Intro; Foreword; Contents; List of Contributors; About the Editors; Part I: Introductory Chapters; 1: The Microbiome: Past, Present, and Future; Past: Surprising Insights into Today's Microbial World; Present: "Democratization of Metagenomics"; Future: Microbiota-Based Therapeutics or Prevention; References; 2: Methods for Microbiota Analysis: Sample Collection and Laboratory Methods; Introduction; Microbiota Research: From Culture- to Molecular-Based Methods; High-Throughput Sequencing of 16S rRNA Genes and Whole Community Profiling; Beyond the 16S rRNA High-­Throughput Sequencing

Quantitative PCRCloning of the 16S rRNA Genes; Microbiota Array; Staining-, Histology-, and Microscopy-Based Methods; Electrophoresis-Based Methods; Flow Cytometry (FCM); Single-Cell Approaches; Combination of Various Methods in Microbiota Studies; Sample Collection and Sampling Strategies in Microbiota Studies; Sample Collection; Choice and Consequences of the Sampling Method on a Microbiota Study; Additional Sources of Variability and Sampling Design; References; 3: Analytic Methods in Microbiome Studies; Universal Marker; Sequence Preprocessing and OTU Binning; Merging and Trimming

Chimera Detection and DenoisingOTU Binning; Classification, Taxonomic Assignment, and Phylogenetic Inference; Phylogenetic Inferences; Diversity Analysis; Alpha and Beta Diversity; Comparing Samples Using Diversity Estimates; Correlating Species with Habitats; Indicator Species Analysis; Differential Abundance (DA) Analysis Based on Count Data; Network Analysis of Co-occurrence/Co-abundance Relationships; Functional Imputation of Amplicon Data; References; Part II: Immunogenetics of the Host Response to Infection; 4: Immunodeficiency and Autoimmunity; Introduction

Autoimmunity due to Quantitative T Cell DefectsDeficiency in Development of Central Tolerance due to Defects in Thymic Education; Autoimmunity due to Defects in Treg Development; Autoimmunity by Haploinsufficiency of Immunoregulatory Genes; Autoimmunity from Dominant Gain-of-Function (GOF) Mutations; Autoimmunity with Selective B Cell Deficiencies; Summary; References; 5: Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases; Background; Innate Recognition of the Microbiota; Interaction of Adaptive Immunity with the Microbiota

Implications for Etiology of RAConcluding Remarks: The Implicated Immunological Mechanisms; References; 6: Animal Models of Rheumatoid Arthritis; Introduction; History of Animal Models of RA; Animal Models of RA; Adjuvant-Induced Arthritis in the Rat; Collagen-Induced Arthritis in the Rat and Mouse; Antigen and/or Antibody-Induced Arthritis Models; Genetically Modified Models of Spontaneous Arthritis; Animal Models Exploring the Role of Microbe-Induced Inflammation in RA; Conclusions: Translating Animal Work to Human Disease; References; Part III: Infectious Agents