A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity

Abstract

BackgroundFew studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.Methodology/Principal FindingsWe tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05).Conclusions/SignificanceThe duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.

The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

“…However, a recent sequencing analysis on five healthy subjects indicated Prevotella and generally Bacteroidetes to be virtually absent from duodenum mucosa 34. More recently the Proteobacteria genera Acinetobacter , Neisseria and Haemophilus , and Prevotella were reported to be the most predominant genera 35.…”

The Intersection of Immune Responses, Microbiota, and Pathogenesis in Giardiasis

“…Furthermore, if biopsy samples are used, they were most likely extracted from patients with gastrointestinal diseases that may already contain perturbed microbiota communities. One study comparing the intestinal microbial composition of obese humans with normal weighted individuals described the dominance of Firmicutes and Actinobacteria in all samples taken from gastric tubes inserted in the gut [38]. However, this result must be further examined as the data was provided from 12 year-frozen samples and were taken from a study that was not designed to examine the intestinal microbiota composition [38].…”

Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

“…The bacteria in the small intestine may be involved in nutrient sensing that potentially affects various host functions [5]. In humans, the predominant phyla in duodenal samples were accounted for by Firmicutes and Actinobacteria, while Bacteroidetes were not detected [6]. This distribution of phyla is distinctly different from the phyla found in both human and mouse faeces, which are mainly accounted for by Firmicutes and Bacteroidetes [7].…”