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

Digestive Diseases and Sciences
Gabriela Guimaraes Sousa LeiteMark Pimentel

Abstract

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

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Citations

Dec 29, 2020·Frontiers in Microbiology·Logan R KilburnMariana C Rossoni Serão
Jan 12, 2021·Computational and Structural Biotechnology Journal·Amy C Engevik, Melinda A Engevik
Feb 4, 2021·Digestive Diseases and Sciences·Stacy WeitsmanMark Pimentel
May 18, 2021·Frontiers in Cellular and Infection Microbiology·Jinyan HanJing Kong
Aug 12, 2021·Computational and Structural Biotechnology Journal·Zhen YangYungang He

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Methods Mentioned

BETA
Assay
biopsy
biopsies

Software Mentioned

CLC Genomics Workbench
GraphPad
MetaboAnalyst
REIMAGINE
Abundance Analysis
GraphPad Prism

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