title: High throughput sequencing methods and analysis for microbiome research.
abstract: High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms. We also discuss commonly used and recently developed bioinformatic tools applied to microbiomes, including analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences. This field is relatively new and rapidly evolving, thus we hope that this review will provide a baseline for understanding these methods of microbiome analyses. Additionally, we seek to stimulate others to solve the many problems that still exist with the sensitivity, specificity and interpretation of high throughput microbiome sequence analysis.
authors.affiliation: Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Di Bella
authors.forename: Yige
authors.initials: Y
authors.lastname: Bao
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Gloor
authors.forename: Jeremy P
authors.initials: JP
authors.lastname: Burton
authors.forename: Gregor
authors.initials: G
authors.lastname: Reid
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota
chemical_list: D004247:DNA
keywords: Bioinformatics; High-throughput sequencing; Metagenome; Metatranscriptome; Microbiome