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

  • Tanzila Afrin
  • Asuka Kounosu
  • Mohammad-Masum Billah
  • Kazunori Murase
  • Taisei Kikuchi
Technical Note


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.


Microbiome 16S-rRNA amplicon sequencing analysis Maxwell RSC automated workstation DNA extraction methods Faecal material 



We thank Atsushi Iguchi and the veterinary parasitology laboratory in University of Miyazaki for providing faecal samples, and Ryusei Tanaka, Yasunobu Maeda and Aya Adachi for technical assistance.

Supplementary material

13355_2018_551_MOESM1_ESM.pdf (1.5 mb)
Supplementary material 1 Fig. S1 (a) Gel electrophoresis of extracted DNA from four extraction methods (PF, CF, BD, and MO). (b) Gel electrophoresis of PCR products: Group A: normal laboratory condition; Group B: antibiotic treatment and parasitic infection; Group C: antibiotic treatment. Marker: 2-log ladder (New England Biolab). Fig. S2 Inhibitory effect of different amounts of extracted DNA sample with qPCR. Ct values (y-axis), which are defined as the number of cycles required for the fluorescent signal to cross the threshold level, showed higher at the highest volume (x-axis) than the regression line thorough the three lower volume points in most samples. (a) Group A: normal laboratory conditions; (b) Group B: antibiotic treatment with parasite infection; (c) Group C: antibiotic treatment without parasite infection. Fig. S3 Alpha diversity metric (Chao1) based on 16 s rRNA variable region 4 bovine faecal extracted DNA (PDF 1521 kb)


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Copyright information

© The Japanese Society of Applied Entomology and Zoology 2018

Authors and Affiliations

  1. 1.Division of Parasitology, Faculty of MedicineUniversity of MiyazakiMiyazakiJapan

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