A majority of archaea was affiliated to Methanomicrobiales, andMathanobacteriales and less to Methanosaetaceae and Methanosarcinaceae(Fig. 6). The Methanococcales abundance wasbelow detection limit in all the samples. Also, it is noted thatMethanosarcinaceae was found to increase in number in all thereactors when the experiment was ended. Methanomicrobiales,which was abundant in the beginning phase of SM-containingflasks, are reduced at the end indicating that methane productionwas limited. In the flasks with CD and CD-SSM the percentage ofMethanobacteriales was increased indicating the higher biogasyields. The evaluation of the different methanogenic speciesrevealed a clear view for co-digestion samples and most specificallyfor sheep addition. As for mono-digestion of SM, the total amountof Methanobacteriales in this treatment has a decreasing trend andreflects the lowest biogas, perhaps due to strong inhibition inmono-digestion of SM which hinders the growth of methanogens.The stable pH and TVFA values from the beginning and the end ofthe experiment (Table 4) indicate that higher amount of substratescan be treated. However, these findings cannot explain the directcorrelation between the methanogenic communities and processconditions. The importance of co-substrate selection for biogaspotential essays is important, as substrates contain specific microbialspecies which is related to different metabolic pathwaysduring the AD as influences between microorganisms occur