UID:
almahu_9949984127102882
Umfang:
1 online resource (840 pages)
Ausgabe:
Second edition.
ISBN:
9780443133213
,
0443133212
Inhalt:
This book, 'Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis,' provides a comprehensive exploration of microbial diversity through advanced genomic technologies. Edited by Surajit Das and Hirak Ranjan Dash, it delves into the study of microbial communities, their functional roles, and the use of molecular tools for community analysis. The work discusses methodologies such as environmental DNA extraction, metagenomics, and next-generation sequencing (NGS) to understand microbial ecology. It also examines the implications of microbial diversity on health, exploring aspects like gut microbiota and its relation to diseases. The book is intended for researchers and practitioners in microbiology, ecology, and related fields, aiming to enhance their understanding of microbial diversity and its applications in environmental and health sciences.
Anmerkung:
Front Cover -- Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis -- Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis -- Copyright -- Contents -- Contributors -- I - Overview of Microbial Diversity -- 1.1 - Molecular Tools for Assessing Bacterial Diversity From Natural Environments -- 1.1.1 INTRODUCTION -- 1.1.2 ANALYSIS OF MICROBIAL COMMUNITIES BASED ON CULTURED APPROACHES -- 1.1.3 ANALYSIS OF MICROBIAL COMMUNITIES USING CULTURE-INDEPENDENT APPROACHES -- 1.1.3.1 Extraction of Environmental DNA (eDNA) From a Natural Sample -- 1.1.3.2 Clone Library and Sanger Sequencing -- 1.1.3.3 Terminal Restriction Fragment Length Polymorphism -- 1.1.3.4 Denaturing Gradient Gel Electrophoresis -- 1.1.3.5 Fluorescence In Situ Hybridization -- 1.1.3.6 Next-Generation Sequencing (NGS) -- 1.1.3.6.1 Illumina Sequencing -- 1.1.4 PROCESSING OF NGS DATA -- 1.1.5 THIRD-GENERATION SEQUENCERS -- 1.1.6 "OMICS"-DRIVEN METAGENOMICS -- REFERENCES -- 1.2 - Importance of Microbial Diversity on Health: Perhaps the Best Tool to Intervene in Emerging and Continuing Di ... -- 1.2.1 BACKGROUND -- 1.2.2 INTRODUCTION -- 1.2.2.1 Gut Microbiota -- 1.2.2.2 Gut Microbial Composition, Host Immunity, and Metabolism -- 1.2.3 GUT MICROBIAL COMPOSITION (ABUNDANCE AND DIVERSITY) AND THEIR IMPORTANCE AND RELATION TO DISEASES -- 1.2.4 MOLECULAR BASIS OF MICROBIOME DISEASE CORRELATION: IN THE PERSPECTIVE OF CONSERVED AND UNIQUENESS OF METAGENOME AND METABOL ... -- 1.2.4.1 Neurological Diseases -- 1.2.4.2 Cardiovascular Diseases -- 1.2.4.3 Oncogenic Diseases -- 1.2.4.4 Gastrointestinal Diseases -- 1.2.4.5 Metabolic Diseases -- 1.2.4.6 Respiratory Diseases -- 1.2.5 IMPLICATION FROM THE PERSPECTIVE OF GUT MICROBIOTA -- 1.2.6 PROSPECTIVE -- AUTHOR CONTRIBUTIONS -- CONFLICT OF INTEREST -- APPENDIX -- Acknowledgments -- REFERENCES.
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1.3 - Computational Tools for Whole Genome and Metagenome Analysis of NGS Data for Microbial Diversity Studies -- 1.3.1 INTRODUCTION -- 1.3.2 COMPUTATIONAL TOOLS FOR CULTURED-DEPENDENT WHOLE GENOME ANALYSIS -- 1.3.2.1 Whole Genome Sequencing Methods -- 1.3.2.2 Sequence Output and Terminologies in NGS -- 1.3.2.2.1 File Formats -- 1.3.2.2.2 Contig -- 1.3.2.2.3 Cluster -- 1.3.2.2.4 Read Length -- 1.3.2.2.5 Sequence Coverage -- 1.3.2.2.6 Coverage Depth -- 1.3.2.2.7 Paired-End Sequencing -- 1.3.2.2.8 Quality Score (Also Known as "Q-Score") -- 1.3.2.2.9 k-mer -- 1.3.2.2.10 Reference Genome -- 1.3.2.3 Quality Control -- 1.3.2.4 Whole Genome Assembly -- 1.3.2.5 Whole Genome Annotation -- 1.3.2.5.1 Structural Annotation -- 1.3.2.5.1.1 Repeats -- 1.3.2.5.1.2 Gene Prediction -- 1.3.2.5.1.3 Structural Annotation Databases -- 1.3.2.5.2 Functional Annotation -- 1.3.2.5.2.1 Functional Annotation Database -- 1.3.2.5.3 Annotation Pipelines -- 1.3.2.5.3.1 Structural Pipelines -- 1.3.2.5.3.2 Functional Pipelines -- 1.3.2.5.3.3 Combined Pipelines -- 1.3.2.5.4 Annotation Visualization -- 1.3.3 COMPARATIVE GENOMICS AND PAN-GENOMIC ANALYSIS -- 1.3.3.1 Comparative Genomics -- 1.3.3.2 Pan Genomics -- 1.3.3.2.1 Integrated Microbial Genomes with Microbiome Samples -- 1.3.3.2.2 MicrobesOnline -- 1.3.3.2.3 The Microbial Genomes Database -- 1.3.3.2.4 ROARY -- 1.3.3.2.5 OrtholugeDB -- 1.3.3.2.6 EzBiocloud -- 1.3.3.2.7 EDGAR -- 1.3.4 COMPUTATIONAL TOOLS FOR MICROBIAL COMMUNITY ANALYSIS -- 1.3.4.1 Metagenomics -- 1.3.4.1.1 Targeted Metagenomics -- 1.3.4.1.1.1 Denoising -- 1.3.4.1.1.2 Detection of Chimera Sequence -- 1.3.4.1.1.3 OTU Clustering -- 1.3.4.1.1.4 Taxonomy-Dependent Approach -- 1.3.4.1.2 Nontargeted Metagenomics (Shotgun Metagenomics and NGS) -- 1.3.4.1.2.1 Assembly -- 1.3.4.1.2.2 Binning -- 1.3.4.1.2.3 Functional Annotation of Metagenomics Sequences.
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1.3.4.1.3 Metagenomic Analysis Databases -- 1.3.4.1.3.1 MG-RAST -- 1.3.4.1.3.2 IMG/M -- 1.3.4.1.3.3 METAREP -- 1.3.4.1.3.4 CoMet -- 1.3.4.1.3.5 CAMERA -- 1.3.4.1.3.6 MEGAN -- 1.3.4.1.3.7 Other Metagenomic Programs -- 1.3.4.2 Metatranscriptomics -- 1.3.4.3 Metabolomics -- 1.3.5 CONCLUSION AND FUTURE PROSPECTS -- REFERENCES -- 1.4 - Microbial Community Structure of the Sundarbans Mangrove Ecosystem -- 1.4.1 INTRODUCTION -- 1.4.2 SUSTENANCE OF MANGROVE ECOSYSTEMS IN ASSOCIATION WITH MICROBIOME -- 1.4.3 THE SUNDARBANS: WORLD'S LARGEST MANGROVE FOREST -- 1.4.4 DIVERSITY AND DISTRIBUTION OF MICROBIAL COMMUNITY STRUCTURE IN THE MANGROVE ECOSYSTEMS OF THE SUNDARBANS -- 1.4.5 CULTURE-INDEPENDENT TECHNIQUES BASED ON NEXT-GENERATION SEQUENCING TECHNOLOGY TO EXPLORE MICROBIAL COMMUNITY STRUCTURE -- 1.4.6 STUDY OF DIVERSITY FROM SUNDARBANS MANGROVE-ASSOCIATED MICROORGANISMS -- 1.4.6.1 Study of Bacterial Communities in Soil Sediments -- 1.4.6.2 Study of Bacterial Communities in Surface Water -- 1.4.6.3 Diversity of Archaea in the Mangrove Sediment of the Sundarbans -- 1.4.6.4 Analysis of Cyanobacterial Diversity in the Sundarbans Mangrove Ecosystem -- 1.4.6.5 Eukaryotic Community Structure of the Sundarbans Mangrove Ecosystem -- 1.4.7 CONCLUSION AND FUTURE PERSPECTIVE -- REFERENCES -- 1.5 - Understanding the Diversity and Evolution of Rhizobia from a Genomic Perspective -- 1.5.1 DIAZOTROPHIC BACTERIA: TYPES OF INTERACTION WITH PLANTS -- 1.5.2 DIVERSITY, EVOLUTION, AND TAXONOMY OF RHIZOBIA: FROM THE CLASSIC METHODS TO THE GENOMIC ERA -- 1.5.3 STATE-OF-THE-ART IN CURRENT RHIZOBIAL CLASSIFICATION -- 1.5.4 SYMBIOSIS GENES: INSIGHTS ABOUT THEIR EVOLUTION AND ORGANIZATION IN THE GENOMES -- 1.5.5 CONSIDERATIONS ABOUT THE ORIGIN OF THE SYMBIOTIC NITROGEN FIXATION -- Acknowledgments -- REFERENCES -- 1.6 - Role of Microbial Diversity in the Constructed Wetlands.
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1.6.1 INTRODUCTION -- 1.6.2 CLASSIFICATION, DESIGN, AND PROPERTY OF THE CONSTRUCTED WETLANDS -- 1.6.2.1 Free Water Surface CW -- 1.6.2.2 Horizontal Flow CW -- 1.6.2.3 Vertical Flow CW -- 1.6.2.4 French Vertical Flow CW -- 1.6.2.5 Hybrid CW -- 1.6.2.6 Baffled Sub-Surface Flow CW -- 1.6.2.7 Aerated CW -- 1.6.3 THE FACTORS THAT AFFECT MICROBIAL GROWTH IN THE CW -- 1.6.3.1 Organic Matter -- 1.6.3.2 Oxidation and Reduction Potential -- 1.6.3.3 Wetland Type -- 1.6.3.4 Operation Mode -- 1.6.3.5 Temperature -- 1.6.3.6 pH -- 1.6.3.7 Wetland Species -- 1.6.3.8 Media/Substrate -- 1.6.4 MICROBIAL DISTRIBUTION IN THE CONSTRUCTED WETLAND -- 1.6.5 THE MICROBIAL ASSOCIATED WITH POLLUTANT REMOVAL IN CONSTRUCTED WETLAND -- 1.6.5.1 Functional Microbial Community for Organic Matter Decomposition -- 1.6.5.2 Functional Microbial Community for Nitrogen Removal -- 1.6.5.3 Functional Microbial Community for Phosphorous Removal -- 1.6.5.4 Functional Microbial Community for Toxic Metals Removal -- 1.6.5.5 Functional Microbial Community for Dye Degradation -- 1.6.5.6 Functional Microbial Community for Emerging Pollutant Removal -- 1.6.6 PLANT-MICROBE SYNERGISM IN THE CW FOR THE TREATMENT OF VARIOUS WASTEWATER -- 1.6.7 CONCLUSION -- REFERENCES -- FURTHER READING -- II - Molecular Tools in Microbial Diversity -- 2.1 - Deriving Microbial Community Fingerprints From Environmental Samples Using Advanced Molecular Fingerprinting ... -- 2.1.1 INTRODUCTION -- 2.1.2 CULTURE-DEPENDENT APPROACHES: ADVANTAGES AND LIMITATIONS -- 2.1.3 MOLECULAR APPROACHES TO DERIVE MICROBIAL COMMUNITY FINGERPRINT FROM ENVIRONMENTAL SAMPLES -- 2.1.3.1 Random Amplified Polymorphic DNA -- 2.1.3.2 Denaturing Gradient Gel Electrophoresis -- 2.1.3.3 Amplified Ribosomal DNA Restriction Analysis -- 2.1.3.4 Ribosomal Intergenic Spacer Analysis -- 2.1.3.5 Single-Strand Conformation Polymorphism.
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2.1.3.6 Terminal Restriction Fragment Length Polymorphism -- 2.1.3.7 Fluorescence In Situ Hybridization -- 2.1.4 LIMITATIONS OF MOLECULAR COMMUNITY ANALYSIS TECHNIQUES -- 2.1.5 CONCLUSION -- Acknowledgments -- REFERENCES -- FURTHER READING -- 2.2 - Planktonic and Benthic Archaea in Brackish Coastal Lagoons -- a Case Study using High-throughput Amplicon Seque ... -- 2.2.1 INTRODUCTION -- 2.2.2 BIOGEOCHEMICAL ROLES OF ARCHAEA -- 2.2.3 BIOLOGY AND ECOLOGY OF ARCHAEA THROUGH APPLICATION OF HIGH-THROUGHPUT SEQUENCING -- 2.2.4 MICROBIAL ECOLOGY OF ARCHAEA FROM CHILIKA LAGOON -- 2.2.4.1 Benthic Archaeal Communities of Chilika Lagoon -- 2.2.4.1.1 Benthic Archaea in Vegetated Sediments -- 2.2.4.1.2 Benthic Archaea in Bulk Sediments -- 2.2.4.1.3 Benthic Archaea in Vegetated Mudflat Sediments -- 2.2.4.2 Planktonic Archaea in Chilika Lagoon: a Case Study using High-throughput Sequencing -- 2.2.4.2.1 Water Sample Collection and Physicochemical Measurements -- 2.2.4.2.2 DNA Extraction, PCR, and Illumina MiSeq Sequencing -- 2.2.4.2.3 Processing of Sequence Data and Statistical Analysis -- 2.2.4.2.4 Data Accessibility -- 2.2.4.3 Results and Discussion -- 2.2.4.3.1 Spatial Variability of Environmental Parameters -- 2.2.4.3.2 General Sequence Data Characteristics -- 2.2.4.3.3 Taxonomic Composition and Functional Potential of Planktonic Archaea -- 2.2.4.3.4 Comparison Between Planktonic and Benthic Archaea Composition -- 2.2.5 CONCLUDING REMARKS AND PERSPECTIVE -- Acknowledgment -- REFERENCES -- 2.3 - Molecular Tools in Microbial Diversity: Functional Assessment for Genomes and Metagenomes by Genomaple -- 2.3.1 INTRODUCTION -- 2.3.2 DEVELOPMENT OF A NEW METHOD FOR EVALUATING THE POTENTIAL FUNCTIONOME -- 2.3.2.1 KEGG Module -- 2.3.2.2 Calculation of the Module Completion Ratio Based on the Boolean Algebra-like Equation.
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2.3.2.3 Assignment of KO IDs to the Query Sequences.
Weitere Ausg.:
ISBN 9780443133206
Weitere Ausg.:
ISBN 0443133204
Sprache:
Englisch
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