Several by-products of tropical fruits, which are often discarded by the food industry, have high fibre content and bioactive compounds. These compounds, as well as certain probiotic strains and some pectins present in the by-products, have the potential to modulate the human gut microbiota, promoting several health benefits, including the attenuation of obesity parameters. The aim of this work was to evaluate the effects of lemon pectin, by-products of tropical fruits and probiotic strains on the gut microbiota from healthy-weight and obese individuals using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Six articles were developed in order to meet the proposed aims. The first article is a mini-review and the other five are original articles. In the first article, we summarized the principal findings on obesityrelated microbiota composition and reviewed new strategies for gut microbiota modulation in favour of obesity treatment. We showed that the composition of the microbiota is essential for understanding the mechanisms involved in the aetiology of obesity and, that several strategies, such as consumption of probiotics and prebiotics, as well as moderate and regular physical activity, can modulate the gut microbiota in favour of obesity treatment. In the second article, the chemical composition, the total phenolic compounds and the in vitro antioxidant capacity of the camu-camu by-product were evaluated. An in vitro gastrointestinal survival essay was also performed using three probiotic strains (Bifidobacterium longum BB-46, Lactobacillus acidophilus LA-5 and L. paracasei L-431) along with the camu-camu byproduct. This study indicated that although the camu-camu by-product might be useful for the development of new food products, increasing its nutritional value, it can have a negative effect on the survival rate of determined probiotic strains during the gastrointestinal passage. In the third article, the impact of a lemon pectin on the survival rate of B. longum BB-4, L. acidophilus LA-5 and L. paracasei L-431 was evaluated using an in vitro gastrointestinal survival essay. The citric pectin was shown to have a positive impact on the survival of B. longum BB-46, but had no positive effects on L. acidophilus LA-5 and L. paracasei L-431 survival. Therefore, B. longum BB-46 with lemon pectin was one of the combinations selected for further experiments in the SHIME® model. In the fourth article, we evaluated the chemical composition, the total phenolic compounds and the in vitro antioxidant capacity of the acerola byproduct. We also evaluated the survival of all studied probiotic strains (LA-5, L-431 and BB-46) combined with acerola by-product using an in vitro gastrointestinal survival essay. This article also includes the effects of Bifidobacterium longum BB-46 in combination with the acerola by-product on the intestinal microbiota of healthy-weight individuals using the SHIME®. The acerola by-product showed an excellent chemical composition and high antioxidant activity. Moreover, the by-product could improve the survival of B. longum BB-46 during the in vitro gastrointestinal assay and was, therefore, the second combination selected for the experiments in SHIME® model. The results suggested that B. longum BB-46 with acerola by-product has a positive effect on the gut microbiota metabolism and might be used in new studies about functional product development. In the fifth article, the effects of Bifidobacterium longum BB-46 in combination with the citric pectin on the intestinal microbiota of healthy-weight individuals were evaluated using the SHIME® and 16S rRNA gene sequencing. We observed that although each treatment (B. longum BB-46 and B. longumBB-46 combined with lemon pectin) could modulate the microbiota, the combination was more effective in decreasing intestinal NH4 + levels and in increasing butyric acid-producing bacteria. These findings indicate that B. longum BB-46, especially when combined with lemon pectin, might have a beneficial impact on human health.In the sixth article, the effects of Bifidobacterium longum BB-46 an d lemon pectin, combined or not, on the intestinal microbiota of obese individuals were evaluated using the SHIME® and the 16S rRNA gene sequencing. The results indicated that both B. longum BB-46 and pectin can modulate the obesity-related microbiota; however, when the pectin is combined with BB-46, the predominant effect of the pectin can be observed. Treatments with pectin and pectin combined with B. longum BB-46 showed a high increase in butyric acid-producer bacteria as well as in bacteria with potential anti-inflammatory effects and a decrease in the Lachnospiraceae family, recently associated with the development of obesity. These findings indicate that the studied pectin canprobably have a protective role in obesity. Finally, with the results reported in this study, we could conclude that both the acerola and camu-camu by-products might be useful in thedevelopment of new functional foods due to their excellent physico-chem ical characteristics. However, we could demonstrate that the by-product of camucamu may be harmful to the survival of certain probiotic strains. Moreover, this study allowed us to conclude that B. longum BB-46 in combination with the acerola by-product can positively alter intestinal metabolites and that B. longum BB-46 in combination with the citric pectin has the ability to modulate the microbiota of both obese and healthy-weight individuals, but in different ways. This study also enabled us to observe that the stimulation or inhibition of certain bacterial families or genera are also dependent on the initial composition of the microbiota. Although this study indicates that B. longum BB46 in combination with the citric pectin may be useful in preventing obesityrelated symptoms, clinical studies including blood parameters and weight control are required to demonstrate the in vitro observed effects. Keywords: Gut microbiota; Obesity; Pectin; By-product of fruits; Probiotics; 16S rRNA.