Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods

Birgitte Smith1, Nan Li1, +, Anders Schou Andersen1, 2, Hans Christian Slotved1, Karen Angeliki Krogfelt1, *
1 Department of Microbiological Surveillance and Research, Statens Serum Institut, DK-2300 S, Copenhagen, Denmark
2 Copenhagen Wound Healing Centre, Bispebjerg University Hospital, DK-2400 N Copenhagen, Denmark

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© Smith et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Department of Microbiological Surveillance and Research, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; Tel: +45 3268 3745; Fax: +45 3268 3147; E-mail:
+ present address Peking University First Hospital, Beijing 100034, China


Culture independent methods are used widely in diagnostic laboratories for infectious disease Isolation of genomic DNA from clinical samples is the first and important step in the procedure. Several procedures for extracting DNA from faecal samples have been described, including different mechanical cell disruptors. To our knowledge, the use of TissueLyser as a mechanical disruptor on faecal samples before DNA extraction has not been previously described. The purpose of the study was to implement a method for preparing faecal samples for optimal DNA extraction. Thus, three different procedures for extracting DNA from human faeces were compared. This was done either by using the mechanical disrupter by Mini BeadBeater 8, or the TissueLyser both followed by DNA purification using QIAamp DNA stool MiniKit, in comparison with DNA extractions using QIAamp DNA stool MiniKit without any prior mechanical disruption, according to manufacturer’s instructions. The obtained DNA from the three procedures was analysed by DGGE, and the number of bands was compared between each procedure. There was no significant difference between the numbers of bacterial bands obtained from DGGE when using a TissueLyser or Mini BeadBeater 8, so the two different mechanical cell disruptors can be used comparably when isolating bacterial DNA from faecal samples. The QIAamp DNA stool MiniKit alone resulted in a reduced number of bands compared to the two mechanical disruption methods.

Keywords: DNA extraction method, faecal samples, Mini BeadBeater 8, TissueLyser.