Ultra-deep shotgun sequencing

Microbiomes influence many aspects of health, but no cost-efficient method precisely characterizes a microbiome's species and genes. Deep shotgun sequencing provides strain-level taxonomic and functional resolution, but is expensive; 16S rRNA gene sequencing limits taxonomic resolution and functional predictions. We find that shallow shotgun sequencing of 500K-1M reads/sample matches ultra-deep sequencing of 2.5B reads/sample on human microbiome samples for species-level taxonomic and functional annotation and clinical biomarker discovery.