The human microbiome encompasses a variety of microorganisms that change dynamically and are in close contact with the body. The microbiome influences health and homeostasis, as well as the immune system, and any significant change in this equilibrium (dysbiosis) triggers both acute and chronic health conditions. Microbiome research has surged, in part, due to advanced sequencing technologies enabling rapid, accurate, and cost-effective identification of the microbiome. A major prerequisite for stool sample collection to study the gut microbiome in longitudinal prospective studies requires standardized protocols that can be easily replicated. However, there are still significant bottlenecks to stool specimen collection that contribute to low patient retention rates in microbiome studies. These barriers are further exacerbated in solid organ transplant recipients where diarrhea is estimated to occur in up to half the patient population. We sought to test two relatively easy sample collection methods (fecal swab and wipes) and compare them to the more cumbersome “gold” standard collection method (scoop) using two different sequencing technologies (16S ribosomal RNA sequencing and shotgun metagenomics). Our comparison of the collection methods shows that both the swabs and the wipes are comparable to the scoop method in terms of bacterial abundance and diversity. The swabs, however, were closer in representation to the scoop and were easier to collect and process compared to the wipes. Potential contamination of the swab and the wipe samples by abundant skin commensals was low in our analysis. Comparison of the two sequencing technologies showed that they were complementary, and that 16S sequencing provided enough coverage to detect and differentiate between bacterial species identified in the collected samples. Our pilot study demonstrates that alternative collection methods for stool sampling are a viable option in clinical applications, such as organ transplant studies. The use of these methods may result in better patient retention recruitment rates in serial microbiome studies.

中文翻译：

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使用 16S rRNA 和宏基因组学方法对健康志愿者和实体器官移植受者的粪便样本收集方法的可行性和比较研究。

人体微生物组包括各种动态变化并与身体密切接触的微生物。微生物群会影响健康和体内平衡以及免疫系统，这种平衡（生态失调）的任何显着变化都会引发急性和慢性健康状况。微生物组研究激增，部分原因是先进的测序技术能够快速、准确且经济高效地识别微生物组。在纵向前瞻性研究中收集粪便样本以研究肠道微生物组的主要先决条件需要可以轻松复制的标准化方案。然而，粪便标本收集仍然存在重大瓶颈，导致微生物组研究中患者保留率低。这些障碍在实体器官移植受者中进一步加剧，据估计，多达一半的患者会发生腹泻。我们试图测试两种相对简单的样本收集方法（粪便拭子和擦拭巾），并使用两种不同的测序技术（16S 核糖体 RNA 测序和鸟枪宏基因组学）将它们与更麻烦的“黄金”标准收集方法（勺子）进行比较。我们对收集方法的比较表明，就细菌丰度和多样性而言，拭子和擦拭巾都与勺子方法相当。然而，与擦拭巾相比，拭子更接近勺子，更容易收集和处理。在我们的分析中，大量皮肤共生体对拭子和擦拭物样品的潜在污染很低。两种测序技术的比较表明它们是互补的，并且 16S 测序提供了足够的覆盖范围来检测和区分收集到的样本中鉴定的细菌种类。我们的试点研究表明，粪便取样的替代收集方法是临床应用（例如器官移植研究）中的可行选择。在连续微生物组研究中，使用这些方法可能会导致更好的患者保留招募率。