Since several decades, lifestyle and nutrition changes (unbalance in lipid intake quality) in the developed countries has leaded to the increased prevalence of inflammatory and metabolic pathologies. These pathologies are associated with an increase in visceral adipose tissue, chronic low-grade inflammation and a gut microbiota dysbiosis. Long-term habits play a crucial role on the gut microbiota community and diversity of these bacterial communities. General population is in deficit in n-3 PUFAs. Nevertheless, these fatty acids can exert a beneficial impact on the gut microbiota composition in these metabolic pathologies, and increase anti-inflammatory compounds for the microbiota fermentation, as short chain fatty acids. Linseed is a plant rich in n-3 polyunsaturated fatty acids (n- 3 PUFAs) and also in lignans and other components. We aimed to study a rebalance in n-6/n-3 PUFAs ratio in two models of rodents (rats and mice) with high fat diet (HFD)-enriched in linseed oil (LS-O) or extruded linseed (LS-E), as a matrix. We analyzed the mucosa-associated gut microbiota on colon samples in both models and demonstrated an impact of LS-E. The β-diversity was significantly different in LS-E compared to LS-O and HFD. Moreover, the α-diversity illustrated by the Shannon index tended to increase with LS-E supplementation. The abundance of the specific features Prevotella, Paraprevotella, Ruminococcus and Clostridiales were increased in LS-E compared to HFD and LS-O. LS-O did not impact the gut mucosa-associated microbiota. Extruded linseed with n-3 PUFAs, lignans and others components may increase the richness of the microbiota and restore its composition compared to an exclusive intake in n-3 PUFAs. A long-term supplementation in extruded linseed, evaluated as a matrix could be an efficient strategy in the prevention of inflammatory and metabolic diseases from its impact on gut microbiota composition