Shotgun metagenomics, from sampling to analysis

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging members and understanding how communities function.
Cheap, high-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methodsthat have transformed microbiology. Still, computational approaches to overcome challenges that affect both assembly-based and mapping-based metagenomic
profiling, particularly of high-complexity samples, or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offer biotechnological promise in therapeutic discovery, or innovative ways to synthesize products using microbial factories, but can also pinpoint the contributions of microorganisms to planetary, animal and human health.