Development of a Novel Biosensor to AccelerateInvestigations of the Gut Microbiome.

PROJECT SUMMARY / ABSTRACT In recent years it has become clear that the human gut microbiome has significant potential to influence health, resulting in intense research interest in areas related to human physiology, including immunology, metabolism, neurodegenerative disease, cancer, and infectious disease. However, despite thousands of published studies linking changes in the microbiome to disease, clinical outcomes, and therapeutic response, clinical translation has been minimal. No FDA-approved microbiome-based therapies or drugs exist, and patients and their doctors have no proven way to leverage their microbiome for improved health. A critical barrier preventing translation is that most microbiome studies only analyze infrequent ‘snapshot’ measurements of the microbial gut community and do not capture the daily variations caused by diet, medical interventions, disease states, environment, or behavior—despite clear scientific evidence that these day-to-day variations are critical to discovery. Collection of dense, time-longitudinal samples from trial participants is an ideal solution to this problem, but to date, there are no existing tools for sample collection outside of collection kits, which suffer from poor patient adherence and are too expensive to be useable for longitudinal collection. Until this is resolved, the pace of microbiome research will remain glacial. Therefore, we have developed a prototype of a novel biosensor specifically to solve the patient adherence and cost concerns, and thereby dramatically accelerate all microbiome research, with significant long-term implications for human health and welfare. Our specific aims are (#1) validate the microbial lysis function of the prototype biosensor using three key metrics: accuracy, precision, and cross-contamination, and (#2) validate the DNA isolation function of the prototype biosensor using the same key metrics: accuracy, precision, and cross-contamination. Upon conclusion, we will have validated the prototype, allowing us to finalize engineering architecture and begin human trials. The contribution is significant as the components to be validated are critical for the biosensor due to their impacts on the accuracy and robustness of the data produced as well as their integral role in ensuring automated and low-cost functionality – given the nature of the device, both equally necessary for successful development. The proposed project is innovative as it is supporting development of a tool to perform complex biochemical processes in the patient home, not a laboratory, which will result in functionality that has no remotely similar predicates available. The device will make microbiome data collection a routine, low-cost exercise, offering a truly unique tool that is applicable to any and all research involving human subjects, even those without direct microbiome-related hypotheses. Thus, the potential impact of the device is significant, encompassing any novel biomarkers, diagnostics, therapeutics, or other interventions that are discovered or confirmed using the data that will become available to researchers.PROJECT NARRATIVE Microbiome research is limited by a fundamental challenge – the microbiome is dynamic, complex, and variable, which sharply limits the ability of scientists to make novel discoveries without dense, time-longitudinal data, but existing data generation tools are so expensive and difficult to use that most studies are forced to rely on limited, biased ‘snapshots’ of the microbiome. This proposal aims to support development of a novel, fully automated, low-cost biosensor that will enable dense time-longitudinal microbiome data generation for a fraction of the cost and difficulty of current, highly manual tools. The completed biosensor will empower investigators with continuous data on patient microbiome compositions during clinical trials, exponentially increasing the level of data available for analysis, revolutionizing how microbiome research is conducted and dramatically accelerating its progress towards a core component of precision medicine.