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Metagenomics for Microbiology

Metagenomics for Microbiology Book
Author : Jacques Izard,Maria Rivera,Maria C. Rivera
Publisher : Academic Press
Release : 2014-10-13
ISBN : 9780124104723
Language : En, Es, Fr & De

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Book Description :

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.

The New Science of Metagenomics

The New Science of Metagenomics Book
Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Publisher : National Academies Press
Release : 2007-05-24
ISBN : 9780309185752
Language : En, Es, Fr & De

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Book Description :

Although we can't usually see them, microbes are essential for every part of human life -- indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying -- one at a time -- the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Metagenomics

Metagenomics Book
Author : Wael N. Hozzein
Publisher : BoD – Books on Demand
Release : 2020-03-25
ISBN : 1838800557
Language : En, Es, Fr & De

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Book Description :

This book is for the students starting their research projects in the field of metagenomics, for researchers interested in the new developments and applications in this field; and for teachers involved in teaching this subject. The book is divided into three sections as indicated from its title, namely; the basics of metagenomics, metagenomic analysis, and applications of metagenomics. It covers the basics of metagenomics from its history and background, to the analysis of metagenomic data as well as its recent applications in different fields. The book contains excellent texts at both the introductory and advanced levels, that describe the latest metagenomic approaches and applications, from sampling to data analysis for taxonomic, environmental, and medical studies. Finally, the publication of this book was an interesting journey for me and I hope the readers will enjoy reading it.

Metagenomics Methods and Protocols

Metagenomics  Methods and Protocols Book
Author : Wolfgang R. Streit,Rolf Daniel
Publisher : Methods in Molecular Biology
Release : 2018-12-14
ISBN : 9781493982745
Language : En, Es, Fr & De

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Book Description :

Download Metagenomics Methods and Protocols book written by Wolfgang R. Streit,Rolf Daniel, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Metagenomics Techniques Applications Challenges and Opportunities

Metagenomics  Techniques  Applications  Challenges and Opportunities Book
Author : Reena Singh Chopra,Chirag Chopra,Neeta Raj Sharma
Publisher : Springer Nature
Release : 2020-09-08
ISBN : 9811565295
Language : En, Es, Fr & De

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Book Description :

This book summarizes the various areas of research in metagenomics and their potential applications in medicine, the environment and biotechnology. The book presents the recent advances in theoretical, methodological and applied aspects of metagenomics and highlights their applications in the fields of environmental microbial forensics, bioremediation, drug-discovery and agriculture. In addition, the book discusses various metagenomics approaches used for understanding the microbial physiology and biochemistry. Lastly the book describes a range of bioinformatics tools and computational methods for metagenomics analysis as well as the functional diversity and dynamics of microbial communities colonizing the human skin.

Functional Metagenomics Tools and Applications

Functional Metagenomics  Tools and Applications Book
Author : Trevor C. Charles,Mark R. Liles,Angela Sessitsch
Publisher : Springer
Release : 2017-10-09
ISBN : 3319615106
Language : En, Es, Fr & De

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Book Description :

In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.

Handbook of Molecular Microbial Ecology I

Handbook of Molecular Microbial Ecology I Book
Author : Frans J. de Bruijn
Publisher : John Wiley & Sons
Release : 2011-10-14
ISBN : 1118010493
Language : En, Es, Fr & De

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Book Description :

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary Approaches, covers such topics as: Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches Species designation in microbiology Metagenomics: Introduction to the basic tools with examples Consortia and databases Bioinformatics Computer-assisted analysis Complementary approaches—microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.

Metagenomics of the Human Body

Metagenomics of the Human Body Book
Author : Karen E. Nelson
Publisher : Springer Science & Business Media
Release : 2010-11-16
ISBN : 9781441970893
Language : En, Es, Fr & De

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Book Description :

The book brings a completely different perspective than available books by combining the information gained from the human genome with that derived from parallel metagenomic studies, and new results from investigating the effects of these microbes on the host immune system. Although there are a number of books that focus on the human genome that are currently available, there are no books that bring to the forefront the mix of the human genome and the genomes and metagenomes of the microbial species that live within and on us.

Microbial Metagenomics Metatranscriptomics and Metaproteomics

Microbial Metagenomics  Metatranscriptomics  and Metaproteomics Book
Author : Anonim
Publisher : Academic Press
Release : 2013-09-19
ISBN : 012407927X
Language : En, Es, Fr & De

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Book Description :

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers microbial metagenomics, metatranscriptomics, and metaproteomics, and includes chapters on such topics as in-solution FISH for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers microbial metagenomics, metatranscriptomics, and metaproteomics Contains chapters on such topics as in-solution fluorescence in situ hybridization (FISH) for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton

Handbook of Molecular Microbial Ecology II

Handbook of Molecular Microbial Ecology II Book
Author : Frans J. de Bruijn
Publisher : John Wiley & Sons
Release : 2011-09-27
ISBN : 0470647191
Language : En, Es, Fr & De

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Book Description :

"Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches is the first comprehensive reference covering the various metagenomics in a large variety of habitats, which could not previously have been analysed without metagenomic methodology. This Volume includes topics such as species designations in microbiology, metagenomics, consortia and databases, bioinformatics, microarrays, and other metagenomics applications. This reference is ideal for researchers in metagenomics, microbiology, environmental microbiology, those working on the Human Microbiome Project, microbial geneticists, molecular microbiology, and bioinformatics"--

Metagenomics and Its Applications in Agriculture Biomedicine and Environmental Studies

Metagenomics and Its Applications in Agriculture  Biomedicine and Environmental Studies Book
Author : Robert W. Li
Publisher : Nova Biomedical Books
Release : 2011
ISBN : 9781616686826
Language : En, Es, Fr & De

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Book Description :

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. DNA sequencing (or alternatively, an assay of functional properties) is applied to the culture-independent analyses of complex and diverse ("meta") populations of microbes. The rapid growth of metagenomics entails an expanded focus on microbes in a wide range of basic and applied research fields, ranging from microbiology to agriculture, biomedicine to bioenergy, and from veterinary to clinical medicine. This new book is an insightful and inclusive study on metagenomics and its applications.

Mining of Microbial Wealth and MetaGenomics

Mining of Microbial Wealth and MetaGenomics Book
Author : Vipin Chandra Kalia,Yogesh Shouche,Hemant J. Purohit,Praveen Rahi
Publisher : Springer
Release : 2017-10-30
ISBN : 9811057087
Language : En, Es, Fr & De

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Book Description :

The existence of living organisms in diverse ecosystems has been the focus of interest to human beings, primarily to obtain insights into the diversity and dynamics of the communities. This book discusses how the advent of novel molecular biology techniques, the latest being the next-generation sequencing technologies, helps to elucidate the identity of novel organisms, including those that are rare. The book highlights the fact that oceans, marine environments, rivers, mountains and the gut are ecosystems with great potential for obtaining bioactive molecules, which can be used in areas such as agriculture, food, medicine, water supplies and bioremediation. It then describes the latest research in metagenomics, a field that allows elucidation of the maximum biodiversity within an ecosystem, without the need to actually grow and culture the organisms. Further, it describes how human-associated microbes are directly responsible for our health and overall wellbeing.“/p>

Metagenomics for Microbiology

Metagenomics for Microbiology Book
Author : Jacques Izard,Maria Rivera
Publisher : Academic Press
Release : 2014-11-07
ISBN : 0124105084
Language : En, Es, Fr & De

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Book Description :

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.

Using Genomics Metagenomics and Other Omics to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications

Using Genomics  Metagenomics and Other  Omics  to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications Book
Author : Diana Elizabeth Marco,Florence Abram
Publisher : Frontiers Media SA
Release : 2019-05-15
ISBN : 2889458148
Language : En, Es, Fr & De

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Book Description :

Most ecosystem services and goods human populations use and consume are provided by microbial populations and communities. Indeed, numerous provisioning services (e.g. food and enzymes for industrial processes), regulating services (e.g. water quality, contamination alleviation and biological processes such as plant-microbial symbioses), and supporting services (e.g. nutrient cycling, agricultural production and biodiversity) are mediated by microbes. The fast development of metagenomics and other meta-omics technologies is expanding our understanding of microbial diversity, ecology, evolution and functioning. This enhanced knowledge directly translates into the emergence of new applications in an unlimited variety of areas across all microbial ecosystem services and goods. The varied topics addressed in this Research Topic include the development of innovative industrial processes, the discovery of novel natural products, the advancement of new agricultural methods, the amelioration of negative effects of productive or natural microbiological processes, as well as food security and human health, and archeological conservation. The articles compiled provide an updated, high-quality overview of current work in the field. This body of research makes a valuable contribution to the understanding of microbial ecosystem services, and expands the horizon for finding and developing new and more efficient biotechnological applications.

Metagenomics

Metagenomics Book
Author : Camilla Benedetti
Publisher : Nova Science Pub Incorporated
Release : 2014-01-01
ISBN : 9781611223583
Language : En, Es, Fr & De

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Book Description :

Metagenomic analysis has extraordinary potential to improve our understanding of microbial populations in their natural environment and identify novel genes of interest. The key feature of such analyses is that they are performed using metagenomic libraries constructed from total DNA isolated from a particular niche rather than a laboratory culture. Thus, metagenomic analyses potentially allow access to all the genetic resources present in an environment, regardless of whether or not they belong to micro-organisms that can be cultured in the laboratory. Sequence-based metagenomic analyses rely on comparisons with databases of known genomic sequences whilst functional analyses rely on screening libraries on the basis of the phenotypes cloned DNA can confer to host bacteria. Therefore, functional analysis allows the identification of novel genes with functions that could not have been predicted from their DNA sequence. This book discusses metagenomics' methods, applications and perspectives.

Metagenomics

Metagenomics Book
Author : Wolfgang Streit,Rolf Daniel
Publisher : Humana Press
Release : 2010-09-21
ISBN : 9781607618225
Language : En, Es, Fr & De

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Book Description :

Metagenomics has proven to be a powerful tool for exploring the ecology, metabolic profiling, and comparison of complex microbial communities as well as its important applications in the mining of metagenomes for genes encoding novel biocatalysts and drug molecules for bioindustries. In Metagenomics: Methods and Protocols, expert researches provide an overview and introduction to basic methods commonly used in laboratories that have a strong background in microbial metagenomics. The book attempts to address all of the working steps involved in this crucial field, beginning with DNA isolation from soils and marine samples and continuing with the construction and screening of libraries, along with key advise involving bioinformatic tools available to analyze large metagenomic sequence data sets. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metagenomics: Methods and Protocols serves as a very complete guide to available screening protocols for all major biocatalysts in order to allow for the easy setup of these screens in any microbiology lab.

Metagenomics of the Human Body

Metagenomics of the Human Body Book
Author : Karen E. Nelson
Publisher : Springer
Release : 2011-07-21
ISBN : 9781441970909
Language : En, Es, Fr & De

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Book Description :

The book brings a completely different perspective than available books by combining the information gained from the human genome with that derived from parallel metagenomic studies, and new results from investigating the effects of these microbes on the host immune system. Although there are a number of books that focus on the human genome that are currently available, there are no books that bring to the forefront the mix of the human genome and the genomes and metagenomes of the microbial species that live within and on us.

From Genes to Species Novel Insights from Metagenomics

From Genes to Species  Novel Insights from Metagenomics Book
Author : Eamonn P. Culligan,Roy D. Sleator
Publisher : Frontiers Media SA
Release : 2016-10-07
ISBN : 2889199754
Language : En, Es, Fr & De

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Book Description :

The majority of microbes in many environments are considered “as yet uncultured” and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing and functional expression of metagenomic DNA in a heterologous host. Metagenomics has revealed an extraordinary degree of diversity and novelty, not only among microbial communities themselves, but also within the genomes of these microbes. This Research Topic aims to showcase the utility of metagenomics to gain insights on the microbial and genomic diversity in different environments by revealing the breadth of novelty that was in the past, largely untapped.

Metagenomics for Gut Microbes

Metagenomics for Gut Microbes Book
Author : Ranjith Kumavath
Publisher : BoD – Books on Demand
Release : 2018-05-09
ISBN : 1789231108
Language : En, Es, Fr & De

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Book Description :

This book focuses on metagenomics for gut microbiomes. The host is deprived of various benefits derived from the numerous gut microbes for food metabolism and health. However, polysaccharides such as cellulose, xylans, resistant starch, and inulin that are found in vegetables in our diet are digested by certain species that colonize the intestines. In contrast, metagenomic studies that reiterate microbiome intrinsic factors from particular communities and lifestyles and are extremely important for bacterial communities traveling over a long distance have entered a new era. Predominantly to understand the behavior of organisms and their action in a host, next-generation sequencing will provide a new insight into analyzing the livestock industry, agriculture, and human health risks and will consider for future development novel therapies for various diseases through identification of advanced tools. Hence, the book will give more precise information on the role of gut microbiomes in the host.

The Science and Applications of Microbial Genomics

The Science and Applications of Microbial Genomics Book
Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Release : 2013-05-02
ISBN : 0309268192
Language : En, Es, Fr & De

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Book Description :

Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.