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Complex gene–environment interactions are considered important in the development of obesity. The composition of the gut microbiota can determine the efficacy of energy harvest from food^,, and changes in dietary composition have been associated with changes in the composition of gut microbial populations^,. The capacity to explore microbiota composition was markedly improved by the development of metagenomic approaches^,, which have already allowed production of the first human gut microbial gene catalogue and stratifying individuals by their gut genomic profile into different enterotypes, but the analyses were carried out mainly in non-intervention settings. To investigate the temporal relationships between food intake, gut microbiota and metabolic and inflammatory phenotypes, we conducted diet-induced weight-loss and weight-stabilization interventions in a study sample of 38 obese and 11 …