Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses

Studies on host-associated microbial communities using faecal samples has been providing important insights into the health, ecology and evolution of various animals. Many gut microbiome studies currently use manual kit-based DNA extraction methods, yet new methods that allow high-throughput sample processing are in demand. In this study, we evaluated magnetic cellulose bead-based DNA extraction methods, which can be automated in a work station, using mouse, Mus musculus (Linnaeus), and bovine, Bos taurus (Linnaeus), faeces as a model. Our data showed that those methods can provide good quantity and quality of extracted DNA suitable for 16S-rRNA-based microbiome analyses for a wide variety of samples, comparable to or more efficiently than the widely used standard method. The automated extraction requires less time and fewer manual steps, which makes these methods suitable for high-throughput faecal microbiome analyses.