| Summary: | With growing demand for clean and cheap energy resources, biogas production is emerging as an ideal solution, as it provides relatively cheap and clean energy, while also tackling the problematic production of excessive organic waste from crops and animal agriculture. Behind this process stands a variety of anaerobic microorganisms, which turn organic substrates into valuable biogas. The biogas itself is a mixture of gases, produced mostly as metabolic byproducts of the microorganisms, such as methane, hydrogen, or carbon dioxide. Hydrogen itself figures as a potent bio-fuel, however in many bioreactors it serves as the main substrate of methanogenesis, thus potentially limiting biogas yield. With help of modern sequencing techniques, we tried to evaluate the composition in eight bioreactors using different input materials, showing shifts in the microbial consortia depending on the substrate itself. In this paper, we provide insight on the occurrence of potentially harmful microorganisms such as <i>Clostridium novyi</i> and <i>Clostridium septicum</i>, as well as key genera in hydrogen production, such as <i>Clostridium</i> <i>stercorarium</i>, <i>Mobilitalea</i> sp., <i>Herbinix</i> sp., <i>Herbivorax</i> sp., and <i>Acetivibrio</i> sp.
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