This thesis focuses on anaerobic digestion and, more specifically, on its role in biorefinery and on the dynamic behaviour of the underlying microbiomes. In recent decades, significant progress has been made in the field of anaerobic digestion. Innovative methods, especially highthroughput sequencing approaches, have allowed for a deeper understanding of biotechnologically relevant biocenosis. However, the exact behaviour of the relevant microbiomes under different conditions has not been thoroughly researched. In order to shed light on the diversity of the underlying biocenosis, this thesis compares multiple biogas production facilities in Germany. It also provides the first multi-OMICs characterization of separated acidification stages at mesophilic and thermophilic conditions. At the phylum level, three key microbiomes are identified, which are specific for sewage sludge, highly viscous codigester sludge, and leachate from leach-bed systems. All three microbiomes are strongly related to their underlying environmental parameters (Chemical oxygen demand, total organic carbon, total nitrogen contents, conductivity, total volatile fatty acids, total solids, volatile solids, pH, and volume of biogas). Through various experiments, new methods for acidifying biomass in pretreatment stages were investigated. One of the main contributions of this thesis is to highlight the importance of separated acidification stages as crossroad for multiple industries. Separated acidification potentially allows for the production of multiple organic acids, the usage of many varieties of waste, and the production of hydrogen simultaneously. Moreover, separated acidification might facilitate the usage of substrates that are difficult to digest, such as lignocellulose grass biomass or nitrogen-rich chicken dung. Indeed, this thesis demonstrates that both substrates can contribute to successful liquefaction. In searching for further possible applications based on acidification stages, we developed the first Microbial Thermoelectric Cell (MTC), which is compatible with anaerobic digestion and suitable for use in the pre-treatment stage. The MTC allows for the simultaneous production of ethanol and electric energy. Remnants might be used in a subsequent methane-producing stage. In addition, in seeking further new pretreatment methods, we investigated the possibility of combining thermal pre-treatment with microbe-driven acidification. Surprisingly, we observed only minimal impacts of heat-shocks in the microbial composition. Therefore, it might be possible in the future to combine heatshocks with acidification processes to improve biomass pre-treatment. Furthermore, this possibility highlights the robustness of microbiomes from anaerobic digestion processes. Finally, we isolated news strains from the acidification of grass biomass, with foreseeable roles in anaerobic digestion.This thesis focuses on anaerobic digestion and, more specifically, on its role in biorefinery and on the dynamic behaviour of the underlying microbiomes. In recent decades, significant progress has been made in the field of anaerobic digestion. Innovative methods, especially highthroughput sequencing approaches, have allowed for a deeper understanding of biotechnologically relevant biocenosis. However, the exact behaviour of the relevant microbiomes under different conditions has not been thoroughly researched. In order to shed light on the diversity of the underlying biocenosis, this thesis compares multiple biogas production facilities in Germany. It also provides the first multi-OMICs characterization of separated acidification stages at mesophilic and thermophilic conditions. At the phylum level, three key microbiomes are identified, which are specific for sewage sludge, highly viscous codigester sludge, and leachate from leach-bed systems. All three microbiomes are strongly related to their underlying environmental parameters (Chemical oxygen demand, total organic carbon, total nitrogen contents, conductivity, total volatile fatty acids, total solids, volatile solids, pH, and volume of biogas). Through various experiments, new methods for acidifying biomass in pretreatment stages were investigated. One of the main contributions of this thesis is to highlight the importance of separated acidification stages as crossroad for multiple industries. Separated acidification potentially allows for the production of multiple organic acids, the usage of many varieties of waste, and the production of hydrogen simultaneously. Moreover, separated acidification might facilitate the usage of substrates that are difficult to digest, such as lignocellulose grass biomass or nitrogen-rich chicken dung. Indeed, this thesis demonstrates that both substrates can contribute to successful liquefaction. In searching for further possible applications based on acidification stages, we developed the first Microbial Thermoelectric Cell (MTC), which is compatible with anaerobic digestion and suitable for use in the pre-treatment stage. The MTC allows for the simultaneous production of ethanol and electric energy. Remnants might be used in a subsequent methane-producing stage. In addition, in seeking further new pretreatment methods, we investigated the possibility of combining thermal pre-treatment with microbe-driven acidification. Surprisingly, we observed only minimal impacts of heat-shocks in the microbial composition. Therefore, it might be possible in the future to combine heatshocks with acidification processes to improve biomass pre-treatment. Furthermore, this possibility highlights the robustness of microbiomes from anaerobic digestion processes. Finally, we isolated news strains from the acidification of grass biomass, with foreseeable roles in anaerobic digestion.