DNA extraction: High yield is not synonymous with high diversity

The quality, amount, and, in the case of polymicrobial samples, diversity of isolated DNA presupposes the precision of downstream application results. As part of a larger study on colorectal cancer, the aim of this work was to identify the DNA extraction procedure that resulted in highest DNA yields and highest bacterial diversity in stool samples. This study evaluates and compares four DNA extraction kits and six different procedures for isolation of bacterial and human DNA from stool samples. The QIAsymphony extraction robot with the DSP Virus/Pathogen kit (Qiagen) was the method that gave the highest yield of both bacterial and human DNA. Additionally, the QIAsymphony possesses advantages in the form of automation, greater work volume, and a more effective use of resources. Bacterial diversity analysis, however, illustrated that DNA yield and diversity are independent factors. DNA extraction using the PSP® Spin Stool DNA Kit (Stratec Molecular) resulted in greater intra-sample and intra-kit diversity compared to the QIAsymphony DNA extraction method. The PSP® Spin Stool DNA Kit (Stratec Molecular), despite its advantages for bacterial diversity studies, is a manual kit, making it a more demanding, less cost-effective kit.