Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

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.

Keywords: 16S metagenomic analysis; Duodenum; Jejunum; Microbiome; Stool.

Fig. 1

a PCoA plot of the duodenal and stool microbial profiles in the same subjects (Group 1, n = 53). Duodenum—red; stool—green. Transparent circles indicate the 95% confidence region. b Volcano plot of OTUs that were statistically different in the duodenal microbiome and stool microbiome in the same subjects (Group 1, n = 53) (FDR P value < 0.05 and fold change (FC) threshold of 2.0 shown in pink)

Fig. 2

The 16S rRNA microbiome profiles of aspirates collected from a—duodenum, b—jejunum, and c—farthest distance (FD), in the same subjects (Group 2, n = 23)

Fig. 3

Relative abundance of microbial populations at the phylum level in the duodenum, jejunum, and farthest distance (FD) and stool, in the same subjects (Group 3, n = 8)

Fig. 4

Relative abundance of the major Firmicutes families in the duodenum, jejunum, FD, and stool, in the same subjects (Group 3, n = 8)