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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.

A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity