When mixed organic waste is used for hydrogen production by dark fermentation, the microbial community which is most adapted to the actual biopolymer composition of the substrate is auto-selected. In this research, six substrates simulating different biopolymers (proteins, fats, carbohydrates) and their mixtures were used to enrich hydrogen-producing bacteria adapted to these substrates from non-pretreated sewage sludge. Phylum Firmicutes dominated in the microbial community (67–100%) regardless of the substrate used, as was shown by high-throughput sequencing. Microbial diversity was low when using carbohydrate-rich substrates and the microbial community was mainly represented by Ruminococcus (26–90%) and Thermoanaerobacterium (6–67%). Dark fermentation of fats and proteins was characterized by higher microbial diversity. Thermoanaerobacterium (21%), Thermobrachium (19%), Tepidiphilus (16%) and Acetomicrobium (14%) dominated when using fats, while Thermobrachium (34%), Acetomicrobium (16%) and Clostridium sensu stricto 7 (12%) dominated when using proteins, as substrate. Different microbial communities and substrates resulted in diverse process performance and metabolic pathways. Dark fermentation of starch achieved the maximum hydrogen yield of 138 mL/g volatile solids with 60.4% hydrogen content in biogas. The dominance of genus Ruminococcus was thought to be responsible for the highest hydrogen production. Minor quantities of methane from proteins and fats were produced by Methanothermobacter and Methanosarcina. Based upon the stable 13C isotope analysis, the hydrogenotrophic pathway was a slightly more predominant methane formation route than the others considered.
