Standard operating procedure for fecal samples DNA Extraction, protocol H INRA

The SOP 07 aims to standardize the fecal samples DNA extraction by giving a step-by-step description of the protocol. This SOP is of first interest for good fecal samples DNA extraction practice in order to characterize the fecal microbiota by metagenomic profiling. As preliminary steps for this SOP, an inventory of protocols for the preparation of the nucleic acids from appropriately identified, with respect to IHMS SOP 001 V1, and collected samples, with respect to IHMS SOP 002, or 003 or 004 or 005 V1, was undertaken. Consideration was given to the requirement for high throughput treatment of large sample sets. Thus obtained DNA has been analysed with respect to sequencing standards (IHMS SOP 009, 010 & 011 V1) and sequence data further analysed with respect to data analysis standards (IHMS SOPs 012,013,014 & 015 V1). Finally, a subset of 3 satisfactory protocols (IHMS SOPs 006, 007 & 008 V1) was further selected for the assessment of inter-laboratory reproducibility. As this time, the results of the data analysis and the comparison between the 3 protocols are not available. Moreover, it must be kept in mind that the specific area of nucleic acids preparation does see constant evolutions and improvements, such that it is hardly conceivable to definitely "freeze" a protocol that will be considered as optimal in the long term.

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  • BMC Microbiology - 2012
  • BMC Microbiology - 2014


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