Shotgun Illumina sequencing is an increasingly common method of studying microbial communities as it allows estimation of functional potential and recovery of population genomes. Studying communities with metagenomics is not subject to the primer biases inherent in traditional amplicon-based approaches.
However, unlike traditional methods which group sequences into operational taxonomic units (OTUs), bioinformatic synthesis of metagenome data does not resolve sequence types and instead simply estimates abundances of taxonomic groups. This presentation will focus on the applications of SingleM, a tool for finding OTUs from metagenomes and determining microbial community structure.
Resolving community profiles into sequence-based rather than taxonomy-based groupings enables community profiles to be resolved more finely. Ecological alpha and beta diversity metrics can be calculated even for complex communities containing novel lineages, and community profiles derived from metagenome sequences can be directly linked to recovered population genomes. Comparison made between unrelated metagenomic studies can also empower genome recovery efforts. An associated NeCTAR-hosted website allows searching of >4 million distinct sequence types from thousands of public metagenomes.