Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.
Scripps Center for Organ Transplantation, La Jolla, California, USA.
Biopreserv Biobank. 2020 Oct;18(5):425-440. doi: 10.1089/bio.2020.0032. Epub 2020 Aug 21.
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.
人类微生物组包含多种微生物，这些微生物动态变化，并与人体密切接触。微生物组影响健康和体内平衡，以及免疫系统，而这种平衡的任何重大变化（失调）都会引发急性和慢性健康状况。微生物组研究的激增部分是由于先进的测序技术能够快速、准确、经济有效地识别微生物组。为了在纵向前瞻性研究中研究肠道微生物组，需要标准化的协议来收集粪便样本，这是一个主要的前提条件，这些协议可以很容易地复制。然而，粪便标本采集仍然存在重大瓶颈，导致微生物组研究中的患者保留率低。这些障碍在实体器官移植受者中进一步加剧，据估计，多达一半的患者会出现腹泻。我们试图测试两种相对简单的样本采集方法（粪便拭子和擦拭物），并使用两种不同的测序技术（16S 核糖体 RNA 测序和鸟枪法宏基因组学）将它们与更繁琐的“黄金”标准采集方法（勺子）进行比较。我们对采集方法的比较表明，在细菌丰度和多样性方面，拭子和擦拭物与勺子方法相当。然而，与擦拭物相比，拭子在代表勺子方面更接近，并且与擦拭物相比，更容易收集和处理。在我们的分析中，拭子和擦拭物样本中丰富的皮肤共生菌潜在污染较低。两种测序技术的比较表明，它们是互补的，16S 测序提供了足够的覆盖范围，可以检测和区分收集样本中鉴定的细菌物种。我们的初步研究表明，替代粪便采样的采集方法是临床应用（如器官移植研究）中的一种可行选择。这些方法的使用可能会导致在连续微生物组研究中更好的患者保留招募率。
