SBIR Phase I: A Microbial Enrichment Device to Reduce the Cost of Sequencing Metagenomes

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) project will be the acceleration of discoveries in microbiome science by wider adoption of whole metagenomic and metatranscriptomic sequencing. These DNA and RNA sequencing techniques are the gold standard for data generation in microbiome-based drugs and diagnostics, but are prohibitively expensive for large-scale research efforts. The high cost is due to two factors: First, customers are required to sequence large quantities of DNA and RNA to adequately analyze the microbiome; and second, research projects are plagued by long turnaround times due to lower sample throughput. The proposed product will enrich microbial cells and will remove contaminants before the sequencing analysis begins. If successful, the commercial impact of this product for end-users will be substantial cost savings and the ability to expand their customer base, enabling scientific progress to accelerate in microbiome research. Accomplishing the technical aims set forth in this Phase I proposal will significantly reduce technical risk in the company's commercialization efforts by demonstrating proof-of-feasibility for a single-use device and bench-top instrument capable of enriching microbes prior to metagenomic sequencing. This SBIR Phase I project proposes to develop a microbial enrichment tool to significantly reduce the cost and difficulty of analyzing microbiomes using DNA and RNA sequencing. At present, sequencing laboratory directors only are able to analyze microbiomes at tremendous expense because samples are highly contaminated with DNA and RNA derived from host cells. The proposed solution is a disposable cartridge and a control instrument that will enable lab personnel to rapidly enrich microbes directly from samples without the use of bioengineered tags or labels that introduce bias, and enable the generation of sequencing libraries composed primarily of bacterial DNA and RNA. The technical challenges in this proposal are to convert the current laboratory method for enriching bacteria demonstrated previously into a bench-top instrument that uses a simple and disposable device compatible with current sequencing workflows that requires minimal operator steps. The system's performance in Phase I will be evaluated using spike-in samples with bacterial isolates and mock communities to simulate realistic microbiomes. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.