Department of Surgery, University of Otago, Christchurch, New Zealand.
Department of Surgery, University of Otago, Christchurch, New Zealand.
Int J Med Microbiol. 2022 Feb;312(2):151549. doi: 10.1016/j.ijmm.2022.151549. Epub 2022 Jan 24.
Advances in genome sequencing have enabled detailed microbiome analysis; however, the ideal specimen type for sequencing is yet to be determined. Rectal swabs may offer a rapid and convenient modality for colonic microbiome analysis. The aim of this study is to evaluate the use of rectal swabs compared to faecal specimens.
Twenty health professionals participated in this study and provided a faecal specimen, a self-collected rectal swab and a rectal swab taken by a clinician. DNA was extracted and 16S rRNA gene sequencing was carried out for microbiome analysis. Alpha diversity was higher in swabs compared to faecal specimens; however, the difference was only significant when comparing clinician-obtained swabs to faeces. Analysis of beta diversity consistently showed that few taxa were affected by sample type. We found sample type accounted for only 6.8% of community variation (R2 = 0.067, p < 0.001, permanova). Notably, there were only six genera identified in clinician-obtained swabs that were not also found in the self-taken swabs.
Both self-collected and clinician obtained rectal swabs are a reliable method of analysing the colonic microbiome. Obtaining specimens for microbiome analysis is often time-critical due to therapy, such as antibiotics, influencing the microbiome. Rectal swabs are shown to be a valid and convenient modality for microbiome analysis.
基因组测序技术的进步使得对微生物组进行详细分析成为可能；然而，目前仍需要确定最适合测序的样本类型。直肠拭子可能是一种快速便捷的结肠微生物组分析方法。本研究旨在评估直肠拭子与粪便标本的应用效果。
本研究纳入了 20 名健康专业人员，他们提供了粪便标本、自行采集的直肠拭子和由临床医生采集的直肠拭子。提取 DNA 后，进行 16S rRNA 基因测序以进行微生物组分析。与粪便标本相比，拭子中的 alpha 多样性更高；然而，只有在比较临床医生采集的拭子与粪便时，差异才具有统计学意义。beta 多样性分析始终表明，很少有类群受到样本类型的影响。我们发现，样本类型仅解释了群落变异的 6.8%（R2=0.067，p<0.001，permanova）。值得注意的是，仅在临床医生采集的拭子中发现了 6 个在自行采集的拭子中未发现的属。
自行采集和临床医生采集的直肠拭子都是分析结肠微生物组的可靠方法。由于治疗（如抗生素）会影响微生物组，因此进行微生物组分析时，获取标本通常具有时间紧迫性。直肠拭子是一种有效的便捷的微生物组分析方法。
