Description: Recent evidence shows that the Space Assembly Facility (SAF) of Jet Propulsion Laboratory environments, such as floors and hardware surfaces, could harbor various microorganisms, and a comprehensive metagenomics framework to characterize organisms relevant to planetary protection is needed. Sequencing-based approaches, especially whole genome non-targeted metagenomics techniques, are preferred ways of microbial detection for planetary protection due to its fast turnaround time and ability to detect a broader spectrum of viable organisms. Current practices for microbe detection in low biomass samples generally do not fit well with NASA needs, due to high requirements in DNA concentration, small sample processing volumes, variability, and high predictive errors. In this project, we will tackle the problems through three modules (1) A sampling or filtration unit that process larger volumes of input solutions, (2) DNA preparations, enrichment, and amplifications followed by NGS sequencing, (3) Bioinformatics pipeline optimizations for error handling, assembly, and annotations, as well as integration with culture-based data for better risk modeling. The core technological contribution would be to validate or compare the use of two recent library preparation techniques 2bRAD-M and TruePrime MDA methods for microbiome diversity estimates. The technology is superior to 16S rRNA in the ability to detect a broader scope of microbes including virus, archaea, bacteria and fungi and other eukaryotes. This would be the first use of these technologies in JPL low biomass samples. The resulting microbe taxa estimates can guide risk-assessment modeling parameterization of planetary protection practices.

Benefits: Potential NASA applications include the detection of microorganisms before and after spacecraft missions to reduce or mitigate the possibility of inadvertent false positives, forward/backward contamination and to ensure the safety and soundness of spaceflight missions. Furthermore, increasing our ability for microbial detection in low biomass samples is also critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space flights, stations, and surface habitats.

Microbiome market is growing in the biotech industry and is expected to reach $1.3B in 5yrs. The growth is due to increasing research in microbiome science, the rising of microbiome-related diseases and the demand for personalized medicine. This technology could improve areas particularly relevant to low biomass microbiome studies. e.g neonatal disease diagnosis, deep ocean microbe communities.