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Anaerobic Digestion (AD), which is mediated by microorganisms, is a highly effective biological method for the treatment of organic waste and the production of biogas. The primary determinants of bacterial community structure and the potential core and distinctive bacterial populations in manure anaerobic digesters are still not fully understood. Using high-throughput 16S rRNA amplicon sequencing, we examined the changes in bacterial community compositions in 20 full-scale anaerobic digesters processing bovine or swine dung for this study. Free Ammonia (FA) and substrate type appeared to be important factors in shaping the organisation of the bacterial population, according to clustering and correlation analysis. The most significant operational indicators that could be used to relate the bacterial populations in the digesters for swine and cow dung, respectively, were the COD: NH+ 4N (C: N) ratio of the substrate and FA. Firmicutes, followed by Bacteroidetes, Proteobacteria, and Chloroflexi, dominated the bacterial populations in all of the digesters. Firmicutes with higher FA content were chosen, indicating that these organisms possibly have more significant roles under high FA concentration. When FA level is high, syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes, and Planctomycetes is likely suppressed. Despite varying manure substrates, operational circumstances, and digester locations, core bacterial populations were found. The phylum Firmicutes, where Clostridium predominated heavily, best described the core communities. Communities that are plentiful and specific to the substrate may indicate operational circumstances and manure substrate characteristics. Our present understanding of the bacterial assembly in large-scale manure anaerobic digesters is expanded by these findings.