Characterizing the Deep Terrestrial Subsurface Microbiome -- Freshwater Viromes: From Sampling to Evaluation -- Characterization of Eukaryotic Microbiome using 18S Amplicon Sequencing -- Culture and Molecular Profiling of the Respiratory Tract Microbiota -- Methods and Strategies to Examine the Human Breastmilk Microbiome -- Quantification of Vitamin B12-related Proteins in Marine Microbial Systems Using Selected Reaction Monitoring Mass Spectrometry -- Single-cell Genomics of Microbial Dark Matter -- 16S rRNA Gene Analysis with QIIME2 -- Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow -- Normalization of Microbiome -- Predicting the Functional Potential of the Microbiome from Marker Genes using PICRUSt -- Using Compositional Data Analysis in Meta-transcriptomics -- Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning For Genome-resolved Metagenomics -- Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions -- Constructing and Analyzing Microbiome Networks in RBayesian Inference of Microbial Community Structure from Metagenomic data using BioMiCo -- Analyzing Metabolomic Pathways in Microbiomes -- Sparse Treatment-E_ect Model for Taxon Identi_cation with High-Dimensional Metagenomic Data.

This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of microbiome research, and the protocols described in this book are complemented with short perspectives about the history, current state, and future directions of protocols in microbiomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbiome Analysis: Methods and Protocols aims to ensure successful results in the further study of this vital field.