Options for treatment of obesity include dietary approaches and bariatric surgery. Previous studies have shown that weight loss interventions have an impact on gut microbiota. However, a pattern of gut microbiota changes associated with weight loss independently of the type of intervention has not been described yet. This study includes 61 individuals who followed different weight loss strategies in three different trials: 21 followed a hypocaloric Mediterranean diet (MedDiet), 18 followed a very-low-calorie ketogenic diet (VLCKD) and 22 patients underwent sleeve gastrectomy bariatric surgery (BS). Gut microbiota profile was assessed by next-generation sequencing. A common taxon that had significantly changed within the three weight loss interventions could not be find. At the family level, Clostiridiaceae significantly increased its abundance with MedDiet and VLCKD, whilst Porphyromonadacean and Rikenellaceae significantly increased with VLCKD and BS. At genus level, in VLCKD and BS, Parabacteroides and Alistipes significantly increased their abundance whilst Lactobacillus decreased. At the species level, BS and VLCKD produced an increase in Parabacteroidesdistasonis and a decrease in Eubactieriumventriosum and Lactobacillusrogosae, whilst Orodibactersplanchnicus increased its abundance after the BS and MedDiet. Predicted metagenome analysis suggested that most of the changes after VLCKD were focused on pathways related to biosynthesis and degradation/utilization/assimilation, while BS seems to decrease most of the biosynthesis pathways. MedDiet was enriched in several pathways related to fermentation to short-chain fatty acids. Our results show that weight loss is not associated with a specific pattern of gut microbiota changes independently of the strategy used. Indeed, gut microbiota changes according to type of weight loss intervention.