From mouth to anus, the gastrointestinal system is one of the most studied ecosystems. Deciphering its microbial composition requires the extraction and sequencing of the DNA of the microorganisms that inhabit it. Between sampling and computer analysis, researchers from INRA and CEA (François-Jacob Institute/ Genoscope) and their partners have studied the impact of the method used for DNA extraction on the microbial composition of human stool samples.

The scientists have shown that although every sample analysis step is critical, DNA extraction is most likely to affect the results. Among 366 bacterial species tested, 90 (25%) are affected by the extraction protocol, and therefore may be underrepresented. The majority of them are Gram-positive bacteria (which account for some 37% of microbiota bacteria) whose wall is more resistant to mechanical forces mobilized during extraction.

The scientists are now proposing a standard protocol for the processing of human stool samples, from sampling to DNA extraction and sequencing, and ultimately, biocomputing analysis.

This work has led to a patent and a press release.