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Table of Contents
Preface; Contents; Contributors; About the Editors; Part I: Next Generation Sequence Technology; 1: The Omics Era and Host Microbiomes; 1.1 Introduction; 1.2 The Human Microbiome; 1.3 The Plant Microbiomes; References; 2: Uncultivated Lineages and Host-Microbe Interaction in Saline Environment; 2.1 Introduction; 2.2 Culture-Independent (Meta-analysis) Approaches; 2.2.1 Metagenomics; 2.2.1.1 Holobionts and Hologenomes ; 2.2.2 Metatranscriptomics; 2.2.3 Metaproteomics; 2.3 Habitats and Host-Microbe Interaction
2.4 Analysis of the Host-Microbe Interaction by Metagenomics, Metatranscriptomics, and Metaproteomics2.5 Detection of Phylogenetic Marker; 2.5.1 Reference Species for Host-Microbe Interaction; 2.6 Detection of Host-Microbe Interaction by Various Techniques Is Displayed in Table 2.1; References; 3: Exploring Metagenomes Using Next-Generation Sequencing ; 3.1 Metagenomics: A Step Ahead in Microbial Ecology; 3.2 Approaches to Study Metagenomes; 3.2.1 Shotgun Metagenomics; 3.2.2 Targeted Metagenomics; 3.2.2.1 Bacterial Community Profiling Through 16S Amplicon Sequencing
3.2.2.2 Fungal Community Profiling Through ITS, LSU and SSU Amplicon Sequencing3.3 Metatranscriptomics (RNA Transcript Sequencing); 3.4 Next-Generation Sequencing Technologies for Metagenomics; 3.4.1 Roche 454 Sequencing (GS20, GS-FLX, GS-FLX Titanium, GS-FLX Titanium Plus); 3.4.2 Illumina Sequencing (GA I, GA II, HiSeq, MiSeq, NextSeq 500, HiSeq 2500, HiSeq X Ten); 3.4.3 Applied Biosystem's SOLiD; 3.4.4 Ion Torrent Sequencing (PGM, Proton, S5); 3.4.5 Pacific Biosciences (PacBio RS II); 3.4.6 Oxford Nanopore Sequencing; 3.4.7 Irys Technology of BioNano Genomics
3.5 Basic Steps in Metagenomic Data Analysis3.6 Future of Metagenomics; References; 4: Metagenomics: An Era of Throughput Gene Mining; 4.1 Introduction; 4.2 Gene Mining from Soil Metagenome; 4.3 Gene Mining from Marine Metagenome; 4.4 Metagenomic Approaches for Gene Mining; 4.4.1 Sequence-Based Approach; 4.4.2 Functional-Based Approach; References; 5: Prospects and Progress in Extreme Biosphere Microbiome; 5.1 Extremophiles and Extreme Environments; 5.2 Metagenomics and Microbial Diversity; 5.3 Environmental Metagenomics; 5.4 Challenges in Environmental DNA Extraction
5.5 Sequencing Platforms5.5.1 PacBio Sequencing; 5.5.2 Oxford Nanopore Sequencing; 5.6 Future Prospects; References; Part II: Human Microbiome; 6: 16S rRNA Metagenomics of Asian Gut Microbiota; 6.1 Introduction of Asian Microbiome Project (AMP); 6.2 Phase I Pilot Study (Nakayama et al. 2015); 6.2.1 Bacterial Composition and Enterotype Clustering of 303 Children Samples; 6.2.2 Predicted Function of Each Enterotype Community; 6.2.3 Local Variation Associated with Country; 6.3 Comparison of 16S rRNA Metagenomic Data from MiSeq Platform to that from 454 Platform
2.4 Analysis of the Host-Microbe Interaction by Metagenomics, Metatranscriptomics, and Metaproteomics2.5 Detection of Phylogenetic Marker; 2.5.1 Reference Species for Host-Microbe Interaction; 2.6 Detection of Host-Microbe Interaction by Various Techniques Is Displayed in Table 2.1; References; 3: Exploring Metagenomes Using Next-Generation Sequencing ; 3.1 Metagenomics: A Step Ahead in Microbial Ecology; 3.2 Approaches to Study Metagenomes; 3.2.1 Shotgun Metagenomics; 3.2.2 Targeted Metagenomics; 3.2.2.1 Bacterial Community Profiling Through 16S Amplicon Sequencing
3.2.2.2 Fungal Community Profiling Through ITS, LSU and SSU Amplicon Sequencing3.3 Metatranscriptomics (RNA Transcript Sequencing); 3.4 Next-Generation Sequencing Technologies for Metagenomics; 3.4.1 Roche 454 Sequencing (GS20, GS-FLX, GS-FLX Titanium, GS-FLX Titanium Plus); 3.4.2 Illumina Sequencing (GA I, GA II, HiSeq, MiSeq, NextSeq 500, HiSeq 2500, HiSeq X Ten); 3.4.3 Applied Biosystem's SOLiD; 3.4.4 Ion Torrent Sequencing (PGM, Proton, S5); 3.4.5 Pacific Biosciences (PacBio RS II); 3.4.6 Oxford Nanopore Sequencing; 3.4.7 Irys Technology of BioNano Genomics
3.5 Basic Steps in Metagenomic Data Analysis3.6 Future of Metagenomics; References; 4: Metagenomics: An Era of Throughput Gene Mining; 4.1 Introduction; 4.2 Gene Mining from Soil Metagenome; 4.3 Gene Mining from Marine Metagenome; 4.4 Metagenomic Approaches for Gene Mining; 4.4.1 Sequence-Based Approach; 4.4.2 Functional-Based Approach; References; 5: Prospects and Progress in Extreme Biosphere Microbiome; 5.1 Extremophiles and Extreme Environments; 5.2 Metagenomics and Microbial Diversity; 5.3 Environmental Metagenomics; 5.4 Challenges in Environmental DNA Extraction
5.5 Sequencing Platforms5.5.1 PacBio Sequencing; 5.5.2 Oxford Nanopore Sequencing; 5.6 Future Prospects; References; Part II: Human Microbiome; 6: 16S rRNA Metagenomics of Asian Gut Microbiota; 6.1 Introduction of Asian Microbiome Project (AMP); 6.2 Phase I Pilot Study (Nakayama et al. 2015); 6.2.1 Bacterial Composition and Enterotype Clustering of 303 Children Samples; 6.2.2 Predicted Function of Each Enterotype Community; 6.2.3 Local Variation Associated with Country; 6.3 Comparison of 16S rRNA Metagenomic Data from MiSeq Platform to that from 454 Platform