A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity

Abstract

Background: Few 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 findings: We 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/significance: The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.

Fig 1. Phylum taxonomic classification.

Ob, Obese individual; Norm, Normal weight individual.

Fig 2. Genus relative abundance by individual.

Obese and normal weight individuals are represented by red and blue nodes, respectively. A colored node corresponds to the identification of a genus for one individual. The node size is proportional to the normalized genus abundance.

Fig 3. Relative abundance of anaerobic and aerobic genera of the duodenal microbiota.

The source black nodes are the obese and the normal weight groups (five individuals by group). The blue and red nodes are the aerobic and anaerobic genera identified in the groups, respectively. The genus node is linked by an edge to it source node. The genus relative abundance is given by the node size. Finally, two genera shared by the obese and normal weight groups are linked by an additional edge. The Cytoscape network visualization tool version 3.1.0 was used for building this figure.

Fig 4. Fatty acid beta-oxidation by duodenal microbiota in obese individuals.

The degradation of fatty acids involves their conversion into Acyl-CoA followed by multiple repetitions of the fatty acid beta-oxidation cycle that leads to the removal each round of two carbon atoms from the acyl chain and to the release of one Acetyl-CoA molecule entering in the Krebs’ cycle. Four key enzymes are involved in the beta-oxidation process, including Acyl-CoA dehydrogenase (FAD), enoyl CoA hydratase, 3-hydroxy acyl CoA dehydrogenase and 3-ketoacyl CoA thiolase. FAD, the first enzyme of fatty acid beta-oxidation, was found to be enriched in the microbiota of obese subjects, suggesting a higher beta-oxidation capacity and energy mobilization in these subjects.