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

Volume editor (Associate), Volume editor (Scientific Advisor, The Golden Helix Foundation, Craven House, London, UK, and Post Doc Researcher, Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, Rio Patras, Greece)
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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 implications of new discoveries for human health, nutrition, disease, cancer research, probiotics, and 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

Recenzijos

"Microbiomics is a broad and still developing field. As the authors point out in the preface, the future of the field is largely unknown. This volume provides a solid overview of the current state of the field and points to multiple areas of likely development. The individual chapters are well sourced with large numbers of appropriate references and occasional suggestions for additional reading." --Doody

List of Contributors
xiii
Chapter 1 Introduction: The Microbiome as a Concept: Vogue or Necessity?
1(4)
Manousos E. Kambouris
Aristea Velegraki
References
4(1)
PART I CLASSES AND KINDS OF MICROBIOMES
5(70)
Chapter 2 Bacteriome and Archaeome: The Core Family Under the Microbiomic Roof
7(22)
George P. Patrinos
Loukia Zerva
Michael Arabatzis
Loannis Giavasis
Manousos E. Kambouris
Introduction
7(2)
DNA Exchange
9(1)
The Pioneers, Their Vision and Their Means
10(2)
Diversity
12(2)
Habitats, Settings, and Formats
14(2)
Environmental Adaptability, Monitoring, and Engineering
16(4)
The (Near-Term) Way Ahead
20(2)
References
22(7)
Chapter 3 Myc(et)obiome: The Big Uncle in the Family
29(24)
Manousos E. Kambouris
Aristea Velegraki
Introduction
29(1)
Emergence and Establishment
29(1)
Definition and Identity
30(3)
Mycobiome: Status, Categories, and Essence
33(3)
Mycobiome: Structure and Composition
36(3)
Studying the Mycobiome
39(6)
Microscopy
42(1)
Culture and Culturomics
42(1)
Immunoassays
43(1)
Metagenomics
43(2)
Select Mycobiomic Research: Some Working Examples
45(2)
Human Mycobiomes
45(2)
Remote Effects, Communication, and Control Functions of Mycobiomes
47(2)
Gut-Brain Axis and the Mycobiome Factor
48(1)
Mycorrhizal Databuses
48(1)
References
49(4)
Chapter 4 Virome: The Prodigious Little Cousin of the Family
53(22)
Yiannis N. Manoussopoulos
Cleo G. Anastassopoulou
Introduction
53(1)
The Viral Components of the Microbiome
54(4)
The Environmental Virome
55(1)
The Plant Virome
55(1)
The Human Virome
56(1)
Methodological Challenges Associated With Virome Studies
56(2)
The Host---Virus Interactome
58(10)
Network Analysis: A Roadmap to Explore Host---Virus Interactions
58(1)
Prospecting the Continuum of Interactions Within the Virosphere
59(2)
The Double-Stranded DNA Virus---Host Interactome
61(2)
Humans, Apes, and Monkeys
63(2)
Dolphins
65(1)
Bats
66(1)
Birds
66(1)
Amoebas
67(1)
Fishes
67(1)
Bacteria
67(1)
Future Perspectives, Aspects, and Prospects
68(1)
References
68(7)
PART II THE STUDY OF MICROBIOTA AND MICROBIOMES
75(126)
Chapter 5 Identifying Microbiota: Genomic, Mass-Spectrometric, and Serodiagnostic Approaches
77(18)
Aristea Velegraki
Loukia Zerva
Introduction---The Romantic Past
77(1)
The Modern Pedigree
78(1)
Metamodernism: The Changing Environment
79(3)
Metamodernism: The Methods
82(8)
Mass Spectrometry
85(1)
Immunoassays
85(1)
Genomics
86(2)
Microscopy
88(2)
Conclusion: A Peek of the Future
90(1)
References
90(5)
Chapter 6 Panmicrobial Microarrays
95(26)
Aristea Velegraki
Introduction
95(1)
Invention, Definition, and Rationale of Microarrays
96(1)
Pedigree and Categories of Microarrays
96(5)
Comparison to the State of the Art
101(1)
Trade-Offs and Prospects
102(2)
Methodology
104(4)
Development and Optimization
104(1)
Types of Labeling Signal
105(1)
Amplification
106(2)
The Microbiomic Aspect of Microarray Concepts
108(5)
The Genomic Aspect
108(3)
Phenotypic Microarrays
111(1)
Live Cell Microarrays
111(2)
Conclusion
113(3)
References
116(5)
Chapter 7 Metagenomics in Microbiomic Studies
121(34)
Martin Laurence
Introduction
121(1)
Commensals and Infectious Agents
122(2)
Five Key Metrics
124(2)
Sensitivity
124(1)
Efficiency
125(1)
Bias/Universality
125(1)
Taxonomic Classification of Novel Microbes
125(1)
Contamination
126(1)
Total DNA or RNA Sequencing Using Illumina
126(7)
Specimen Collection and Storage
127(1)
DNA/RNA Extraction
127(2)
Isolation of Relevant DNA/RNA
129(1)
Library Preparation
129(1)
Sequencing
129(4)
Alignment
133(1)
Tabulation
133(1)
Ribosomal RNA Genes rrs and rrl
133(6)
Conserved Sequences
135(1)
Divergent Sequences
136(2)
Modified Bases
138(1)
Introns
139(1)
Sensitivity (Metagenomics)
139(2)
Sensitivity (Aliquoting and Consensus PCR)
141(1)
Nearly Universal Consensus PCR
142(1)
Nearly Universal Consensus PCR With Blocking Primers
143(1)
Nearly Universal Consensus RT-PCR With Blocking Primers
144(4)
Custom Illumina Library Preparation
148(1)
Bioinformatics
149(3)
Multiple Alignment Passes
149(1)
Gapped Alignment
150(1)
Word Length
150(1)
Host Versus Non-Host
150(2)
Databases
152(1)
Aligning Ribosomal RNA Against SILVA
152(1)
Conclusion
152(1)
Disclosures
153(1)
References
153(2)
Chapter 8 Culturomics: The Alternative From the Past
155(20)
Manousos E. Kambouris
Introduction
155(1)
Culturomics: Inventing or Recasting?
156(2)
Phylogenesis of Culturomics
158(3)
The Technical Dimension: Instrumentation and Devices
161(3)
Simulating Infectivity: Legacy and Innovative Applications
164(3)
Affiliations, Opportunities, and Impact
167(1)
References
168(7)
Chapter 9 Next-Generation Sequencing: The Enabler and the Way Ahead
175(26)
Sonja Pavlovic
Kristel Klaassen
Biljana Stankovic
Maja Stojiljkovic
Branka Zukic
Introduction
175(1)
Next-Generation Sequencing: A General Overview
176(1)
Next-Generation Sequencing: General Technical Aspects
177(1)
Next-Generation Sequencing Platforms Used for Metagenomics
178(3)
Roche 454 Pyrosequencing
178(1)
Illumina Sequencing
179(1)
Ion Torrent Sequencing
179(1)
Sequencing by Oligonucleotide Ligation and Detection
180(1)
Third-Generation Sequencing
181(6)
Single-Molecule Real-Time Sequencing
181(2)
Nanosequencing
183(1)
Helicos Sequencing
184(1)
GnuBIO Sequencing
184(1)
DNA Nanoball Sequencing
185(2)
Big Data in Genomics
187(1)
Bioinformatic Methods for Analyzing Metagenomic Data
187(6)
Preprocessing of Sequence Data
188(1)
16S rRNA Analysis
189(1)
Whole-Genome Shotgun Analysis
190(3)
Conclusion
193(1)
Acknowledgment
194(1)
References
194(7)
PART III NOVEL AND LEGACY FIELDS OF MICROBIAL APPLICATIONS
201(166)
Chapter 10 Cancer Microbiomatics?
203(22)
Georgios Gaitanis
Martin Laurence
Introduction
203(1)
Important Holdouts
203(1)
Microbiomics and Cancer
204(1)
Koch's Blind Spots
205(1)
Breakthroughs in Establishing Microbiomic Causality in Cancer
206(1)
Becoming Wiser
207(1)
Malassezia as an Inducer
208(1)
Skin Microbiome and Carcinogenesis
208(5)
Malassezia in Internal Organs and Cancer
213(3)
Conclusion
216(1)
Disclosures
216(1)
References
216(9)
Chapter 11 A Prerequisite for Health: Probiotics
225(20)
Rodnei Dennis Rossoni
Felipe de Camargo Ribeiro
Patricia Pimentel de Barros
Eleftherios Mylonakis
Juliana Campos Junqueira
Introduction: Definitions and Terminology
225(2)
Mechanisms of Action of Probiotics Against Pathogens
227(5)
Competitive Exclusion of Pathogens by Blocking Binding Sites
227(1)
Production of Bioactive Compounds
228(3)
Modulation of Immune System
231(1)
Bioengineering for Enhancing the Functional Properties of Probiotics Strains
232(1)
Clinical Applications
233(4)
Bacterial Infections of the Gastrointestinal Tract
233(1)
Oral Infections
234(2)
Vulvovaginal Candidiasis
236(1)
Conclusion
237(1)
Acknowledgment
237(1)
References
237(8)
Chapter 12 Microbiomic Prospects in Fermented Food and Beverage Technology
245(34)
Paraskevi Bouki
Chrysanthi Mitsagga
Manousos E. Kambouris
Ioannis Giavasis
Introduction
245(2)
The Microbiome of Naturally Fermented Dairy Products
247(8)
Resolving the Composition of the Microbiomes
250(2)
Wild Lactococci
252(1)
Mesophilic Lactobacilli
252(1)
Thermophilic Lactic Acid Bacteria
253(2)
The Microbiome of Naturally Fermented Meat Products
255(4)
The Microbiome of Naturally Fermented Olives and Pickles
259(3)
Table Olives
259(2)
Pickles
261(1)
The Microbiome of Naturally Fermented Wine and Beer
262(5)
Wine
262(3)
Beer
265(2)
References
267(12)
Chapter 13 Legacy and Innovative Treatment: Projected Modalities for Antimicrobial Intervention
279(20)
Mohammad Al Sorkhy
Rose Ghemrawi
Introduction
279(1)
A Brief History of the Antimicrobial Struggle
279(1)
The History of Chemotherapy Originated With Paul Ehrlich
279(1)
Fleming's Observation of the Penicillin Effect Ushered in the Era of Antibiotics
280(1)
The Current Antibacterial Arsenal
280(6)
Metabolic Antagonists
280(1)
Nucleic Acids Inhibitors
281(1)
Cell Wall Synthesis Inhibitors
282(2)
Protein Synthesis Inhibitors
284(2)
Nonbacterial Microbes
286(3)
Antiviral Drugs
286(1)
Antifungal Agents
287(1)
Antiprotist Agents
288(1)
Antihelminthic Drugs
289(1)
Antibiotic Resistance
289(3)
Offensive Resistance Strategies
290(1)
Defensive Resistance Strategies
291(1)
New Approaches of Antimicrobial Discovery
292(3)
The Two-Component System
293(1)
Beta-Lactamase Inhibitors
294(1)
Efflux Pump Inhibitors
294(1)
Outer Membrane Permeabilizers
295(1)
Conclusion Remarks
295(1)
References
296(3)
Chapter 14 Electromagnetism and the Microbiome(s)
299(34)
Stavroula Siamoglou
Mas Boltsis
Constantinos A. Chassomeris
Manousos E. Kambouris
Introduction
299(2)
History and Lore
299(1)
Electrons and Microbes: The Formal Meeting
300(1)
Formats, Conditions, and Effects
301(22)
Magnetic Fields
303(4)
Electric Fields
307(4)
Electromagnetic Fields
311(1)
Currents
312(3)
The New Generation of Electrostimulation: WMCS-NCCT
315(4)
Electroresistance and Electrostimulation Interaction With Antibiotics
319(4)
References
323(10)
Chapter 15 Microbiomics: A Focal Point in GCBR and Biosecurity
333(28)
Manousos E. Kambouris
Konstantinos Grivas
Basilis Papathanasiou
Dimitris Glistras
Maria Kantzanou
Introduction
333(1)
Emergence of New, Aggressive, and Better Adapted Pathogens
334(2)
Into the Future: Projecting a Responsive Strategy and Defining Operational Procedures
336(9)
Surveillance---Vigilance
338(5)
Intervention---Containment---Management
343(2)
Fresh From the Past: Adapting Our Cognitive Dimension to an Evolving Universe
345(6)
Traits of the Threats/Compilation of a Threat Library
346(3)
"Measured, Weighed and Found... Threatening". Assessing the Threat Factor of an Agent
349(2)
Conclusion---Is It a Dream or a Nightmare?
351(2)
References
353(8)
Chapter 16 Epilogue
361(6)
Manousos E. Kambouris
References
364(3)
Index 367
Dr. Manousos E. Kambouris serves as a Scientific Advisor for the Golden Helix Foundation, Craven House, London, UK, an international non-profit research organization aiming to advance research and education in the area of genomic and personalized medicine and as a Post Doc Researcher in the Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras. Dr. Kambouris has long participated in different aspects and applications of microbiology, human genomics, biosecurity and cancer research. In his own work, he pursues an integrative approach to microbiomics, employing various -omics-driven approaches and realizing their application in human health, selective and personalized medicine, and panbiosurveillance among other areas. He has published widely in such peer-reviewed journals as OMICS-JIB, Hemoglobin, Medical Mycology, FEMS Immunology & Medical Microbiology, Public Health Genomics, and Future Microbiology. Dr. Aristea Velegraki is Associate Professor of Mycology at the National Kapodistrian University of Athens, Athens, Greece. She is founder and curator of the Hellenic Collection for Pathogenic Fungi http://www.eccosite.org/ (UOA/HCPF under Greece), and specializes in aspects and applications of mycology, from clinical infectious disease to toxicology, with extensive applied experience in microbiomic identification and sequencing technologies. She has served as Vice President of the International Society of Human and Animal Mycology (ISHAM) from 2006 to 2012, and has published widely in peer reviewed journals as Medical Mycology, OMICS, Clinical Microbiology and Infection, PLOS pathogens, Journal of Investigative Dermatology, Journal of Clinical Microbiology, Environmental Microbiology, Natural Product Communications, Journal of Ethnopharmacology, Fungal Genetics and Biology, and the American Journal of Clinical Pathology.
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