1. Part I: Microbiome of Finfish 1: Introduction to Finfish Microbiome and Its Importance 1.1 Introduction 1.2 Techniques Used to Study the Microbiota 1.2.1 Culture-Dependent Techniques 1.2.2 Molecular Techniques 1.2.3 Next-Generation Sequencing 1.2.4 ``Omics´´ Technologies 1.2.5 Use of Gnotobiotic Fish 1.3 Finfish Microbiome 1.3.1 Microbe-Microbe Interactions 1.3.1.1 Prebiotics 1.3.1.2 Probiotics 1.3.1.3 Antibiosis 1.3.2 Microbe-Host Interactions 1.3.2.1 Immunity 1.3.2.2 Nutrition (Animal Productivity) 1.3.2.3 Health 1.4 Effect of Anthropogenic Substances on the Gut Microbiota of Finfish 1.5 Importance of the Fish Microbiome 1.6 Conclusion References 2: Isolation and Identification of Fish Gut Microbiome 2.1 Introduction 2.2 Sample Collection from Different Geographical Locations 2.3 Procedures for Bringing the Samples to the Laboratory for Analysis 2.4 Dissection and Removal of Different Parts of the Gut System 2.5 Isolation of Microbes and Determine the Complexity of Composition 2.6 Identification Based on Molecular Gene Structure (Use of Conventional and Advanced Methods of NGS or Any Other Latest Meth... 2.7 Differentiation of Genetic Composition and Their Interpretation of Pathogenic and Healthy Microbes Based on Their Genetic ... 2.8 Data Collection and Development of Microbiome Libraries Using Adequate Software 2.8.1 Metatranscriptomics, Metaproteomics, and Metabolomics 2.9 Use of Such Data Libraries for Undertaking Metagenomic Studies References 3: Gut Microbiome and Fish Health: An Overview in Finfish Aquaculture Prospective 3.1 Introduction 3.2 Ontogenetic Characterization of the Intestinal Microbiota 3.3 Gut Microbiome of Aquacultured Finfishes 3.4 Gut Microbiota and Fish Health 3.4.1 Gut Microbiota and Immune Response 3.4.2 Gut Microbiota Correlates with Occurrence of Diseases in Finfish 3.5 Modulation of Fish Gut Microbiota for Improved Health: Supplementation of Synbiotics 3.6 Conclusion References 4: Fish Microbiome and Metagenomics 4.1 Introduction 4.2 Gut Microbiota of Marine Fishes 4.3 Factors Influencing the Diversity and Function of the Gut Microbiome of Fish 4.4 Host Habitat or Environment 4.5 Salinity of the Sampling Site 4.6 Fish Diet 4.7 Host Immunity Status 4.8 Role of the Fish Gut Microbiome 4.9 Microbiome and Aquaculture Productivity 4.10 Metagenomics 4.11 Significance of Metagenomics in Aquaculture 4.12 Role of the Microbiome in Fish Health 4.13 Specific Host Receptor Activation by Chemicals from Microorganisms References 5: Ready Reckoner for Using Bioinformatics Tools in Fish and Shellfish Microbiome Analysis 5.1 Introduction: Microbiome Analysis in Fish and Shellfish 5.1.1 Factors Influencing the Microbiome in Fish and Shellfish 5.1.2 Ontogeny of the Microbiome in Fish and Shellfish 5.1.3 Challenges and Future Perspectives in Metagenomics 5.2 Fish Microbiome Diversity and Metagenomics 5.2.1 Introduction to Fish Microbiome 5.2.2 Significance of Fish Microbiome 5.2.3 Early Research in Fish Microbiome Analysis 5.2.4 Metagenomics in Fish Microbiome 5.3 Shellfish Microbiome Diversity and Metagenomics 5.3.1 Introduction to Shellfish Microbiome 5.3.2 Importance of Shellfish Microbiome 5.3.3 Early Research in Shellfish Microbiome Analysis 5.3.4 Metagenomics in Shellfish Microbiome 5.4 Bioinformatics Skills in Fish and Shellfish Microbiome Research 5.4.1 Computational Protocol for Microbiome Acquisition 5.4.1.1 Target Gene Approach Taxonomy Functional Annotation Data Visualization 5.4.1.2 Shotgun Metagenomics Approach Quality Filtering Reference-Based Analysis Taxonomy Functional Annotation Assembly-Based Analysis Contig Assembly Assembly Statistics Comparative Analysis Binning Refinement 5.4.2 Taxonomic Profile Based on 16S Amplicon Data 5.4.2.1 Picking Operational Taxonomic Units 5.4.2.2 Assigning Taxonomy 5.4.2.3 Measuring Alpha and Beta Diversity 5.4.3 Application of NGS Technologies in Recent Studies of Fish Gut-Associated Microbiota 5.4.3.1 Illumina Sequencing Platforms 5.4.3.2 Roche Platforms 5.4.3.3 Ion Torrent PGM 5.4.3.4 PacBio Sequencers 5.4.3.5 Oxford Nanopore Technologies 5.4.3.6 Other NGS Platforms 5.4.4 Functional Profile Based on Metagenomic and Metatranscriptomic Data 5.4.4.1 Gene Prediction and Functional Gene Annotation 5.4.4.2 Assigning Taxonomy 5.4.4.3 Genome Assembly from Metagenomic Data 5.4.5 Hypothesis-Driven Functional Analyses 5.4.5.1 Homology-Based Tools 5.4.5.2 Motif- or Pattern-Based Tools 5.4.5.3 Context-Based Tools 5.4.5.4 Other Functional Predictions 5.4.6 Assembly-Independent Strain-Level Characterization 5.4.7 Long-Read Sequencing and Other Advances 5.4.8 Machine Learning and Data Science 5.4.9 Systems Biology Approaches to Understand the Host-Microbiome Interactions 5.5 Microbiome Research and Development of Probiotics, Aquaculture Sector and Bioindustry References 6: Microbiome Applications for the Growth and Development of the Aquaculture/Biopharma Industry 6.1 Introduction 6.2 Fish and Shellfish Gut Microbiome and Their Ingredients 6.3 Fish and Shellfish Gut Microbiomes and Their Functionality 6.4 Metagenomics of the Microbiome and the Aquaculture Industry 6.5 Gut Microbiomes Controlling the Outbreak of Diseases and the Health of the Cultivable Organisms 6.6 Microbiome and Probiotic Development 6.7 Bioinformatics Skills in Microbiome Research for Augmenting the Aquaculture Industry 6.8 Conclusions References Part II: Microbiome of Shellfish 7: Shellfish Microbiome 7.1 Introduction 7.2 Shellfish 7.3 Types of Shellfish 7.3.1 Crustaceans 7.3.1.1 Shrimp 7.3.1.2 Lobsters 7.3.1.3 Crab 7.3.2 Mollusks 7.3.2.1 Bivalves Clams Mussels Oyster Scallops 7.3.2.2 Cephalopods Octopus Squid Cuttlefish 7.3.2.3 Gastropods Abalone Conch Snails 7.3.3 Echinoderms 7.3.3.1 Sea Urchin 7.4 Shellfish Microbiome 7.4.1 Microbiome 7.4.2 Crab 7.4.3 Chinese Mitten Crab (Eriocheir sinensis) 7.4.4 Horseshoe Crab (Limulus polyphemus) 7.4.5 White Shrimp (Litopenaeus vannamei) 7.5 Conclusion References 8: Shellfish Microbiome and Its Significant Role in Immune Response and Health Management 8.1 Introduction 8.2 Microbial Diversity and Microbiome Study 8.3 Gut Microbiome Composition in Shellfish 8.4 Factors Effecting Microbial Diversity 8.5 Host-Microbiome Interaction 8.6 Pathobiome/Signature Microbiome 8.7 Probiotics Role for Healthy Gut Microbiota 8.8 Heterotrophic Production System 8.9 Growth Enhancement and Microbial Colonization 8.10 Microbial Community and Health Management 8.11 Conclusion References 9: Shrimp Health and Microbiome 9.1 Introduction 9.2 Shrimp Culture Environment: A Microbial Perspective 9.2.1 Shrimp Aquaculture and Diseases 9.2.2 Major Diseases of Shrimp 9.2.2.1 Bacterial Diseases 9.2.2.2 Viral Diseases 9.2.2.3 Other Microbial Diseases 9.2.2.4 Diseases of Unknown Etiology 9.3 Shrimp Microbiome and Its Role in Health and Disease 9.3.1 Microbiome of Farmed Shrimp 9.3.2 Vibrio Species in Health and Diseases of Shrimp 9.3.3 Sequence-Based Microbiome of Shrimp 9.3.4 Biofloc-Associated Microbiome 9.3.5 Microbiome of Shrimps Farmed in Inland Saline Water 9.4 Microbiome and Disease Prediction 9.5 Conclusions References 10: Microbial Metagenomics and the Shellfish Microbiome 10.1 Introduction 10.2 Shellfish Symbionts 10.3 Shellfish Disease 10.4 Environmental Influence on Community Function 10.5 Applied Metagenomics 10.6 Conclusions References 11: Shellfish Microbiome and Probiotics: A Decade in Review 11.1 Introduction 11.2 Bioprospecting and Production 11.2.1 Probiont Isolation 11.2.2 Desired Probiotic Characteristics 11.2.3 Commercial Production 11.3 Commonly Used Probiotics 11.3.1 Bacillus 11.3.2 Lactic Acid Bacteria 11.3.2.1 Other Probiotic Organisms 11.3.3 The Consortia Effect 11.4 Mechanisms of Action 11.4.1 Improvement in Water Quality 11.4.2 Competitive Exclusion 11.4.3 Digestion and Nutrient Assimilation 11.4.4 Immunomodulatory Capability 11.4.5 Microbiome Manipulation 11.5 Beyond Probiotics 11.5.1 Synbiotics 11.5.2 Paraprobiotics 11.5.3 Living Therapeutics 11.6 Conclusions References 12: Impact of Climate Change on the Gut Microbiome of Fish and Shellfish 12.1 Introduction 12.2 Fish Gut Microbiome 12.2.1 The Influence of Environmental and Host-Related Intrinsic Factors 12.2.1.1 Host-Specific Intrinsic Factors 12.2.1.2 Impact of Trophic Level 12.2.1.3 Impact of Season 12.2.2 Microbial Composition of Fish in Wild and Captive Conditions 12.2.2.1 Variations Within a Species at Different Geographical Locations 12.2.3 Colonization and the Factors Affecting the Fish Gut Microbiome 12.2.3.1 Environment and Host-Microbe Interactions 12.2.4 Impact of Climate Change on Shellfish Gut Microbiome 12.2.5 Microbial Composition in Wild and Domesticated Shrimp 12.2.6 Microbial Composition in Diseased Shrimp 12.2.7 Changes in the Gut Microbiome and the Incidence of Disease 12.2.8 Gut Microbiota of Oysters and Mussels 12.2.8.1 Impact of Thermal Stress 12.2.8.2 Freshwater Mussel 12.3 Conclusions