Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior

The quest to manipulate microbiomes has intensified, but many microbial communities have proven to be recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping microbiomes by advancing an understanding of community interactions. We developed a model community with representatives from three dominant rhizosphere taxa, the , , and We chose as a model rhizosphere firmicute and characterized 20 other candidates, including "hitchhikers" that coisolated with from the rhizosphere. Pairwise analysis produced a hierarchical interstrain-competition network. We chose two hitchhikers, from the top tier of the competition network and from the bottom of the network, to represent the and , respectively. The model community has several emergent properties, induction of dendritic expansion of colonies by either of the other members, and production of more robust biofilms by the three members together than individually. Moreover, produces a novel family of alkaloid antibiotics that inhibit growth of , and production is inhibited by We designate this community THOR, because the members are he itchhikers f the hizosphere. The genetic, genomic, and biochemical tools available for dissection of THOR provide the means to achieve a new level of understanding of microbial community behavior. The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and genetically tractable model community would be useful to dissect microbiome assembly, maintenance, and processes. We have developed a tractable model rhizosphere microbiome, designated THOR, containing , , and , which represent three dominant phyla in the rhizosphere, as well as in soil and the mammalian gut. The model community demonstrates emergent properties, and the members are amenable to genetic dissection. We propose that THOR will be a useful model for investigations of community-level interactions.