A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis
Fangchao Song, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin
Abstract
Understanding bacterial interactions and assembly in complex microbial communities using 16S rRNA sequencing normally requires a large experimental load. However, the current DNA extraction methods, including cell disruption and genomic DNA purification, are normally biased, costly, time-consuming, labor-intensive, and not amenable to miniaturization by droplets or 1,536-well plates due to the significant DNA loss during the purification step for tiny-volume and low-cell-density samples. A direct PCR method could potentially solve these problems. In this study, we developed a direct PCR method which exhibits similar efficiency as the widely used method, the DNeasy PowerSoil protocol, while being 1,600 times less expensive and 10 times faster to execute. This simple, cost-effective, and automation-friendly direct-PCR-based 16S rRNA sequencing method allows us to study the dynamics, microbial interaction, and assembly of various microbial communities in a high-throughput fashion.