EFRI-MIKS: Innovations for Next Generation Biomanufacturing and Microengineering

微生物在其栖息地之间的相互作用使微生物群落或“微生物群”能够进行超过群落中任何单个有机体的化学过程。成功地执行这种复杂的过程需要协调组成物种的新陈代谢。这种协调是通过在社区成员之间直接发送和接收信号来实现的。有些信号是间接的，比如它们的新陈代谢引起的局部环境的变化。通过了解这些信号传递过程，有可能操纵这些群落并在工业规模上利用它们的能力。低层白蚁肠道内的微生物群落就是这样一个群落。这个群落中的有机体由细菌、古生菌和原生生物组成，共生，分解木质纤维素等复杂的碳源，造福于所有人。白蚁肠道的物理和化学生境在微米级的空间尺度上变化，并影响其微生物群落的结构和功能。我们假设白蚁肠道群落的木质纤维处理能力取决于其组成、其成员的空间分布以及它们之间的相互作用。我们进一步假设，群落的维持是通过一个复杂的信号网络来调节的，该网络由细胞-细胞接触依赖信号和细胞间化学信号组成。通过了解这些过程是如何运作的，就有可能利用白蚁微生物群作为化学生产的平台。为了验证我们的假设，我们将在人造微生境中重现低层白蚁肠道的微观物理和化学特征，即人造白蚁肠道。我们将追求以下具体目标来实现我们的目标：1.元基因组学：通过对从整个群落中提取的DNA进行测序并对序列进行分析，来评估下白蚁的肠道群落。信号传递：识别关键的信号传递分子和它们相互作用的生物体，并检查它们控制的功能。建模：进行数学分析，确定S信令网的结构和控制流程。工程学：开发一种模拟黄粉菌肠道微生境的微流控培养阵列，允许进行物理化学控制和实时监测。集成：在体外建立、维护和控制具有功能的白蚁微生物群。这项工作的变革性在于对白蚁肠道信号网络的理解，并将其用于设计一个化工生产平台。通过人工白蚁肠道的开发和我们合理操纵其微生物种群的能力，工程学知识将实现重大飞跃。微生境？S种群将通过将适当的信号分子引入其供给流中或通过破坏自然的细胞间信号来操纵。这项拟议的研究将通过为新的生物燃料开发平台奠定基础来满足国家需求。我们的长期战略是开发微生境阵列，用于将木质纤维素加工成生物燃料或生物燃料生产的中间化合物，如其他能够生产乙醇或丁醇的微生物的原料。此外，我们将开展一些外展活动，包括高中教师培训倡议和关于这项研究的当地电台广播。为了接触到更广泛的受众，并提供教育补充，将在当地博物馆开发播客和研讨会和演示文稿。一个iPod/iPad应用程序和PC教育视频游戏/教育工具将被创建，并以英语和西班牙语免费提供。所有计算机代码都将是开源的，并免费提供。

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.