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Four full-scale anaerobic digesters with a long history of stable operation were characterized in terms of active microbiome and metagenome. Isotopic fractionation of biogas demonstrated that acetotrophy was rather prevalent in reactors operated at 6 gTAN L−1, suggesting that syntrophic acetate oxidizing bacteria (SAOB) played a significant role in the latter. These results were generally coherent with the observed active bacterial and archaeal communities but no known SAOB were observed. Metagenome descriptions yielded 73 assembled population genomes, of which only 7 could be assigned at the species level. Gene annotation and association to relevant metabolic pathways indicated that the phyla Chloroflexi and Bacteroidales might encompass new, currently undescribed, SAOB/formate producing species that would metabolize acetate via the glycine cleavage system. The predominant hydrogenotrophic counterpart at a high ammonia content belonged to the genus Methanoculleus, which could also grow on acetate to a certain extent.