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

This Phase II proposal advances NASA's planetary protection mission by developing an innovative lysis-based sample collection tool that significantly enhances current swab-based procedures. While NASA's existing protocol uses swabs for microbial collection followed by the NASA standard assay, this method struggles to detect low biomass, unculturable species, and microbial dark matter. Spores are resilient to the extreme conditions of space, and though culturable, often remain undetected in metagenomic sequencing and other nucleic acid-based analyses, creating a critical gap in planetary protection protocols. Our solution builds upon our successful automated grinding lysis system developed in Phase I. This integrated platform combines traditional swab collection with novel mechanical disruption to effectively release genomic material from difficult-to-lyse, low-biomass samples. By automating and optimizing the lysis process through precision grinding mechanisms, our system overcomes the limitations of conventional techniques, ensuring more comprehensive nucleic acid extraction for planetary protection applications. The Phase II work will rigorously evaluate our technology against industry-standard bead beating methods through metagenomic sequencing. Our testing protocol encompasses diverse NASA-relevant surfaces—including steel, aluminum, and polycarbonate—and a broad spectrum of challenging-to-lyse, NASA relevant microbial species. We will demonstrate system effectiveness using Nanopore sequencing with Carrier-Seq, a method to enable low biomass sequencing. This innovative system promises to enable detecting and analyzing low biomass, resistant spores that currently evade standard detection methods. By enhancing the reliability and comprehensiveness of microbial detection, our technology will strengthen NASA's planetary protection capabilities, helping safeguard both Earth and celestial bodies from cross-contamination during space exploration.