Obesity has been linked to the composition of the gut microbiota but this relationship is not completely understood. Moreover, dietary interventions aiming to treat obesity have mostly focused on non-digestible carbohydrates. Although the effect of polyphenols on the intestinal microbiota has been studied using culture and molecular techniques, research is needed to determine whether these widely available compounds are capable of modulating the gut microbiota in obese individuals. Additionally, the gut microbiota consists of hundreds of microbial taxa, an ecosystem that can only be fully approached using highthroughput sequencing systems. Unfortunately, very few papers are available that have made use of these technologies to obtain a better insight on the effect of polyphenolics-rich fruits on the intestinal microbiota. The use of animal models is common to study the gut microbiota because mammals share the most predominant gut phylotypes and therefore the obtained results may help guide future interventions, Emodin either dietary or therapeutic, in human populations. Zucker rats possess a mutation in the leptin receptor and develop metabolic syndrome 8-Hydroxy-2-deoxyguanosine symptoms, including insulin resistance and dyslipidemia, at 4�C5 weeks of age. This animal model has been very well characterized as a model of obesity and therefore makes it attractive for studies of the gut microbiota. The present study aimed to investigate the effect of carbohydrate-free peach and plum juice on fecal microbial ecology using obese Zucker rats as the animal model. Animals were assigned to three groups, the lean wild-type was used as control lean. Quantitative real-time PCR revealed a significantly higher abundance of the phylum Bacteroidetes, the family Ruminococcacea, and the genera Faecalibacterium, Lactobacillus, and Turicibacter in the plum group when compared to the control and the lean groups. These changes were accompanied by a significant difference between control and treatment groups in principal coordinate analysis, differences in fecal fatty acids among the animal groups as well as by a significantly lower body weight in the plum group. There has been an increased interest in the characteristics and potential modifications of the intestinal microbiota to improve health in obese individuals.