Integrated de novo metagenomics and metatranscriptomics to study natural products and microbial ecology in situ

Biosynthetic pathways that make secondary metabolites are widespread amongst bacteria, and the resulting small molecules presumably confer a selective advantage to producers. Because bacteria live in complex mixed communities in the environment and in association with higher host organisms, a variety of functions have been suggested for secondary metabolites. These include the suppression of competitors, modulation of behavior or communication, as well as functions that align with the interests of a eukaryotic host. Discerning the roles of small molecules in the environment may uncover therapeutically relevant bioactivities, but natural bacterial communities are hard to study as most environmental bacteria are recalcitrant to culture. These uncultured communities can be accessed directly through sequencing of environmental DNA (metagenomics) or RNA (metatranscriptomics). Methods to deconvolute and assemble the genomes of multiple bacteria from metagenomes will be presented, with results from two model systems, the tunicate Lissoclinum sp. and the bryozoan Bugula neritina. In the latter system we have also integrated metatranscriptomics to give a snapshot of the global gene expression in a complex microbial assemblage.

*These authors contributed equally to this work.