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

Author: Francis Martin

Publisher: Humana

Published: 2016-01-21

Total Pages: 0

ISBN-13: 9781493933679

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This volume seeks to understand how organisms and gene functions are influenced by environmental cues while accounting for variation that takes place within and among environmental populations and communities. Microbial Environmental Genomics (MEG) guides readers through methods to analyse the diversity of different organism types (archaea, bacteria, fungi, protists and microfauna), interactions between fungi and trees, and methods to identify and characterize functions and functional diversity of both pro- and eukaryotes. Written for the Methods in Molecular Biology series, chapters include 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 practical, Microbial Environmental Genomics (MEG) will serve as a primary research reference for researchers and research managers in environmental microbiology working in the expanding field of molecular ecology and environmental genomics.

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 Genomics in Sustainable Agroecosystems
Microbial Genomics in Sustainable Agroecosystems

Author: Vijay Tripathi

Publisher: Springer Nature

Published: 2019-11-05

Total Pages: 285

ISBN-13: 9811387397

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In recent decades, significant advances in new methodologies like DNA sequencing and high-throughput sequencing have been used to identify microorganisms and monitor their interactions with different environments. Microbial genomics techniques are opening new approaches to microbiology by revealing how microorganisms affect human beings and the environment. This book covers four major areas: 1) Environmental microbial genomics, 2) Microbial genomics in human health, 3) Microbial genomics in crop improvement and plant health protection, and 4) Genome analysis of microbial pathogens. Within these areas, the topics addressed include: microbial genome diversity, evolution, and microbial genome sequencing; bioinformatics and microarray-based genomic technologies; functional genomics of bioremediation of soil and water from organic and inorganic pollutants and carbon management; functional genomics of microbial pathogens and relevant microorganisms; functional genomics of model microorganisms; and applied functional genomics. Given its scope, the book offers a comprehensive source of information on the latest applications of microorganisms and microbial genomics to enhance the sustainability of agriculture and the environment.

Environmental Microbiology
Environmental Microbiology

Author: Eugene L. Madsen

Publisher: John Wiley & Sons

Published: 2015-07-06

Total Pages: 592

ISBN-13: 1118439589

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New and expanded for its second edition, Environmental Microbiology: From Genomes to Biogeochemistry¸ Second Edition, is a timely update to a classic text filled with ideas, connections, and concepts that advance an in-depth understanding of this growing segment of microbiology. Core principles are highlighted with an emphasis on the logic of the science and new methods-driven discoveries. Numerous up-to-date examples and applications boxes provide tangible reinforcement of material covered. Study questions at the end of each chapter require students to utilize analytical and quantitative approaches, to define and defend arguments, and to apply microbiological paradigms to their personal interests. Essay assignments and related readings stimulate student inquiry and serve as focal points for teachers to launch classroom discussions. A companion website with downloadable artwork and answers to study questions is also available. Environmental Microbiology: From Genomes to Biogeochemistry, Second Edition, offers a coherent and comprehensive treatment of this dynamic, emerging field, building bridges between basic biology, evolution, genomics, ecology, biotechnology, climate change, and the environmental sciences.

Metagenomic Data Analysis
Metagenomic Data Analysis

Author: Suparna Mitra

Publisher: Springer Nature

Published: 2023-05-31

Total Pages: 443

ISBN-13: 1071630725

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This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis using most used R packages. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.

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.

Microbial Metagenomics, Metatranscriptomics, and Metaproteomics
Microbial Metagenomics, Metatranscriptomics, and Metaproteomics

Author:

Publisher: Academic Press

Published: 2013-09-19

Total Pages: 683

ISBN-13: 012407927X

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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

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.

Microbial Functional Genomics
Microbial Functional Genomics

Author: Jizhong Zhou

Publisher: John Wiley & Sons

Published: 2004-03-19

Total Pages: 624

ISBN-13: 9780471071907

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Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.

Insight on Environmental Genomics
Insight on Environmental Genomics

Author: Denis Faure

Publisher: Elsevier

Published: 2016-07-11

Total Pages: 176

ISBN-13: 0081010915

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Bringing together the latest methodological and scientific progress in the various research areas in the field of Environmental Genomics, this book discusses the characterization of the structure and dynamics of life, the study of the evolution and adaptation of genes and genomes, the analysis of degraded and/or old DNA, and the functional and genomic ecology of populations and communities. It also considers access to the production and sharing of NGS data and the quality of this data.As the product of the collective discussion of the active French scientific community, the book presents not only the latest technologies in the development of new sequencing methods, but also the resulting issues, challenges and prospects, in order to identify those aspects with the greatest potential for modeling and exploring the function of ecosystems. Includes recent updates from the field of environmental genomics Provides details of advances of methods and perspectives of their use Contains a multidisciplinary overview of the environmental sciences including taxonomy, ecology, evolution, and diversity Focuses on the impact of recent technology advances in high-throughput sequencing