Division of Rheumatology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA.
Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA.
Microbiol Spectr. 2022 Apr 27;10(2):e0244621. doi: 10.1128/spectrum.02446-21. Epub 2022 Mar 28.
Newer 'omics approaches, such as metatranscriptomics and metabolomics, allow functional assessments of the interaction(s) between the gut microbiome and the human host. However, in order to generate meaningful data with these approaches, the method of sample collection is critical. Prior studies have relied on expensive and invasive means toward sample acquisition, such as intestinal biopsy, while other studies have relied on easier methods of collection, such as fecal samples that do not necessarily represent those microbes in contact with the host. In this pilot study, we attempt to characterize a novel, minimally invasive method toward sampling the human microbiome using mucosal cytology brush sampling compared to intestinal gut biopsy samples on 5 healthy participants undergoing routine screening colonoscopy. We compared metatranscriptomic analyses between the two collection methods and identified increased taxonomic evenness and beta diversity in the cytology brush samples and similar community transcriptional profiles between the two methods. Metabolomics assessment demonstrated striking differences between the two methods, implying a difference in bacterial-derived versus human-absorbed metabolites. Put together, this study supports the use of microbiome sampling with cytology brushes, but caution must be exercised when performing metabolomics assessment, as this represents differential metabolite production but not absorption by the host. In order to generate meaningful metabolomic and microbiome data, the method of sample collection is critical. This study utilizes and compares two methods for intestinal tissue collection for evaluation of metabolites and microbiomes, finding that using a brush to sample the microbiome provides valuable data. However, for metabolomics assessment, biopsy samples may still be required.
更新的“组学”方法，如宏转录组学和代谢组学，可以评估肠道微生物组与人类宿主之间的相互作用。然而，为了用这些方法生成有意义的数据，样本采集的方法是至关重要的。先前的研究依赖于昂贵且有创的样本采集方法，如肠道活检，而其他研究则依赖于更容易的样本采集方法，如粪便样本，而这些样本不一定代表与宿主接触的微生物。在这项初步研究中，我们尝试使用黏膜细胞学刷采样的新的微创方法来描述人类微生物组，与 5 名接受常规筛查结肠镜检查的健康参与者的肠道活检样本进行比较。我们比较了两种采集方法的宏转录组学分析，发现细胞学刷样本中的分类均匀度和β多样性增加，两种方法之间的群落转录谱相似。代谢组学评估表明两种方法之间存在显著差异，这意味着细菌衍生代谢物与人体吸收代谢物之间存在差异。综上所述，这项研究支持使用细胞学刷进行微生物组采样，但在进行代谢组学评估时必须谨慎，因为这代表了不同的代谢物产生而不是宿主吸收。为了生成有意义的代谢组学和微生物组数据，样本采集的方法至关重要。本研究利用并比较了两种用于肠道组织采集以评估代谢物和微生物组的方法，发现使用刷子采样微生物组可提供有价值的数据。然而，对于代谢组学评估，可能仍需要活检样本。
