Biosynthetic pathways that make secondary metabolites are widespread amongst bacteria, which naturally live in complex mixed assemblages in the environment. The resulting small molecules may play many roles in intra- and inter-species interactions, and likely confer a survival advantage to the producing bacterium. The extent of chemical diversity produced in nature is likely under explored because many pathways remain silent in isolated strains under laboratory conditions and the majority of bacteria are recalcitrant to culture. Bacterial communities, however, 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, along with the integration of metatranscriptomic data with de novo assemblies. These methods were used to assemble bacterial symbiont genomes in two model systems, the tunicate Lissoclinum sp. and the bryozoan Bugula neritina, providing insights into the producing organisms and biosynthetic pathways for the mandelalides and the bryostatins (both trans-AT PKS systems), respectively. Several other bacterial genomes were assembled from B. neritina, and the behavior of the whole microbiome was investigated with metatranscriptomics. The bioinformatic workflows presented will be used in the future to investigate the dynamics of natural product biosynthesis in native systems, to potentially shed light on the roles of small molecules in complex bacterial communities.