NSF Award
2426904
Understanding the microorganisms that live together in an environment, known as the microbiome, and how they convert hundreds to thousands of chemicals is critical for revealing their impact on biological systems and improving any microbiome applications, from probiotic supplements to waste treatment technologies. This project aims to uncover the interactions between microbes using a new approach that combines experiments, scientific and engineering principles, and computer simulations. Recent biotechnological advances have allowed scientists to study microbiomes in great detail. Microbial members, their genes, and the molecules present in an environment can be identified. However, despite the wealth of microbiome data, it is still challenging to directly determine how different groups of microbes interact due to the complexity of these communities. This project aims to overcome this challenge and apply a new approach to a new waste treatment technology – Rewired Anaerobic Digestion (RAD). RAD shifts from producing traditional biogas, which primarily consists of methane and CO2, to sustainably producing more valuable chemicals such as butyric acid, a biofuel precursor. In addition to scientific advances, this project will also support the development of a Course-based Outreach and Research Experience (CORE) at Colorado State University. CORE will enable undergraduate students to gain hands-on experience in both scientific research and science communication. The research component of CORE is a laboratory class where students conduct research and learn how to isolate and culture of microbial communities. The outreach component involves students in communicating science to the public and stakeholders of the RAD technology. The project will track whether these experiences improve students’ awareness, retention and readiness for careers in integrative biotechnology.<br/><br/>Multi-omics has become a powerful approach in revealing what microbial members, functions, and molecules are present in the microbiome. However, multi-omics data does not directly indicate what individual groups of microbes are doing and how they evolve to function and interact in a specific way. The overarching goal of this research project is to develop a novel microbiome modeling platform that integrates omics data, thermodynamics principles, metabolic models, and artificial intelligence to unravel the metabolism, interactions, and evolution of microbiomes. The modeling approach, coupled with omics data generated from RAD reactors and enrichment cultures, will be applied to address specific research questions regarding the RAD microbiome metabolism: (1) identify the butyric-acid-producing microbes, their interacting members, and the metabolites through which they interact; (2) simulate how the RAD microbiome evolves using a novel artificial intelligence algorithm; and (3) test whether thermodynamic driving force determines the microbial division of labor within the microbiome. The project will result in a generalizable integrated experiment-modeling approach for studying microbiomes and reveal principles of microbiome interactions that could also inform other systems such as the butyrate production in the gut microbiome. The knowledge and predictions generated will suggest new strategies for optimizing the product profile of RAD.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
