December 1, 2020

Download Ebook Free High Throughput Next Generation Sequence Analysis For Food Microbiologists

Game Changer-Next Generation Sequencing and Its Impact on Food Microbiology

Game Changer-Next Generation Sequencing and Its Impact on Food Microbiology
Author : Jennifer Ronholm,Sabah Bidawid,Sandra Torriani
Publisher : Frontiers Media SA
Release Date : 2018-04-26
Category :
Total pages :129
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Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.

Fermented Meat Products

Fermented Meat Products
Author : Nevijo Zdolec
Publisher : CRC Press
Release Date : 2017-11-22
Category : Technology & Engineering
Total pages :572
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This book presents recent developments on the health and safety of fermented meat products. It discusses health aspects of select topics in fermented meat microbiology, veterinary public health, chemistry, technology, biotechnology, nutrition, toxicology, and quality assurance, and gives a broad insight into the product’s safety and health hazards. The book considers the safety of fermented meat products through a whole food chain approach. It focuses on requirements for strict hygienic and technological procedures to prevent potential risk during the production of ready-to-eat products. The book does not aim to serve as negative publicity for meat products. Just the opposite – it points out to the complexity of prevention and control of potential hazards/risks in the production which greatly contributes to a higher total value of fermented meat products. This reference book is a result of collaborative efforts of a number of distinguished authors with international reputation from renowned institutions and it is intended to both academic and professional audience.

Advances in Food and Nutrition Research

Advances in Food and Nutrition Research
Author : Fidel Toldra
Publisher : Academic Press
Release Date : 2020-02-05
Category : Technology & Engineering
Total pages :336
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Advances in Food and Nutrition Research, Volume 91 provides updated knowledge about nutrients in foods and how to avoid their deficiency, especially for those essential nutrients that should be present in the diet to reduce disease risk and optimize health. Specific topics covered in this new release include Polyphenols in the management of brain disorders: Modulation of the microbiota-gut-brain axis, Protein and amino acids in skeletal muscle health in aging, Chemical composition and health properties of coffee and coffee by-products, Seaweed and seaweed-derived metabolites as prebiotics, Bioactive potential of fruit and vegetable wastes, and more. The series provides the latest advances on the identification and characterization of emerging bioactive compounds with putative health benefits, as well as up-to-date information on food science, including raw materials, production, processing, distribution and consumption. Contains contributions that have been carefully selected based on their vast experience and expertise on the subject Includes updated, in-depth, and critical discussions of available information, giving the reader a unique opportunity to learn Encompasses a broad view of the topics at hand

Food Molecular Microbiology

Food Molecular Microbiology
Author : Spiros Paramithiotis,Jayanta Kumar Patra
Publisher : CRC Press
Release Date : 2019-02-14
Category : Science
Total pages :252
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With the advances in the field of molecular biology, new tools make it possible to conduct in-depth studies in food microbial communities from a molecular perspective. Information from genomic, transcriptomic, proteomic and metabolomic studies can be integrated through bioinformatic applications, thereby improving our understanding of the interactions between biotic and abiotic factors and concomitantly the physiology of starter cultures, spoilage and pathogenic microbiota. Improvements in the speed, accuracy and reliability of food quality and safety assessment have made the foundation stronger for future developments including the exploitation of gene networks and applications of nanotechnology and systems biology. This book reviews all these developments, provides an integrated view of the subject and helps in identifying areas of future development.

Plant Genomes

Plant Genomes
Author : Jean-Nicolas Volff
Publisher : Karger Medical and Scientific Publishers
Release Date : 2008-01-01
Category : Medical
Total pages :145
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Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.

Molecular Techniques in the Microbial Ecology of Fermented Foods

Molecular Techniques in the Microbial Ecology of Fermented Foods
Author : Luca Cocolin,Danilo Ercolini
Publisher : Springer Science & Business Media
Release Date : 2007-12-15
Category : Technology & Engineering
Total pages :280
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With the application of new analytical techniques, the field of food fermentation has grown in recent years. This book provides the latest information and relevant advances on the microbial ecology of fermented foods and the application of molecular methods. This book serves as a guide for students and researchers on the most advanced techniques to identify bacteria and helps in choosing the most appropriate tools to study fermented food from a microbiological point of view.

High-Throughput Next Generation Sequencing

High-Throughput Next Generation Sequencing
Author : Young Min Kwon,Steven C. Ricke
Publisher : Humana Press
Release Date : 2011-03-23
Category : Medical
Total pages :308
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Due to their novel concepts and extraordinary high-throughput sequencing capacity, the “next generation sequencing” methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.

Manual of Environmental Microbiology

Manual of Environmental Microbiology
Author : Cindy H. Nakatsu,Robert V. Miller,Suresh D. Pillai
Publisher : John Wiley & Sons
Release Date : 2020-08-11
Category : Science
Total pages :129
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The single most comprehensive resource for environmental microbiology Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manual is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation and biotransformation. This wealth of information is divided into 18 sections each containing chapters written by acknowledged topical experts from the international community. Specifically, this new edition of the Manual Contains completely new sections covering microbial risk assessment, quality control, and microbial source tracking Incorporates a summary of the latest methodologies used to study microorganisms in various environments Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.

Microbial Diversity in the Genomic Era

Microbial Diversity in the Genomic Era
Author : Surajit Das,Hirak Ranjan Dash
Publisher : Academic Press
Release Date : 2018-09-20
Category : Medical
Total pages :710
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Microbial Diversity in the Genomic Era presents insights on the techniques used for microbial taxonomy and phylogeny, along with their applications and respective pros and cons. Though many advanced techniques for the identification of any unknown bacterium are available in the genomics era, a far fewer number of the total microbial species have been discovered and identified to date. The assessment of microbial taxonomy and biosystematics techniques discovered and practiced in the current genomics era with suitable recommendations is the prime focus of this book. Discusses the techniques used for microbial taxonomy and phylogeny with their applications and respective pros and cons Reviews the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments Provides a uniform, standard methodology for species designation

Molecular Microbiology

Molecular Microbiology
Author : David H. Persing,Fred C. Tenover,Randall T. Hayden,Margareta Ieven,Melissa B. Miller,Frederick S. Nolte,Yi-Wei Tang,Alex van Belkum
Publisher : John Wiley & Sons
Release Date : 2020-07-24
Category : Science
Total pages :835
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Presenting the latest molecular diagnostic techniques in one comprehensive volume The molecular diagnostics landscape has changed dramatically since the last edition of Molecular Microbiology: Diagnostic Principles and Practice in 2011. With the spread of molecular testing and the development of new technologies and their opportunities, laboratory professionals and physicians more than ever need a resource to help them navigate this rapidly evolving field. Editors David Persing and Fred Tenover have brought together a team of experienced researchers and diagnosticians to update this third edition comprehensively, to present the latest developments in molecular diagnostics in the support of clinical care and of basic and clinical research, including next-generation sequencing and whole-genome analysis. These updates are provided in an easy-to-read format and supported by a broad range of practical advice, such as determining the appropriate type and quantity of a specimen, releasing and concentrating the targets, and eliminating inhibitors. Molecular Microbiology: Diagnostic Principles and Practice Presents the latest basic scientific theory underlying molecular diagnostics Offers tested and proven applications of molecular diagnostics for the diagnosis of infectious diseases, including point-of-care testing Illustrates and summarizes key concepts and techniques with detailed figures and tables Discusses emerging technologies, including the use of molecular typing methods for real-time tracking of infectious outbreaks and antibiotic resistance Advises on the latest quality control and quality assurance measures Explores the increasing opportunities and capabilities of information technology Molecular Microbiology: Diagnostic Principles and Practice is a textbook for molecular diagnostics courses that can also be used by anyone involved with diagnostic test selection and interpretation. It is also a useful reference for laboratories and as a continuing education resource for physicians.

Microbial Forensics

Microbial Forensics
Author : Bruce Budowle,Steven E. Schutzer,Stephen A. Morse
Publisher : Academic Press
Release Date : 2019-11-30
Category : Law
Total pages :526
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Microbial Forensics, Third Edition, serves as a complete reference on the discipline, describing the advances, challenges and opportunities that are integral in applying science to help solve future biocrimes. New chapters include: Microbial Source Tracking, Clinical Recognition, Bioinformatics, and Quality Assurance. This book is intended for a wide audience, but will be indispensable to forensic scientists and researchers interested in contributing to the growing field of microbial forensics. Biologists and microbiologists, the legal and judicial system, and the international community involved with Biological Weapons Treaties will also find this volume invaluable. Presents new and expanded content that includes a statistical analysis of forensic data, legal admissibility and standards of evidence Discusses actual cases of forensic bioterrorism Includes contributions from editors and authors who are leading experts in the field, with primary experience in the application of this fast-growing discipline

Advances in Applied Microbiology

Advances in Applied Microbiology
Author : Geoffrey M. Gadd,Sima Sariaslani
Publisher : Academic Press
Release Date : 2012-07-25
Category : Medical
Total pages :172
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Annotation Published since 1959, 'Advances in Applied Microbiology' offers comprehensive reviews of the latest techniques and discoveries in this rapidly moving field.

Metagenomics for Microbiology

Metagenomics for Microbiology
Author : Jacques Izard,Maria Rivera
Publisher : Academic Press
Release Date : 2014-11-07
Category : Science
Total pages :188
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Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Applied Genomics of Foodborne Pathogens

Applied Genomics of Foodborne Pathogens
Author : Xiangyu Deng,Henk C. den Bakker,Rene S. Hendriksen
Publisher : Springer
Release Date : 2017-01-23
Category : Science
Total pages :205
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This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential in studying, surveying and controlling foodborne microbial pathogens. The vast opportunities brought by this trend are often at odds with the lack of bioinformatics know-how among food safety and public health professionals, since such expertise is not part of a typical food microbiology curriculum and skill set. Further complicating the challenge is the large and ever evolving body of bioinformatics tools that can obfuscate newcomers to this area. Although reviews, tutorials and books are not in short supply in the fields of bioinformatics and genomics, until now there has not been a comprehensive and customized source of information designed for and accessible to microbiologists interested in applying cutting-edge genomics in food safety and public health research. This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts at the forefront of foodborne pathogen genomics research.

Viruses in Food and Water

Viruses in Food and Water
Author : N Cook
Publisher : Elsevier
Release Date : 2013-05-10
Category : Technology & Engineering
Total pages :560
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Viruses can be highly infectious and are capable of causing widespread disease outbreaks. The significance of viral pathogens in food and waterborne illness is increasingly being recognised and viruses transferred by these routes are important areas of research. Viruses in food and water reviews the risks, surveillance and control of food and waterborne viral disease. Part one provides an introduction to food and environmental virology. Part two goes on to explore methods of detection, surveillance and risk assessment of viruses in food and water; it includes chapters on molecular detection of viruses in foods and food processing environments, quality control in the analytical laboratory, and quantitative risk assessment for food and waterborne viruses. Part three focuses on virus transmission routes and control of food and water contamination. It contains chapters on fresh produce, shellfish and viral presence, and control methods in waste water and sewage. Finally, part four highlights particular pathogens including norovirus, hepatitis A and emerging zoonotic viruses. Viruses in food and water is a standard reference book for microbiologists in academia, analytical labs and the food and water treatment industries, as well as environmental health professionals and researchers working on foodborne viruses. Explores methods of detection, surveilance and risk assessment of viruses in food and water Considers virus transmission routes and control of food and water contamination Highlights advances in the understanding of specific pathogens, including norovirus, hepatitis A and rotaviruses and the advances in vaccine development