Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
Department of Internal Medicine, Ersta Hospital, Stockholm, Sweden.
J Dig Dis. 2018 Dec;19(12):745-752. doi: 10.1111/1751-2980.12688.
Fecal samples are often used to characterize gut microbiota. However, whether or not fecal microbiota differs from mucosa-associated microbiota remains largely unknown. This may be specifically relevant in conditions that are characterized by complex mucosal microbe-host interactions, such as Crohn's disease. We aimed to determine the degree of agreement between fecal and mucosal microbiota profiles in 'healthy' individuals, using two commonly used collection procedures.
The gut microbiota composition of fecal samples (sent at ambient temperature before storage at -70°C) and of colonic biopsies (obtained at endoscopy and immediately stored at -70°C) was determined by sequencing the 16S rRNA gene. Altogether 31 randomly selected 'healthy' individuals from the population-based colonoscopy (Popcol) study were included.
The fecal samples were characterized by a reduced degree of richness (P < 0.0001) and diversity (P = 0.016), and also differences in several phyla, including a lower relative abundance of Proteobacteria (P < 0.0001) and Verrucomicrobia (P = 0.008) than in biopsies. Only three of 30 individuals had a similar fecal and mucosal microbiota profile, based on weighted UniFrac analysis. A difference in Crohn's disease dysbiosis-associated bacteria was observed, including a lower relative abundance of Faecalibacterium (P = 0.004) and a higher relative abundance of Ruminococcus (P = 0.001) in feces than in biopsies.
The observed differences between fecal samples, transported at ambient temperature, and the colonic mucosa-associated microbiota have implications for the interpretation of the previous literature, and may be specifically relevant to studies on Crohn's disease.
粪便样本常用于描述肠道微生物群。然而，粪便微生物群与黏膜相关微生物群是否存在差异在很大程度上仍不清楚。在以黏膜微生物-宿主相互作用复杂为特征的情况下，如克罗恩病，这种差异可能尤为重要。我们旨在通过两种常用的采集方法，确定“健康”个体的粪便和黏膜微生物群谱之间的一致性程度。
通过测序 16S rRNA 基因，检测粪便样本（在常温下寄送，然后在-70°C 下储存）和结肠活检样本（在内镜检查时获得，然后立即在-70°C 下储存）中的肠道微生物群组成。总共纳入了来自基于人群的结肠镜检查（Popcol）研究的 31 名随机选择的“健康”个体。
粪便样本的丰富度（P < 0.0001）和多样性（P = 0.016）降低，几个门的相对丰度也存在差异，包括变形菌门（Proteobacteria）和疣微菌门（Verrucomicrobia）的相对丰度降低（P < 0.0001 和 P = 0.008）。仅基于加权 UniFrac 分析，30 名个体中有 3 名个体的粪便和黏膜微生物群谱相似。观察到克罗恩病失调相关细菌存在差异，粪便中粪杆菌（Faecalibacterium）的相对丰度较低（P = 0.004），而真杆菌属（Ruminococcus）的相对丰度较高（P = 0.001）。
在常温下运输的粪便样本与结肠黏膜相关微生物群之间存在差异，这对解释以前的文献具有重要意义，并且可能与克罗恩病的研究特别相关。
