Proper management of food waste has become a major cause of concern over the past few years in both developed and developing countries. This work aimed to properly treat food leftovers through 2-stage anaerobic fermentation at mesophilic temperature for biofuel production (H2 and CH4) and correlate this with the metabolic fingerprints of the most dominant bacterial strains in the two biofermenters. The diversity of bacterial communities in the surface, middle and bottom levels of the hydrogen fermenter as well as in the methane fermenter was examined. Moreover, the phenotypic identification and metabolic fingerprints for the bacterial strains was carried out using Biolog GEN III. The dominant bacterial strain responsible for hydrogen production was Bacillus amyloliquefaciens. While, Stenotrophomonas rhizophila was the most dominant in the methane fermenter. The total energy production was improved by 22.2% in case of increasing HRT for the first fermenter from 17h to 34h.