Alcohol dependence has traditionally considered as a brain disorder. Alteration of gut microbiota composition has been recently shown in psychiatric disorders, which suggest the possibility of gut to brain interactions in the development of alcohol dependence. The aim of the present study was to explore whether the changes in gut permeability are linked to gut microbiota composition and activity in alcohol-dependent subjects. We also investigated whether gut dysfunctions are associated with the psychological symptoms of alcohol-dependence. Finally, we tested the reversibility of the biological and behavioural parameters after a short-term detoxification program. We found that some, but not all, alcohol-dependent subjects develop gut leakiness which was associated with altered composition and activity of gut microbiota. Moreover, subjects with gut dysfunctions remained with higher scores of depression, anxiety and alcohol craving after three weeks of abstinence. These results suggest the existence of a gut-brain axis in alcohol-dependence which implicates the gut microbiota as an actor in the occurrence of the gut barrier and behavioural disorders. Thus, gut microbiota appears as a new target in the management of alcohol-dependence.