BMC Research Notes | |
Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples | |
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
【 预 览 】
Files | Size | Format | View |
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RO202309154610465ZK.pdf | 741KB | download | |
Fig. 2 | 106KB | Image | download |
Fig. 3 | 155KB | Image | download |
Fig. 1 | 74KB | Image | download |
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【 参考文献 】
- [1]
- [2]
- [3]
- [4]
- [5]
- [6]
- [7]
- [8]
- [9]
- [10]
- [11]
- [12]
- [13]
- [14]
- [15]
- [16]