Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Abstract

The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.

Bacterial communities in the feces of insectivorous bats in South Korea

“…Conventional methods for analyzing microbes involve bacterial culture; however, these methods do not capture the entire microbial diversity, especially uncultured microbes (Abdelfattah et al 2018;Hahn et al 2019). Therefore, using next-generation sequencing to explore intricate bacterial communities in guano has facilitated comprehensive research into these distinctive microhabitats, enhancing our understanding of their role in health and disease (Elie et al 2023;Knight et al 2018). This study aimed to establish a foundation for disease research within ecosys-tems by comparing the bacterial community compositions in the feces of four insectivorous bat species in South Korea during July and August.…”