Metagenomics and Microbial Ecology
Metagenomics and Microbial Ecology

Author: Surajit De Mandal

Publisher: CRC Press

Published: 2021-11-29

Total Pages: 266

ISBN-13: 1000482235

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Microorganisms comprise the greatest genetic diversity in the natural ecosystem, and characterization of these microbes is an essential step towards discovering novel products or understanding complex biological mechanisms. The advancement of metagenomics coupled with the introduction of high-throughput, cost-effective NGS technology has expanded the possibilities of microbial research in various biological systems. In addition to traditional culture and biochemical characteristics, omics approaches (metagenomics, metaproteomics, and metatranscriptomics) are useful for analyzing complete microbial communities and their functional attributes in various environments. Metagenomics and Microbial Ecology: Techniques and Applications explores the most recent advances in metagenomics research in the landscape of next-generation sequencing technologies. This book also describes how advances in sequencing technologies are used to study invisible microbes as well as the relationships between microorganisms in their respective environments. Features: Covers a wide range of concepts, investigations, and technological advancement in metagenomics at the global level. Highlights the novel and recent approaches to analyze microbial diversity and its functional attributes. Features a range of chapters that present an introduction to the field and functional insight into various ecosystems.

Handbook of Molecular Microbial Ecology I
Handbook of Molecular Microbial Ecology I

Author: Frans J. de Bruijn

Publisher: John Wiley & Sons

Published: 2011-07-26

Total Pages: 0

ISBN-13: 9780470644799

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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.

The New Science of Metagenomics
The New Science of Metagenomics

Author: National Research Council

Publisher: National Academies Press

Published: 2007-06-24

Total Pages: 170

ISBN-13: 0309106761

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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.

Handbook of Molecular Microbial Ecology II
Handbook of Molecular Microbial Ecology II

Author: Frans J. de Bruijn

Publisher: John Wiley & Sons

Published: 2011-09-27

Total Pages: 632

ISBN-13: 0470647191

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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 second volume, Metagenomics in Different Habitats, covers such topics as: Viral genomes Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones Biodegradation Biocatalysts and natural products A special feature of this book 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. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats. Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.

Metagenomics for Microbiology
Metagenomics for Microbiology

Author: Jacques Izard

Publisher: Academic Press

Published: 2014-11-07

Total Pages: 188

ISBN-13: 0124105084

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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.

Functional Metagenomics: Tools and Applications
Functional Metagenomics: Tools and Applications

Author: Trevor C. Charles

Publisher: Springer

Published: 2017-10-09

Total Pages: 256

ISBN-13: 3319615106

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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.

Encyclopedia of Metagenomics
Encyclopedia of Metagenomics

Author: Karen E. Nelson

Publisher: Springer

Published: 2015-02-18

Total Pages: 1528

ISBN-13: 9781461446743

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Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Phytomicrobiome Interactions and Sustainable Agriculture
Phytomicrobiome Interactions and Sustainable Agriculture

Author: Amit Verma

Publisher: John Wiley & Sons

Published: 2021-01-08

Total Pages: 320

ISBN-13: 111964481X

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A guide to the role microbes play in the enhanced production and productivity of agriculture to feed our growing population Phytomicrobiome Interactions and Sustainable Agriculture offers an essential guide to the importance of ‘Phytomicrobiome’ and explores its various components. The authors – noted experts on the topic – explore the key benefits of plant development such as nutrient availability, amelioration of stress and defense to plant disease. Throughout the book, the authors introduce and classify the corresponding Phytomicrobiome components and then present a detailed discussion related to its effect on plant development: controlling factors of this biome, its behaviour under the prevailing climate change condition and beneficial effects. The book covers the newly emerging technical concept of Phytomicrobiome engineering, which is an advanced concept to sustain agricultural productivity in recent climatic scenario. The text is filled with comprehensive, cutting edge data, making it possible to access this ever-growing wealth of information. This important book: Offers a one-stop resource on phytomicrobiome concepts Provides a better understanding of the topic and how it can be employed for understanding plant development Contains a guide to sustaining agriculture using phytomicrobiome engineering Presents information that can lead to enhanced production and productivity to feed our growing population Written for students, researchers and policy makers of plant biology, Phytomicrobiome Interactions and Sustainable Agriculture offers a clear understanding of the importance of microbes in overall plant growth and development.

Microbial Environmental Genomics (MEG)
Microbial Environmental Genomics (MEG)

Author: Francis Martin

Publisher: Springer Nature

Published: 2022-12-15

Total Pages: 370

ISBN-13: 1071628712

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This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

Microbial Ecology of Extreme Environments
Microbial Ecology of Extreme Environments

Author: Caroline Chénard

Publisher: Springer

Published: 2017-03-15

Total Pages: 254

ISBN-13: 3319516868

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This book explores microbial lifestyles, biochemical adaptations, and trophic interactions occurring in extreme environments. By summarizing the latest findings in the field it provides a valuable reference for future studies. Spark ideas for biotechnological and commercial exploitation of microbiomes at the extremes of life are presented. Chapters on viruses complement this highly informative book. In a vertical journey through the microbial biosphere it covers aspects of cold environments, hot environments, extreme saline environments, and extreme pressure environments, and more. From the deep sea, through polar deserts, up to the clouds in the air - the diversity of microbial life in all habitats is described, explored, and comprehensively reviewed. Possible biotechnical applications are discussed. This book aims to provide a useful reference for those who want to start a research program in extreme microbiology and, hopefully, inspire new research directions.