Abstract View
Application of Long-read Nanopore Sequencing for the Analysis of Airborne Microbes
AUSTIN MARSHALL, Daniel Fuller, Kavindra Kumaragama, Suresh Dhaniyala, Shantanu Sur, Clarkson University - Potsdam, NY
Abstract Number: 327
Working Group: Bioaerosols
Abstract
The ongoing COVID-19 pandemic has raised global awareness of airborne diseases, generating a larger interest in the microbial population in the air. Next-generation sequencing (NGS) offers a robust approach to analyze the microbiome, however, one major challenge to analyze airborne microbes arises from their extremely low concentration in air compared with other environments such as soil, water, and gut. This, thus, necessitates the use of high-pressure drop, high flow-rate sampling devices or long collection time periods to capture sufficient amount of bioaerosol samples for analysis, a severe restriction for several applications. In this work, we explored how long-read nanopore sequencing technology could be utilized to establish an analytical workflow to obtain sequencing data from a small quantity of genomic material without compromising the quality and resolution of measurements. Bacterial abundance and diversity in bioaerosol samples were estimated by 16S rRNA amplicon analysis using a MinIon flow-cell device, which enables a full-length read of the 16S rRNA gene, thus increasing the sequencing read depth. We found that by modifying and optimizing the sample preparation procedure, we could extract reliable and accurate results from less than 0.5 ng of genomic DNA, which is over an order of magnitude lower than the amount needed for conventional NGS platforms such as Illumina. Additionally, the ability to perform the sequencing locally in the laboratory without the need for expensive instrumentation and the capability of multiplexing samples on a single run enable a fast, cost-effective means to get sequencing results following sample collection. Using this workflow, we have successfully analyzed bioaerosol samples collected by a low pressure-drop, low power, portable bioaerosol sampler deployed at various outdoor and indoor locations.