Background

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.

Methods and results

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.

Conclusions

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.

中文翻译：

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直肠拭子是评估结肠微生物组的可靠方法

背景

基因组测序的进步使详细的微生物组分析成为可能；然而，用于测序的理想标本类型尚未确定。直肠拭子可以为结肠微生物组分析提供一种快速便捷的方式。本研究的目的是评估直肠拭子与粪便样本相比的使用。

方法和结果

20 名卫生专业人员参与了这项研究，并提供了粪便样本、自收集的直肠拭子和临床医生采集的直肠拭子。提取 DNA 并进行 16S rRNA 基因测序以进行微生物组分析。

与粪便样本相比，拭子中的 Alpha 多样性更高；然而，只有将临床医生获得的拭子与粪便进行比较时，差异才显着。

对β多样性的分析一致表明，很少有分类群受到样本类型的影响。我们发现样本类型仅占群落变异的 6.8%（R2 = 0.067，p < 0.001，permanova）。值得注意的是，在临床医生获得的拭子中仅发现了六个属，而在自取的拭子中也没有发现。

结论

自行收集和临床医生获得的直肠拭子都是分析结肠微生物组的可靠方法。由于抗生素等疗法会影响微生物组，因此获取用于微生物组分析的标本通常是时间紧迫的。直肠拭子被证明是一种有效且方便的微生物组分析方式。