Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples

BMC Research Notes

Research Note

James Sinclair¹  Amanda J Cox²  Nicholas P West² 

[1] Menzies Health Institute Queensland, Griffith University, Parklands Drive, 4215, Southport, QLD, Australia;Menzies Health Institute Queensland, Griffith University, Parklands Drive, 4215, Southport, QLD, Australia;School of Pharmacy and Medical Sciences, Griffith University, Parklands Drive, 4215, Southport, QLD, Australia;

关键词: Gut microbiota;    Faecal samples;    16s rRNA;    DNA extraction;   

DOI  :  10.1186/s13104-023-06451-7

 received in 2023-05-28, accepted in 2023-08-08,  发布年份 2023

来源: Springer

【 摘 要 】

ObjectiveGrowth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34–69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods.ResultsDiversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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