Microbiome-Host Interactions

Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont," and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment. The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans , and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents. Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology). FEATURES Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences Cover Half Title Title Page Copyright Page Table of Contents Foreword Preface Editors Contributors 1. An Insight of Microbiome Science 1.1 Introduction 1.2 Ecological Theory in Understanding of the Microbiome 1.3 Different Types of Microbiome 1.3.1 Microbiome 1.3.2 Types of Microbiome 1.3.2.1 Soil Microbiome 1.3.2.2 Marine Microbiome 1.3.2.3 Animal Microbiome 1.3.2.4 Plant Microbiome 1.3.2.5 Human Microbiome 1.4 Classification of Microbiomes in Human Health 1.4.1 The Skin Microbiome 1.4.2 Oral Microbiome 1.4.3 The Respiratory Microbiome 1.4.4 Gut Microbiome 1.4.5 Genital Microbiome 1.5 Future Perspectives References Section I: Omics and Computational Techniques Used for Microbiome Analysis 2. Multi-Omics: Overview, Challenges, and Applications 2.1 Introduction 2.2 Assemblers/Tools Used for Metagenome Analysis 2.2.1 AbySS 2.0 2.2.2 MEGAHIT v1.0 2.2.3 SGA 2.2.4 Kraken 2.2.5 SUPER-FOCUS 2.2.6 StrainPhlAn 2.3 Assemblers/Tools Used for Metatranscriptome Analysis 2.3.1 Leimena-2013 2.3.2 MetaTrans 2.3.3 SAMSA 2.4 Functional Analysis Using Different Databases 2.4.1 MG-RAST 2.4.2 MEGAN 2.4.3 COG 2.5 Multi-Omics—A Future Full of Promises and Challenges References 3. Computational Techniques Used for Microbial Diversity Analysis 3.1 Introduction 3.1.1 16S rRNA Amplicon Sequencing 3.1.2 Approaches for Data Analysis of 16S rRNA Amplicon Sequences 3.2 Materials 3.2.1 Software 3.2.2 Sequence and Sample Metadata 3.3 Methods 3.3.1 Merging Paired-End Reads, Quality Analysis, and Filtering 3.3.2 Chimera Removal 3.3.3 OTU-Picking Strategies 3.3.3.1 Closed Reference 3.3.3.2 De novo 3.3.3.3 Open Reference 3.3.4 OTU Table 3.3.5 Converting BIOM Table into Phyloseq Object 3.4 DADA2 Tutorial 3.4.1 Preparation of Data 3.4.2 Sequence Quality Check 3.4.3 Filtering and Trimming 3.4.4 Learning Error Rates 3.4.5 Sample Inference 3.4.6 Merging Paired-End Reads 3.4.7 Construct Sequence Table and Remove Chimeras 3.4.8 Assign Taxonomy 3.4.9 Constructing Phyloseq Object 3.5 Downstream Analysis 3.5.1 Alpha Diversity 3.5.2 Beta Diversity 3.5.3 Bar Charts 3.5.3.1 Tax_glom 3.5.4 Differential Abundance Testing 3.6 Conclusions References 4. Downstream Analysis and Visualization-Knowledge Discovery – Alpha and Beta Diversity 4.1 Introduction 4.2 Genesis of Downstream Analysis and Visualization Technologies 4.3 Challenges 4.4 Experimental Bias (Narrow Spectrum) 4.4.1 Sample Collection and Handling 4.4.2 Nucleic Acid Extraction and Preparation 4.5 Computational Bias (Broad Spectrum) 4.5.1 Amplicon Sequencing Analysis 4.5.2 Metagenomic Sequencing Analysis 4.6 Quality of Nucleic Acids 4.6.1 Short-Read Metagenomic Analysis (NGS) 4.6.2 Long-Read Metagenomic Analysis (Third-Gen.) 4.6.2.1 Applications of HTS 4.6.3 Limitations 4.7 Knowledge Discovery 4.8 Knowledge Discovery Protocol 4.9 Alpha and Beta Diversities 4.9.1 α-Diversity 4.9.2 β-Diversity 4.9.3 Limitations 4.10 Conclusions References 5. Biostatistics Including Multivariate Analysis Commonly Used for Microbiome Analysis/Study 5.1 Introduction 5.2 Hypothesis of Microbiome Study 5.3 Statistical Methods Commonly Used for Microbiome Studies 5.4 Multivariate Statistical Tools Used in Microbiome Studies 5.5 Statistical Tests to Signify the Multivariate Plots 5.6 Limitations and Future Direction Acknowledgments References Section II: Human Microbiome 6. Structure and Functional Role of Microbiome Associated with Specific Organs of Healthy Individuals 6.1 Introduction 6.2 Microbiome of the Gastrointestinal Tract 6.3 Microbiome of the Upper Gastrointestinal Tract of Healthy Individuals 6.4 Microbiome of the Small Intestine of Healthy Individuals 6.5 Microbiome of the Large Intestine of Healthy Individuals 6.6 Microbiome of the Oral Cavity of Healthy Individuals 6.7 Microbiome of the Nasal Region of Healthy Individuals 6.8 Microbiome of the Skin of Healthy Individuals 6.9 Microbiome of Urogenital Organs of Healthy Individuals Acknowledgments References 7. Structure and Function of Healthy Human Microbiome: Role in Health and Disease 7.1 Introduction 7.1.1 Structure and Functions of the Healthy Human Microbiome 7.2 Nasal Microbiome 7.3 Lung Microbiome 7.3.1 The Healthy Human Lung Bacteria 7.4 The Oral Microbiome 7.4.1 Dental-Associated Microbes 7.4.2 Tongue- and Saliva-Associated Microbes 7.4.3 The Human Oral Microbiome Database (HOMD) 7.5 Gut Microbiome 7.5.1 In Utero Colonization 7.5.2 Factors Affecting Colonization – Mode of Delivery 7.5.3 Breastfeeding 7.5.4 Effect of Environment on the Early Colonization of Microbiome 7.5.5 Effect of Pregnancy on Microbiota 7.5.6 Longitudinal Distribution of Healthy Gut Bacteria 7.5.6.1 Esophageal Microbiome 7.5.6.2 Stomach Microbiome 7.5.6.3 Microbiota of the Small Intestine 7.5.6.4 Microbiota of the Large Intestine 7.5.7 Axial Distribution of Gut Bacteria 7.6 The Urogenital Microbiome 7.6.1 Vaginal Microbiome 7.6.2 Male Genital Microbiome 7.6.3 Urinary Bladder and Urinary Tract Microbiome 7.7 The Skin Microbiome 7.7.1 Sweat Glands 7.7.2 The Skin Topology 7.7.3 Role of Microbiome in Diseases 7.7.4 Diabetes and Gut Microbiota 7.7.5 Obesity and Gut Microbiota 7.7.6 Inflammatory Bowel Disease (IBD) and Gut Microbiota 7.8 Conclusions References 8. Human Microbiome’s Role in Disease 8.1 Introduction 8.2 Human Gut Microbiome and Diabetes 8.3 Microbiome and Obesity 8.4 Role of Human Gut Microbiome in IBD 8.5 Therapeutic Implications of the Human Microbiome 8.6 Probiotics 8.7 Prebiotics 8.8 Fecal Microbiota Transplantation 8.9 Conclusion References 9. Role of Human Gut Microbiome in Health and Disease 9.1 Introduction 9.2 Distribution of Microbial Communities in the Human Gastrointestinal Tract 9.2.1 The Microbiota of the Stomach 9.2.2 The Microbiota of the Small Intestine 9.2.3 The Microbiota of the Large Intestine 9.3 The Function of the Human Gut Microbiota 9.3.1 Fermentation of Undigested Polysaccharides, Synthesis, and Conversion of Bioactive Compounds 9.3.1.1 Production of SCFAs 9.3.1.2 Conversion of Daidzein to Bioactive Equol 9.3.1.3 Vitamin K Production 9.3.1.4 Drug Metabolism and Other Metabolic Phenotypes of the Gut Microbiota 9.3.2 Alterations of Intestinal Morphology and Angiogenesis 9.3.3 Maturation of the Immune System 9.3.4 Prevention of Pathogenic Infection 9.3.5 The Gut Microbiota Affects Energy Homeostasis, Adiposity, and Obesity 9.3.6 Effects of Gut Microbiota on Host Behavior 9.4 Gut Microbiome and Diseases 9.4.1 Inflammatory Bowel Diseases 9.4.2 Obesity 9.4.3 Colorectal Cancer 9.4.4 Autism Spectrum Disorders (ASD) 9.4.5 Clostridium difficile Infection (CDI) 9.5 Conclusion References 10. The Role of Probiotics and Prebiotics in the Composition of the Gut Microbiota and Their Influence on Inflammatory Bowel Disease, Obesity, and Diabetes 10.1 Gut Microbiota, Probiotics, and Their Impacts on the Human Health 10.2 Gut Microbiota, Prebiotics, and Their Impacts on the Human Health 10.3 Paraprobiotics, Postbiotics, Psychobiotics and More to Come 10.4 Influence of Probiotics, Prebiotics and Postbiotics in Chronic Non-Communicable Diseases 10.4.1 Inflammatory Bowel Diseases 10.4.2 Diabetes Mellitus 10.4.3 Obesity 10.5 Final Considerations References 11. Skin Microbiome, Its Impact on Dermatological Diseases, and Intervention of Probiotics 11.1 Introduction 11.2 The Skin Microbiome 11.2.1 Bacterial Skin Microbiome 11.2.2 Fungal Skin Microbiome 11.2.3 Other Microbiomes 11.2.4 Factors Affecting Skin Microbiome 11.2.4.1 Host-Related Factors 11.2.4.2 Environmental Factors 11.2.5 Skin Microbiome and Host Interaction 11.3 Skin Microbiome of Different Dermatological Conditions 11.3.1 Psoriasis 11.3.2 Seborrheic Dermatitis 11.3.3 Atopic Dermatitis 11.3.4 Acne 11.3.5 Rosacea 11.3.6 Vitiligo 11.4 Relationship between Skin and Gut Microbiome 11.5 Role of Prebiotics in the Improvement of Skin Health 11.6 In vivo Animal and Human Clinical Studies on Probiotics for Skin Health 11.6.1 Animal Studies 11.6.2 Human Studies 11.7 Beneficial Effects of Probiotics in Amelioration of Dermatological Diseases 11.7.1 Dermatitis 11.7.1.1 Atopic Dermatitis 11.7.1.2 Allergic Dermatitis 11.7.2 Skin Infections 11.7.2.1 Acne 11.7.2.2 Chronic Wounds 11.7.3 Psoriasis 11.7.4 Vitiligo 11.8 Future Perspectives 11.9 Conclusions Acknowledgments Abbreviations References 12. Role of Dysregulation of the Human Oral and Gastrointestinal Microbiome in Chronic Inflammatory Disease 12.1 Oral Flora during Health 12.1.1 Composition of the Oral Microbiome 12.1.2 Development of the Oral Microbiome 12.1.3 Methods of Studying the Oral Microbiome 12.2 Dysbiosis of Oral Flora: Dental Caries to Periodontal Disease 12.2.1 Leaving the Mouth: Blood and Gastrointestinal Colonization 12.2.2 Pathogenic Oral Bacteria and Chronic Inflammatory Disease 12.2.2.1 Fusobacterium Nucleatum 12.2.2.2 Porphyromonas Gingivalis and Aggregatibacter actinomycetemcomitans 12.2.3 Oral Bacteria and Autoimmune Disease 12.2.3.1 Rheumatoid Arthritis 12.2.3.2 Systemic Lupus Erythematosus (SLE) and Sjögren’s Syndrome (SS) 12.2.4 Oral Bacteria and Cardiovascular Disease 12.2.5 Oral Bacteria and Tumors 12.3 Gastrointestinal Flora during Health 12.3.1 Composition of the Gastrointestinal Microbiome 12.3.2 Development of the Gastrointestinal Microbiome 12.3.3 Methods of Studying the Gastrointestinal Microbiome 12.4 Dysbiosis of Gastrointestinal Flora and Disease 12.4.1 Gastrointestinal Dysbiosis and Autoimmune Diseases 12.4.1.1 Ankylosing Spondylitis 12.4.1.2 Crohn’s Disease 12.4.1.3 Other Autoimmune Diseases 12.4.2 Gastrointestinal Dysbiosis and Osteoarthritis 12.4.3 Gastrointestinal Dysbiosis and Tumors 12.5 Future Directions and Final Thoughts 12.5.1 Removal of Oropathogens by Vaccines 12.5.2 Removal and Reduction of Oropathogens by Antimicrobial Agents 12.5.3 Re-Establishing Gastrointestinal Health 12.5.4 Final Thoughts References 13. Microbiome in Women Reproductive Health 13.1 Introduction 13.2 Microbiome in Female Reproductive System 13.2.1 Microbiome in Vagina 13.2.2 Microbiota in Other Parts of Female Reproductive System 13.3 Microbial Dysbiosis and Women Health Issues 13.3.1 Bacterial Vaginosis 13.3.2 Pelvic Inflammatory Disease 13.3.3 Endometriosis 13.3.4 Polycystic Ovarian Syndrome 13.3.5 Ectopic Pregnancy and Spontaneous Abortion 13.3.6 Infertility and Implantation Failures 13.3.7 Gynecological Cancers 13.4 Manipulation of Microbiome/Restoration of Microbiome 13.5 Conclusion References 14. Crosstalk between Bacteria and Host Immune System with Special Emphasis on Foodborne Pathogens 14.1 Introduction 14.2 Virulence Factors 14.3 Capsule 14.4 Cell Wall 14.5 Lipopolysaccharides (LPS) 14.6 Secretion System 14.7 Outer Membrane Vesicles (OMVs) 14.8 Adhesins 14.9 Invasins 14.10 Exotoxins 14.11 Innate Immunity 14.12 Subversion of Cell Signaling by Pathogens 14.13 Bacterial Metabolism: A Prerequisite for Virulence 14.14 Role of Iron in Host–Pathogen Interaction 14.15 Novel Areas of Host–Pathogen Interactions 14.15.1 MiRNAs in Host–Pathogen Interaction 14.15.2 Polyamines 14.15.3 Prenylated Proteins 14.16 Host–Pathogen Interaction Studies 14.17 Conclusion References Section III: Animal Microbiome 15. Reproductive Tract Microbiome in Animals: Physiological versus Pathological Condition 15.1 Introduction 15.2 Vaginal and Uterine Microbiome in Animals 15.3 Factors Affecting Reproductive Tract Microbiome 15.4 Vaginal and Uterine Microbiome during Pregnancy in Animals 15.4.1 The Influence of the Vaginal and Uterine Microbiome on Fertility and Pregnancy Outcome 15.5 Penile and Preputial Microbiome in Animals 15.6 The Reproductive Tract Microbiome of Animals in Pathological Condition 15.6.1 Metritis 15.6.2 Endometritis 15.6.3 Pyometra 15.7 Conclusions References 16. Community Structures of Fecal Actinobacteria in Animal Gastrointestinal System 16.1 Actinobacteria as Typical Inhabitants of Animal GI Tract 16.2 Diversity and Biological Attributes of Animal Fecal Actinobacteria 16.3 Community Structures of Fecal Actinobacteria in Chicken and Goat 16.4 Population Density of Cultivable Actinobacteria in Animal Feces 16.5 Diversity and Distribution Pattern of Animal Fecal Actinobacteria 16.6 Conclusions Acknowledgments References 17. Microbiota Functions in Caenorhabditis elegans 17.1 Introduction 17.2 Caenorhabditis elegans 17.3 Microbiome Composition and Diversity 17.4 Genetics versus Environmental Factors on Gut Microbiome 17.5 Functionality of Gut Microbiota 17.6 A Gateway for Understanding Host–Microbe Cometabolism 17.6.1 Vitamin B12 17.6.2 Folate 17.6.3 Colonic Acid 17.6.4 Nitric Oxide 17.6.5 Reactive Oxygen Species 17.6.6 A Metabolic Communication between Pathogen and the Commensal 17.7 Future Perspective References 18. Impact of Microbial Communities on the Female Reproductive Tract of Bovine 18.1 Introduction 18.2 Vaginal Microbiota 18.2.1 Estrus and Pregnancy Microbiota 18.2.2 Cervico-Vaginal Microbiota 18.3 Uterine Microbiota 18.4 Functional Role of Bacterial Flora in Reproductive Disorders and Failures 18.4.1 Metritis Microbiome Biomarker 18.4.2 Clinical and Subclinical Endometritis Microbiome Biomarker 18.5 Conclusions and Future Recommendations Acknowledgments References Section IV: Plant Microbiome 19. Insights into the Structure, Function, and Dynamics of Rice Root and Rhizosphere-Associated Microbiome 19.1 Introduction 19.2 Global Importance and Cultivation Strategies of Rice 19.3 Strategies of Microbiome Profiling 19.4 Rice Root Anatomy and Microbial Distribution Therein 19.4.1 Rhizosphere 19.4.2 Iron Root Plaque 19.4.3 Rhizoplane 19.4.4 Endosphere 19.4.5 Bulk Soil 19.5 Functional Characterization of Rice Rhizosphere Microbiome 19.5.1 Cycling of Methane 19.5.2 Nitrogen Cycling 19.6 Community Dynamics of Rice Microbiome References 20. Mangrove Ecosystem and Microbiome 20.1 Introduction 20.1.1 Mangrove Forests 20.1.2 Adaptation Strategies of Mangrove Plant Species 20.1.3 Mangroves around the World 20.1.4 Mangroves in Asia 20.1.4.1 Mangrove Ecosystems in India 20.1.4.2 Mangroves in Indonesia 20.1.5 Mangroves in Africa 20.1.6 Mangrove in America 20.2 Mangroves as an Ecosystem 20.2.1 Creatures in the Mangrove Ecosystem 20.2.2 Detritus as an Important Element in the Mangrove Ecosystem 20.3 Physicochemical Parameters of the Mangrove Ecosystem 20.4 Microbial Diversity in the Mangrove Ecosystem 20.4.1 Culturable Diversity 20.4.1.1 Bacterial Diversity 20.4.1.2 Sulfur-Oxidizing and Sulfate-Reducing Bacteria 20.4.1.3 Phosphate-Solubilizing Bacteria 20.4.1.4 Nitrogen-Fixing Bacteria 20.4.1.5 Methanogenic Bacteria 20.4.1.6 Photosynthetic Anoxygenic Bacteria 20.4.1.7 Algae 20.4.1.8 Fungi and Actinomycetes 20.4.1.9 Cellulose Degraders 20.4.2 Unculturable Diversity 20.5 Biotechnological Potential of Mangrove Microbiome 20.6 Need for Conservation of Mangrove Ecosystem Acknowledgment References 21. Role of the Mycobiome in Agroecosystems 21.1 Introduction 21.1.1 Achnatherum inebrians (Drunken Horse Grass) 21.1.2 Acer campestre L. and A. platanoides L. (Field and Temperate Norway Maple) 21.1.3 Aerva javanica Juss. Ex. Schult 21.1.4 Anoectochilus roxburghii 21.1.5 Arabidopsis thaliana 21.1.6 Arachis hypogaea L. (Peanut) 21.1.7 Artemisia annua L 21.1.8 Camellia oleifera 21.1.9 Cannabis sativa 21.1.10 Castanea sativa (Chestnut) 21.1.11 Cullen plicata 21.1.12 Dendrobium exile Schlechter (Orchidaceae) 21.1.13 Dicranum scoparium (Bryophyta) 21.1.14 Dysosma versipellis (Hance) M. Cheng ex Ying (Berberidaceae) 21.1.15 Debregeasia salicifolia 21.1.16 Euphorbia geniculata 21.1.17 Glycine max L 21.1.18 Glycyrrhiza glabra L. (liquorice; Leguminosae) 21.1.19 Halophyte Plants (Anabasis iranica, Seidlitzia rosmarinus, Salsola tomentos, Salsola yazdiana, Rubia tinctorum, and Artemisia annua) 21.1.20 Hordeum brevisubulatum (Wild Barley) 21.1.21 Helianthus annuus L., Solanum xanthocarpum, S. melongena, and Allium cepa L 21.1.22 Jacaranda mimosifolia D. Don 21.1.23 Jatropha curcas L. (Family: Euphorbiaceae) 21.1.24 Lactuca sativa L 21.1.25 Lactuca serriola L. (wild lettuce) 21.1.26 Lolium perenne (Perennial Ryegrass; Poaceae) 21.1.27 Medicago truncatula 21.1.28 Mangrove Plants 21.1.29 Mentha piperita 21.1.30 Mitrephora wangii 21.1.31 Marchantia polymorpha L 21.1.32 Musa acuminata (Banana) 21.1.33 Neurachne alopecuroidea 21.1.34 Ocimum basilicum (Sweet Basil) 21.1.35 Oryza sativa L. (Rice) 21.1.36 Oxalis corniculata 21.1.37 Panax notoginseng 21.1.38 Polystichum munitum (Western Sword Fern; Dryopteridaceae) 21.1.39 Pinus sylvestris var. mongolica 21.1.40 Pinus tabulaeformis Carr 21.1.41 Pisum sativum L 21.1.42 Pisum sativum L. and Triticum spelta L 21.1.43 Phaseolus vulgaris L. (Common Bean) 21.1.44 Polygonum acuminatum and Aeschynomene fluminensis 21.1.45 Populus tremula (Aspen) 21.1.46 Phalaris arundinacea and Scirpus sylvaticus 21.1.47 Securinega suffruticosa (Pall.) Rehd 21.1.48 Solanum lycopersicum 21.1.49 Schedonorus arundinaceus (Schreb.) Dumort.; syn. Festuca arundinacea (Tall Fescue) 21.1.50 Trisetum spicatum (Poaceae) 21.1.51 Triticum aestivum (Wheat) 21.1.52 Vachellia farnesiana (L.) Wight & Arn, (syn. Acacia farnesiana (L.) Willd) 21.1.53 Vitis vinifera L 21.1.54 Zea mays L. (maize) 21.2 Conclusion References 22. Root Nodule Microbiome from Actinorhizal Casuarina Plant 22.1 Introduction 22.2 Actinorhizal Casuarina Root Nodule Microbiome Diversity Experimental Workflow 22.3 Actinorhizal Casuarina Root Nodule Microbiome Statistical Data Analysis Workflow 22.4 MetaVxTM Library Preparation and Illumina MiSeq Sequencing 22.5 Casuarina Root Nodule Microbiome Data Analysis 22.6 Plant Microbiome 22.7 The Rhizosphere Environment 22.8 The Phyllosphere Atmosphere 22.9 The Endosphere Atmosphere 22.10 Effect of Plant Host Microbiome 22.11 Various Applications of the Plant Microbiome References 23. Growth Promotion Utility of the Plant Microbiome 23.1 Introduction 23.1.1 Mechanism of the Plant Microbiome 23.2 Diversity, Functional Potential, and Adaptation to the Plant Environment 23.3 Rhizosphere 23.4 Root Microbiota Transformation 23.5 Endosphere 23.6 Phyllosphere 23.7 Factors Affecting Plant Microbiota 23.8 Core and Satellite Microbiomes 23.9 Functions of Plant Microbiota 23.10 Application of Microbial Consortia 23.11 Modern Tools to Explore PM Interactions 23.12 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas Systems 23.13 Conclusions and Future Challenges References Section V: Environmental Microbiome 24. Microbiome of Speleothems – Secondary Mineral Deposits 24.1 Introduction 24.2 Speleothems: Origin and Types 24.3 History of Speleothems’ Microbiome 24.4 Methods to Study Speleothems’ Microbiome 24.4.1 Culture-Dependent Methods 24.4.2 Culture-Independent Methods 24.5 Microbes Reported from the Caves References 25. Microbiome of Marine Shallow-Water Hydrothermal Vents 25.1 Introduction 25.2 Difference between Deep-Sea and Shallow-Water Hydrothermal Vents 25.3 Life at Shallow-Water Hydrothermal Vents 25.4 Microbiome Studies in Shallow-Water Hydrothermal Vents 25.5 Role of Microorganisms in Shallow-Water Hydrothermal Vents 25.6 Biotechnological Applications of Hydrothermal Vent Microorganisms 25.7 Concluding Remarks Acknowledgments References 26. Diversity and Bioprospecting Potentials of Antarctic (Polar) Microbes 26.1 Introduction 26.1.1 Microbial Diversity in Extreme Environments 26.1.2 The Polar Environments (Cryosphere) 26.1.3 Psychrophiles – Cryosphere Microbes 26.2 Antarctica 26.3 Microbial Diversity in Antarctica 26.3.1 Bacteria 26.3.2 Actinobacteria 26.3.3 Fungi 26.3.4 Algae 26.4 Bioprospecting Potentials of Antarctic Microbes 26.5 Bioactive Compounds/Products 26.5.1 Enzymes 26.5.2 Proteins 26.5.3 Pigments 26.5.4 Biosurfactants 26.5.5 Polysaccharides 26.5.6 Nanoparticle synthesis 26.6 Polar Microbial Research: Opportunities and Challenges Acknowledgment References 27. Alterations in Microbial Community Structure and Function in Response to Azo Dyes 27.1 Introduction 27.2 Azo Dyes and Their Hazards 27.3 Mechanisms of Microbial Azo Dye Reduction 27.3.1 Oxidative Mechanism of Decolorization 27.3.2 Reductive Mechanism of Decolorization 27.3.3 Alternative Oxidative-Reductive Mechanisms for Decolorization 27.3.4 Acceleration of Dye Reduction by Redox Mediators: Artificial and Biological 27.4 Importance of Microbiome Interaction in Bioremediation 27.4.1 Plant-Microbe Interaction 27.4.2 Metal-Microbe Interaction 27.4.3 Soil-Microbe Interaction 27.4.4 Microbe-Microbe Interaction 27.5 Dye-Induced Microbial Community Shifts and Adaptations 27.5.1 In Soil 27.5.2 In Bioreactors 27.5.3 In the Human Intestine 27.5.4 In Microbial Fuel Cells 27.6 Role of Microbes in Natural Remediation of Dyes in Rivers and Sediments 27.7 Prospective Implications of Microbial Cooperation in Dye Reduction 27.8 Summary Abbreviations References 28. Soil Microbiome 28.1 Introduction 28.2 Benefits of the Soil Microbiome 28.2.1 Regulation of Greenhouse Gases 28.2.2 Food Security and Agriculture 28.2.3 Assessing the Soil Microbiome 28.2.3.1 Technologies to Study the Soil Microbiome 28.2.3.2 Indicators for Soil Health 28.2.4 Pressures on the Soil Microbiome 28.2.4.1 Farming 28.2.4.2 Urbanization 28.2.4.3 Climate Change 28.2.5 Restoring the Soil Microbiome 28.2.5.1 Incentivizing Good Practice 28.2.5.2 Targeted Approaches 28.2.5.3 Changing Land-Management Practices 28.2.5.4 Degradative Mechanisms of Persistent Organic Pollutants by Soil Microbes 28.2.5.5 Plant Breeding and Microbiome Engineering 28.2.5.6 Role of Microbial Enzymes and Encoding Genes 28.2.6 Social Interactions of Soil Microbes 28.2.6.1 Quorum Sensing 28.2.6.2 Biofilms 28.2.7 Conditions of Soil Environment 28.2.8 Bioremediation 28.2.8.1 Indigenous Microbes 28.2.8.2 Bioavailability of Pollutants and Biosurfactants 28.9 Conclusions References Index "Microbiome a promising and fascinating subject in the modern Biology. It integrates the microbial communities in human, animal, plant and environment. In human, the microbiota associated with gut, skin, genital organs, oral and respiratory organs. Plant microbial community is referred as 'holobiont' exerted in maintenance and health of the plants further it influenced its role in the animal health and environment. The contents of the Microbiome and Host Interactions book covered all area and new research trends in the fields of plant, animal, human and environmental microbiomes and their interactions. This book covered the details about the microbiome in soil environment to polar (Antarctic) microbiota, microbiome role in health and disease, microbiota functions in Caenorhabditis elegans, mycobiome in agroecosystem, rice root and actinorhizal root nodule microbiome, speleothems, microbiome of marine shallow water hydrothermal vents. Moreover, this book also provides a comprehensive account on advanced Next-Generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing and understand nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial and archaeal communities using QIIME software (Quantitative Insights Into Microbial Ecology). Salient features: Summarize the recent insight in the Microbiome and host interactions in distinct habitat including antarctic, hydrothermal vents water, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forest and mangroves. Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, multivariate analysis commonly used for microbiome analysis. Describe the probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, microbial communities in the reproductive tract of human and animals. Information presented in a reachable way for valuable to students, teachers, researchers, microbiologists, computational biologist and other professionals who interested to strengthen and enlarge their knowledge about microbiome analysis by with Next-Generation DNA Sequencing in different branches of sciences"-- Provided by publisher "Microbiome a promising and fascinating subject in the modern Biology. It integrates the microbial communities in human, animal, plant and environment. In human, the microbiota associated with gut, skin, genital organs, oral and respiratory organs. Plant microbial community is referred as 'holobiont' exerted in maintenance and health of the plants further it influenced its role in the animal health and environment. The contents of the Microbiome and Host Interactions book covered all area and new research trends in the fields of plant, animal, human and environmental microbiomes and their interactions. This book covered the details about the microbiome in soil environment to polar (Antartic) microbiota, microbiome role in health and disease, microbiota functions in Caenorhabditis elegans, mycobiome in agroecosystem, rice root and actinorhizal root nodule microbiome, speleothems, microbiome of marine shallow water hydrothermal vents. Moreover, this book also provides a comprehensive account on advanced Next-Generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing and understand nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial and archaeal communities using QIIME software (Quantitative Insights Into Microbial Ecology). Salient features: Summarize the recent insight in the Microbiome and host interactions in distinct habitat including antarctic, hydrothermal vents water, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forest and mangroves. Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, multivariate analysis commonly used for microbiome analysis. Describe the probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, microbial communities in the reproductive tract of human and animals. Information presented in a reachable way for valuable to students, teachers, researchers, microbiologists, computational biologist and other professionals who interested to strengthen and enlarge their knowledge about microbiome analysis by with Next-Generation DNA Sequencing in different branches of sciences"-- .Résumé de l'éditeur