We read with great interest the recent study by Dewulf and coworkers1 reporting encouraging results on a prebiotic-based dietary intervention trial in obese patients. This work enlightens that even subtle changes in the gut microbiota may influence the metabolomic signature both inside and outside the gut. Interplay among diet, immunity and microbial and host metabolism results in a complex multidirectional signalling that is critical in the maintenance of a healthy gut functionality, reducing risks for inflammatory bowel diseases and metabo-inflammation states associated with obesity.2 ,3 In parallel, the ‘omics’ era has produced many observations associated with disease states,4 and the correlation among the presence, absence or specific ratios of certain bacterial phyla, orders or genera can be considered as a strategy to directly or indirectly manipulate the microbiome. However, a clear causal molecular link between a specific microbial community and a specific metabolic or immune profile is …