Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples

Sandrine Le Gall-David; Gaëlle Boudry; Sylvie Buffet-Bataillon

doi:10.2144/fsoa-2022-0072

Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples

Future Sci OA. 2023 Mar 9;9(1):FSO837. doi: 10.2144/fsoa-2022-0072. eCollection 2023 Jan.

Authors

Sandrine Le Gall-David¹, Gaëlle Boudry¹, Sylvie Buffet-Bataillon^{1

2}

Affiliations

¹ Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France.
² Bacteriology, Pontchaillou University Hospital, Rennes, France.

Abstract

Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum).

Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles.

Results: The quantity and quality of DNA varied among the four kits. The microbiota of the stool samples showed similar diversity and compositional profiles for the 4 kits.

Conclusion: Despite differences in DNA quality and quantity, the 4 kits yielded similar results for stool samples, while all kits were not sensitive enough for low biomass samples.

Keywords: 16S rRNA gene sequencing; DNA binding; Illumina; bacterial DNA extraction; bead-beating; data analysis; enzymatic lysis; human microbiota; low biomass; next generation sequencing.

Plain language summary

DNA extraction is a major factor affecting the microbial profile of various samples. Considering that different kits are commonly used such as QIAamp PowerFecal Pro DNA kit (QPFPD, QIAGEN), Macherey Nucleospin Soil (MNS, MACHEREY-NAGEL) Macherey Nucleospin Tissue (MNT, MACHEREY-NAGEL) and MagnaPure LC DNA isolation kit III (MPLCD, ROCHE), this study aimed to assess their performance using high (feces) and low-biomass samples. The kits were equally effective for feces samples but not sensitive enough for low biomass samples (chyme, bronchoalveolar lavage fluid and sputum).