High throughput sequencing methods and analysis for microbiome research

• We discuss bioinformatic tools applied to microbiomes.
• Amplicon, metagenome shotgun and metatranscriptome sequences
• Stimulate overcoming problems with sensitivity, specificity and interpretation
• Elucidate how bacteria interact with each other and their environment
• A new paradigm of microbiology and the organisms that make up most life on Earth

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.