EFRI-MIKS: Innovations for Next Generation Biomanufacturing and Microengineering

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The interplay that occurs among microbes in their habitat allows the microbial community, or "microbiome", to carry out chemical processes exceeding that of any individual organism in the community. The successful execution of such complex processes requires a coordination of the metabolisms of the component species. Such coordination is accomplished by directly sending and receiving signals among members of the community. Some signals are indirect, such as those resulting from changes in the local environment caused by their metabolisms. By understanding these signaling processes, it may be possible to manipulate these communities and harness their capabilities on an industrial scale.The microbial community inside the gut of the lower termite represents one such community. Consisting of bacteria, archaea, and protists, the organisms in this community exist symbiotically, breaking down complex carbon sources, such as lignocellulose, to the benefit of all. The physical and chemical habitat of the termite gut varies at a spatial scale of microns and affects the structure and function of its microbial community. We hypothesize that the lignocellulosic processing capabilities of the termite gut community are dependent on its composition, the spatial distribution of its members, and their interactions. We further hypothesize that maintenance of the community is regulated through a complex signaling network composed of cell-cell contact dependent signaling and intercellular chemical signaling. By understanding how these processes function, it will be possible to harness the termite microbiome as a platform for chemical production. To test our hypotheses, we will reproduce the micro-scale physical and chemical features of a lower termite gut in manufactured microhabitats, i.e. artificial termite guts. We will pursue the following specific aims to accomplish our goal:1. Metagenomics: Evaluate the gut community of the lower termite Reticulitermes flavipes by sequencing DNA extracted from the entire community and analyzing those sequences.2. Signaling: Identify key signaling molecules and the organisms they interface with and examine the functions that they control.3. Modeling: Carry out mathematical analysis to determine the signaling network?s structure and control processes.4. Engineering: Develop a microfluidic culture array mimicking the microhabitat of the R. flavipes gut allowing physicochemical control and real time monitoring.5. Integration: Establish, maintain, and control a functional termite microbiome in vitro.Intellectual Merit. The transformative nature of this work lies in developing an understanding of the termite gut signaling network and using it to engineer a chemical production platform. A significant leap in engineering knowledge will be realized through the development of the artificial termite gut and our ability to rationally manipulate its microbial population. The microhabitat?s population will be manipulated by the introduction of appropriate signal molecules into its feed stream or through disruption of natural intercellular signals.Broader Impacts. The proposed research will address a national need by laying the groundwork for a new biofuels development platform. Our long-term strategy is to develop the microhabitat array for use in processing lignocellulose to a biofuel or to an intermediate compound for biofuel production, such as feedstock for other microorganisms capable of ethanol or butanol production. Additionally, we will carry out a number of outreach activities, including high school teacher training initiatives and local radio broadcasts about the research. To reach a wider audience, and to provide educational supplements, podcasts will be developed along with workshops & presentations at local museums. An iPod/iPad application and PC educational video game/educational tool about building an in silico functional termite microbiome will be created and made freely available in both English and Spanish. All computer code will be open sourced and made freely available.