The quality (yield, purity, and integrity) of microbial DNA extracted from digesta samples is crucial for downstream analysis of amplicon sequencing, and influenced by Chemical and mechanical lysis. However, contributions of chemical and mechanical lysis have not been investigated in DNA extraction methodology.

Recently, researchers from the Institute of Subtropical Agriculture (ISA), Chinese Academy of Sciences compared the effects of chemical and mechanical lysis on microbial DNA quality and downstream amplicon analysis, including QIAamp Fast DNA Stool Mini Kit (QIA) and RBB + C (YM), bead (BB), and sand beating (SB). The study has been published in Frontiers in microbiology on Nov.16.

The researchers found that chemical lysis (QIA and YM) showed similar efficiency to harvest DNA. Although chemical lysis did not affect the overall bacterial community, YM increased some fibrolytic bacterial genera with relative abundance being ranged from 0.33 to 0.78%. The QIA increased the unclassified protozoa than YM about 24-fold and tended to generate more protozoal amplicons and had higher richness in amplicon length polymorphism than YM. Including BB greatly increased DNA yield without affecting DNA quality and richness of bacterial but decreased the richness of protozoa. Both BB and SB had similar efficiency to harvest DNA yield and had no difference in DNA quality and bacterial and protozoal community.

These findings might reveal that DNA extraction methodology should be slightly different for analyzing the bacterial and protozoal community. Chemical lysis provided by YM and QIA should be better to extract DNA for analyzing bacterial and protozoal community, respectively. Sand can be an alternative beater for DNA extraction, and mechanical lysis is not recommended for protozoal community analysis.

Contact: Kang Jinhe

E-mail: kangjh@isa.ac.cn

Institute of Subtropical Agriculture, Chinese Academy of Sciences