Pearls and pitfalls of genomics-based microbiome analysis

Next generation sequencing (NGS) has supplanted traditional methods for microbiome analyses. Advantages include higher resolution and lower costs. Analyses have evolved from basic 16S rRNA surveys to metagenomic shotgun sequencing analyses. Limitations and obstacles still exist, e.g. 16S bias, bioinformatics bottlenecks, classification accuracies, and genome assembly using short reads. New tools are being developed to improve output and deal with larger amounts of data generated.