Microorganisms Genome Enrichment and Amplification Sequencing (MGEAS)

Recent evidence shows that the cleanrooms 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. Current metagenomics 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. MGEAS addresses these issues with 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 optimization for reads classification and genome assembly. As part of the phase I project ChromoLogic i) successfully evaluated two state-of-the-art genome amplification or enrichment techniques for NGS library preparation. ii) optimized kmers and various bioinformatics parameters for microbial taxa classification based on raw reads and iii) provided taxa reports for JPL environmental samples (wipes and swabs) and identified taxa with radiation, disinfectant resistance. In Phase II we propose to combine our achievements with a) the novel use of SMART accessory blocks for lab-work automations, and various techniques to improve nucleic acids yield and assay repeatability, b) state of the art DNA preparations, enrichment and amplifications followed by NGS sequencing, and c) Bioinformatics pipeline optimization for reads classification, genome assembly and adjacent DNA linked reads sequencing (Hi-C) for radiation/disinfectant resistant elements origin tracing (in species and environments). We will also expand our statistical modeling tests to improve accuracy and sensitivity of assays to fit NASA needs and we will build interactive software visualization tools for easier user navigation of taxa data and sample statistics. To our knowledge, this is the first application of 2bRAD-M and TruePrime MDA technology in ultra-low biomass samples of NASA’s Jet Propulsion Laboratory.  Upon successful validation of these techniques, the more accurate species classifications and taxa abundance estimates they provide will pave the way for NASA planetary protection biological risk modeling and other microbe detection markets areas, such as real time pathogen identification for the medical care industry and microbial monitoring for pharmaceutical manufacturers. Main objectives of the work to be done:   Objective 1. Optimize MGEAS sample preparation subsystem for efficient sample collection, concentration and nucleic acid extraction.   Objective 2. Optimize MGEAS NGS (Next Generation Sequencing) library preparation and analytical subsystems for rapid, accurate and reproduceable metagenomics.   Objective 3. Reconstruct the reference database to minimize biases and improve the accuracy of classification and abundance estimation.   Objective 4. Expand statistical modeling and integrate it with historical culture-based based data to improve risk assessment modeling.   Objective 5. Develop interactive software tools and visualization techniques to foster taxa discovery and the comparison of samples over time and across locations.   Proposed deliverables to NASA at the end of the contract:   1. Market Requirement document that will specify how MGEAS would service the needs of NASA Planet Protection program.   2. Validation data that specifies the performance of MGEAS. This will include the sensitivity, specificity and accuracy of the system.   3. Demonstration and cross validation of MGEAS capability to NASA stake holders.   4.Interim and final reports, prototypes for commercialization.  

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. MGEAS tech has potential applications in the medical device field as a point-of-care (POC) deep DNA/RNA sequencing service for real-time pathogen identification.  MEGAS technology can also be useful for pharmaceutical manufacturer’s environmental monitoring programs where the technology can be marketed as a rapid way to identify microbes found as part of their environmental monitoring procedures.

This is early/mid-stage (TRL 4) — the most realistic path in is NASA SBIR/STTR, which funds small businesses and research institutions to develop technology aligned with NASA's needs (equity-free, phased funding). Check whether a current SBIR/STTR solicitation topic overlaps with this project's technology area, or contact the project directly (above) to ask.

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