Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research (Translational and Applied Genomics)

Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research describes a new, holistic approach to microbiomics. International experts provide in-depth discussion of current research methods for studying human, environmental, viral and fungal microbiomes, as well as the implications of new discoveries for human health, nutrition, disease, cancer research, probiotics and in the food and agricultural industries. Distinct chapters covering culturomics and sub-microbiomes, such as the viriome and mycetobiome, provide an integrative framework for the expansion of microbiomics into new areas of application, as well as crosspollination between research areas. Detailed case studies include the use of microbiomics to develop natural products with antimicrobial properties, microbiomic enhancements in food and beverage technology, microbes for bioprotection and biopreservation, microbial tools to reduce antibiotic resistance, and maintenance and cultivation of human microbial communities. * Provides an integrated approach for realizing the potential of microbiomics across the life, environmental, food and agricultural sciences * Includes thorough analysis of human, environmental, viral and mycetol microbiomes, as well as methods and technology for identifying microbiotes * Features chapter contributions from international leaders in microbiomic methods, technology and applications Cover Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research Copyright Contents List of Contributors 1 Introduction: The Microbiome as a Concept: Vogue or Necessity? References Part I: Classes and Kinds of Microbiomes 2 Bacteriome and Archaeome: The Core Family Under the Microbiomic Roof Introduction DNA Exchange The Pioneers, Their Vision and Their Means Diversity Habitats, Settings, and Formats Environmental Adaptability, Monitoring, and Engineering The (Near-Term) Way Ahead References 3 Myc(et)obiome: The Big Uncle in the Family Introduction Emergence and Establishment Definition and Identity Mycobiome: Status, Categories, and Essence Mycobiome: Structure and Composition Studying the Mycobiome Microscopy Culture and Culturomics Immunoassays Metagenomics Select Mycobiomic Research: Some Working Examples Human Mycobiomes Remote Effects, Communication, and Control Functions of Mycobiomes Gut–Brain Axis and the Mycobiome Factor Mycorrhizal Databuses References 4 Virome: The Prodigious Little Cousin of the Family Introduction The Viral Components of the Microbiome The Environmental Virome The Plant Virome The Human Virome Methodological Challenges Associated With Virome Studies The Host–Virus Interactome Network Analysis: A Roadmap to Explore Host–Virus Interactions Prospecting the Continuum of Interactions Within the Virosphere The Double-Stranded DNA Virus–Host Interactome Humans, Apes, and Monkeys Dolphins Bats Birds Amoebas Fishes Bacteria Future Perspectives, Aspects, and Prospects References Part II: The Study of Microbiota and Microbiomes 5 Identifying Microbiota: Genomic, Mass-Spectrometric, and Serodiagnostic Approaches Introduction—The Romantic Past The Modern Pedigree Metamodernism: The Changing Environment Metamodernism: The Methods Mass Spectrometry Immunoassays Genomics Microscopy Conclusion: A Peek of the Future References 6 Panmicrobial Microarrays Introduction Invention, Definition, and Rationale of Microarrays Pedigree and Categories of Microarrays Comparison to the State of the Art Trade-Offs and Prospects Methodology Development and Optimization Types of Labeling Signal Amplification The Microbiomic Aspect of Microarray Concepts The Genomic Aspect Phenotypic Microarrays Live Cell Microarrays Conclusion References 7 Metagenomics in Microbiomic Studies Introduction Commensals and Infectious Agents Five Key Metrics Sensitivity Efficiency Bias/Universality Taxonomic Classification of Novel Microbes Contamination Total DNA or RNA Sequencing Using Illumina Specimen Collection and Storage DNA/RNA Extraction Isolation of Relevant DNA/RNA Library Preparation Sequencing Alignment Tabulation Ribosomal RNA Genes rrs and rrl Conserved Sequences Divergent Sequences Modified Bases Introns Sensitivity (Metagenomics) Sensitivity (Aliquoting and Consensus PCR) Nearly Universal Consensus PCR Nearly Universal Consensus PCR With Blocking Primers Nearly Universal Consensus RT-PCR With Blocking Primers Custom Illumina Library Preparation Bioinformatics Multiple Alignment Passes Gapped Alignment Word Length Host Versus Non-Host Databases Aligning Ribosomal RNA Against SILVA Conclusion Disclosures References 8 Culturomics: The Alternative From the Past Introduction Culturomics: Inventing or Recasting? Phylogenesis of Culturomics The Technical Dimension: Instrumentation and Devices Simulating Infectivity: Legacy and Innovative Applications Affiliations, Opportunities, and Impact References Further Reading 9 Next-Generation Sequencing: The Enabler and the Way Ahead Introduction Next-Generation Sequencing: A General Overview Next-Generation Sequencing: General Technical Aspects Next-Generation Sequencing Platforms Used for Metagenomics Roche 454 Pyrosequencing Illumina Sequencing Ion Torrent Sequencing Sequencing by Oligonucleotide Ligation and Detection Third-Generation Sequencing Single-Molecule Real-Time Sequencing Nanosequencing Helicos Sequencing GnuBIO Sequencing DNA Nanoball Sequencing Big Data in Genomics Bioinformatic Methods for Analyzing Metagenomic Data Preprocessing of Sequence Data 16S rRNA Analysis Whole-Genome Shotgun Analysis Conclusion Acknowledgment References Part III: Novel and Legacy Fields of Microbial Applications 10 Cancer Microbiomatics? Introduction Important Holdouts Microbiomics and Cancer Koch’s Blind Spots Breakthroughs in Establishing Microbiomic Causality in Cancer Becoming Wiser Malassezia as an Inducer Skin Microbiome and Carcinogenesis Malassezia in Internal Organs and Cancer Conclusion Disclosures References 11 A Prerequisite for Health: Probiotics Introduction: Definitions and Terminology Mechanisms of Action of Probiotics Against Pathogens Competitive Exclusion of Pathogens by Blocking Binding Sites Production of Bioactive Compounds Modulation of Immune System Bioengineering for Enhancing the Functional Properties of Probiotics Strains Clinical Applications Bacterial Infections of the Gastrointestinal Tract Oral Infections Vulvovaginal Candidiasis Conclusion Acknowledgment References 12 Microbiomic Prospects in Fermented Food and Beverage Technology Introduction The Microbiome of Naturally Fermented Dairy Products Resolving the Composition of the Microbiomes Wild Lactococci Mesophilic Lactobacilli Thermophilic Lactic Acid Bacteria The Microbiome of Naturally Fermented Meat Products The Microbiome of Naturally Fermented Olives and Pickles Table Olives Pickles The Microbiome of Naturally Fermented Wine and Beer Wine Beer References Further Reading 13 Legacy and Innovative Treatment: Projected Modalities for Antimicrobial Intervention Introduction A Brief History of the Antimicrobial Struggle The History of Chemotherapy Originated With Paul Ehrlich Fleming’s Observation of the Penicillin Effect Ushered in the Era of Antibiotics The Current Antibacterial Arsenal Metabolic Antagonists Nucleic Acids Inhibitors Cell Wall Synthesis Inhibitors Natural penicillins Semisynthetic penicillins Other beta-lactam antibiotics Protein Synthesis Inhibitors Nonbacterial Microbes Antiviral Drugs Antifungal Agents Inhibitors of ergosterol biosynthesis Fungal membrane disrupters Fungal cell wall inhibitors Sphingolipids biosynthesis inhibitors Nucleic acid synthesis inhibitors Protein synthesis inhibitors Microtubules inhibitors Antiprotist Agents Antihelminthic Drugs Antibiotic Resistance Offensive Resistance Strategies Defensive Resistance Strategies New Approaches of Antimicrobial Discovery The Two-Component System Beta-Lactamase Inhibitors Efflux Pump Inhibitors Outer Membrane Permeabilizers Conclusion Remarks References Further Reading 14 Electromagnetism and the Microbiome(s) Introduction History and Lore Electrons and Microbes: The Formal Meeting Formats, Conditions, and Effects Magnetic Fields Static magnetic fields Alternating magnetic fields Mechanism of action Electric Fields Mechanism of action Electromagnetic Fields Currents The New Generation of Electrostimulation: WMCS-NCCT Mechanism of action Electroresistance and Electrostimulation Interaction With Antibiotics References 15 Microbiomics: A Focal Point in GCBR and Biosecurity Introduction Emergence of New, Aggressive, and Better Adapted Pathogens Into the Future: Projecting a Responsive Strategy and Defining Operational Procedures Surveillance–Vigilance Conceptual and organizational issues Technological solutions for detection and identification and their restrictions Intervention–Containment–Management Generic suppression Selective treatment Fresh From the Past: Adapting Our Cognitive Dimension to an Evolving Universe Traits of the Threats/Compilation of a Threat Library Effectiveness Logistics Upgrade/evolutionary potential “Measured, Weighed and Found... Threatening”. Assessing the Threat Factor of an Agent Conclusion—Is It a Dream or a Nightmare? References Further Reading 16 Epilogue References Index Back Cover