Helicos Single Molecule Sequencing of Bacterial Genomes -- Whole Genome Sequencing of Unculturable Bacterium Using Whole Genome Amplification -- RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System -- Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing -- Discovery of Bacterial sRNAs by High-Throughput Sequencing -- Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform -- Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications -- Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities -- Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment -- Pyrosequencing of Chaperonin-60 (cpn60) Amplicons as a Means of Determining Microbial Community Composition -- Prescreening of Microbial Populations for the Assessment of Sequencing Potential -- Metagenomics -- Metagenomic Analysis of Intestinal Microbiomes in Chickens -- Gene Expression Profiling: Metatranscriptomics -- High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens -- Determining DNA Methylation Profiles Using Sequencing -- Preparation of Next-Generation Sequencing Libraries Using Nextera™ Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition -- Amplification-Free Library Preparation for Paired-End Illumina Sequencing -- Target-Enrichment through Amplification of Hairpin-Ligated Universal Targets for Next-Generation Sequencing Analysis -- 96-Plex Molecular Barcoding for the Illumina Genome Analyzer.

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the "next generation sequencing" methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes.  In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms.  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 key tips on troubleshooting and avoiding known pitfalls.   Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.