
Pros And Cons ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Since the publication of the first draft of the human genome 20 years ago, several novel sequencing technologies have emerged. Whilst some drive the cost of DNA sequencing down, others address the difficult parts of the genome which remained inaccessible so far. But the next-generation sequencing (NGS) landscape is a fast-changing environment and one can easily get lost between second- and third- generation sequencers, or the pros and cons of short- versus long-read technologies. In this beginner’s guide to NGS, we will review the main NGS technologies available in 2021. We will compare sample preparation protocols and sequencing methods, highlighting the requirements and advantages of each technology.

The Green Revolution and the Gene Revolution in Pakistan: Policy Implications (The Quaid-i-Azam Memorial Lecture)

2005 ◽  
Vol 44 (4I) ◽  
pp. 359-386 ◽  
Author(s):  
Robert E. Evenson
Keyword(s):  
Food Safety ◽  
Green Revolution ◽  
Policy Implications ◽  
Gm Crops ◽  
Regulatory Environment ◽  
Memorial Lecture ◽  
Regulatory Systems ◽  
Cost Reductions ◽  
The Cost ◽  
Export Crops

Pakistan achieved high levels of Green Revolution Modern Variety (GRMV) adoption in the Green Revolution. Pakistan out-performed India and Bangladesh in the Green Revolution. Only China, among major countries, out-performed Pakistan in the Green Revolution. Pakistan does not have the food safety and environmental risk studies in place to support a regulatory environment for biotechnology. In effect, Pakistan is following the “precautionary principle” and applying it to science policy. This paper argues that this is a mistake. Pakistan is paying a “double penalty” for its inability to develop the regulatory systems required to take advantage of genetically modified (GM) crops. Not only does it lose the cost reductions enabled by GM crops, but because other countries have adopted GM crops, world prices are lower as a result and affect Pakistan’s export crops.

Development and Application of Computational Methods in Phage Display Technology

2020 ◽  
Vol 26 (42) ◽  
pp. 7672-7693 ◽  
Author(s):  
Bifang He ◽  
Anthony Mackitz Dzisoo ◽  
Ratmir Derda ◽  
Jian Huang
Keyword(s):  
Phage Display ◽  
Computational Methods ◽  
Peptide Ligands ◽  
Next Generation ◽  
Phage Display Technology ◽  
Next Generation Sequencing Technology ◽  
Screening Experiments ◽  
Display Technology ◽  
Comprehensive Search ◽  
Generation Sequencing

Background: Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. Methods: We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. Results: We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. Conclusion: The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.

A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

2020 ◽  
Vol 15 ◽  
Author(s):  
Zheng Jiang ◽  
Hui Liu ◽  
Siwen Zhang ◽  
Jia Liu ◽  
Weitao Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Instability ◽  
Liquid Biopsy ◽  
Tumor Tissue ◽  
High Sensitivity ◽  
Next Generation ◽  
Tissue Samples ◽  
Next Generation Sequencing Technology ◽  
Medication Selection ◽  
Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

scholarly journals Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 539
Author(s):  
Urška Kuhar ◽  
Diana Žele Vengušt ◽  
Urška Jamnikar-Ciglenečki ◽  
Gorazd Vengušt
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Manifestation ◽  
Skin Tumor ◽  
Wild Animals ◽  
Stone Marten ◽  
Sequencing Technology ◽  
Martes Foina ◽  
Tumor Sample ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

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