Abstract

Background

Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease.

Aims

To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome.

Methods

Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench.

Results

16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria.

Conclusions

The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.

中文翻译：

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绘制人类小肠中的分段微生物组与粪便比较：一项 REIMAGINE 研究。

摘要

背景

大多数肠道微生物组研究都是使用粪便样本进行的。然而，小肠对消化、营养吸收和免疫功能至关重要，表征其微生物种群对于阐明它们在人类健康和疾病中的作用至关重要。

目标

表征不同小肠段的微生物群，并将其与粪便微生物组进行对比。

方法

前瞻性招募了在没有结肠准备的情况下接受食管胃十二指肠镜检查的男性和女性受试者。从十二指肠、空肠和到达的最远距离获得管腔抽吸物。一个子集还提供了粪便样本。使用 CLC Genomics Workbench 进行 16S rRNA 测序和分析。

结果

16S rRNA 测序确定了小肠和粪便微生物组之间 2000 多个操作分类单元的差异。厚壁菌门和变形菌门是小肠中最丰富的门，而拟杆菌门则较少。在小肠中，厚壁菌门主要以乳酸菌为代表，包括链球菌科、乳杆菌科和肉杆菌科，变形菌门以奈瑟菌科、巴斯德菌科和肠杆菌科为代表。十二指肠和 FD 微生物特征明显不同，但十二指肠和空肠之间以及空肠和 FD 微生物特征之间存在重叠。在粪便中，厚壁菌门以瘤胃球菌科、毛螺菌科、克里斯滕森菌科、

结论

小肠微生物组与粪便中的微生物组显着不同，并且在不同部位之间也存在差异。这些发现对于确定小肠微生物群的组成变化如何导致人类疾病状态可能很重要。