GRIND: Genomic Rapid Inspection of Non-abundant bacteria after Decontamination

This Phase I proposal focuses on advancing NASA’s planetary protection mission by introducing an innovative lysis-based sample collection tool to enhance the existing swab-based sampling procedures. NASA currently employs swabs for microbial collection on diverse surfaces, followed by concentration and a lysis technique to extract nucleic acids from low biomass samples. However, the detection of challenging-to-lyse spores remains elusive in metagenomic sequencing and other nucleic acid techniques, despite being observable through culture methods. This underscores the critical need for enhanced, efficient, and integrated sample collection and processing techniques in planetary protection. In response to this challenge, our proposal introduces the development of an automated grinding lysis system. This cutting-edge system utilizes a standard collection swab to release genomic components from difficult-to-lyse, low-biomass samples. By automating the lysis process and integrating grinding mechanisms, our approach aims to surpass the limitations of conventional techniques, ensuring a more thorough and effective collection of nucleic acids for planetary protection purposes. During the Phase I work, we will demonstrate and quantitatively benchmark this technology on various contrived surfaces, featuring a diverse set of relevant microbes. Demonstrations will include the quantification of bioburden using qPCR and the identification of unknown samples using Nanopore sequencing. This novel system has the potential to significantly enhance and streamline sample collection methodologies, especially in scenarios involving elusive spores. Through these advancements, we aim to supplement the capabilities of NASA's planetary protection efforts, contributing to a more robust and reliable approach to safeguarding celestial bodies from microbial contamination.