Towards Reconstruction of Individual Gut Microbiomes.

Numerous studies have identified gut microbiome compositions and bacterial taxa associated with various host phenotypes of interest. Mechanistic study of how individual strains contribute to these phenotypes in a realistic context has remained challenging due to a lack of tools to precisely edit intact natural communities. An emerging approach to study host-microbe interactions involves the use of complex synthetic communities like hCom2 that have comparable complexity as natural microbiomes (100+ strains) and allow studies that involve the inclusion of exclusion of specific strains. Here we describe our progress towards reconstructing individual microbiomes as modular synthetic communities. By combining high-throughput enrichment and cultivation of strains and long read sequencing we are able to deeply characterize existing phylogenetic diversity within individual samples and identify efficient strategies for obtaining pure cultures of specific taxa. Future efforts will be geared towards reconstruction of microbiomes with transferrable phenotypes of interest related to human health.