Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research

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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
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