. 2021 Oct 7;11:19913. doi: 10.1038/s41598-021-99389-4

Table 3.

Identified genera in animal manure samples and their predicted metabolic contributions to biogas production.

Genus	Relative abundance in animal manure	Predicted metabolic contribution	References
Bacteria genera in consortia likely playing roles in pathways related to growth and the synthesis and degradation of growth metabolites in manure
Escherichia	Horse < cow < pig	Facultatively anaerobic with wide spectrum capability for several organic carbon sources necessary for heterotrophic growth, also known to be involved in acidogenesis. Mostly harmless but some species and strains are pathogenic	^{57, 58}
Glutamicibacter	Horse < cow < pig	Members of the genus are involved in lignocellulosic material saccharification, amino acid metabolism	^{59, 60}
Psychrobacter	Pig < Horse < cow	Psychrobacter spp. are capable of producing cold-active enzymes with involvement in the physiological strategies that off-set low temperature effects on cellular ATP and ADP generation, a key requirement in metabolic and energy conservation reactions The KEGG pathway shows involvement in riboflavin and tryptophan metabolism (see P. cryohalolentis and P. articus)	⁶¹
Aerococcus	Horse < cow < pig	Members of the genus produce acids from a variety of carbohydrates and are directly involved in acidogenesis The KEGG pathway shows involvement of A. urinae in anaerobic energy and selenocompound metabolism. Some species are considered pathogenic	^62–64
Oceanisphaera	Pig	The KEGG pathway shows involvement of Oceanisphaera profunda in selenocompounds, arachidonic and 2-oxocarboxylic acid metabolism	⁶⁵
Turicibacter	Horse = pig = cow	Members of the genus have been identified as being involved in fat metabolism e.g. T. sanguinis, might be important for host lipid and steroid metabolism The KEGG pathway shows the involvement of Turicibacter sp. H121 in Tryptophan metabolism and T. sanguinis involvement in carbohydrate, amino acid, lipid and nucleic acid metabolism	^66–68
Romboutsia	Pig < cow = horse	Members of the genus have a broad range of capabilities in carbohydrate utilisation but not necessarily cellulose and xylose, fermentation of single amino acids, anaerobic respiration and metabolic end products. Although, there are variations in these abilities with different strains in the manner in which they utilise carbohydrates to synthesize vitamins and nitrogen as well as nitrogen assimilation capabilities	^{69, 70}
Bacteria genera in consortia likely playing roles in pathways related to complex lignocellulose degradation and represented within other hydrocarbon pathways
Glutamicibacter	Horse < cow < pig	Members of the genus are involved in lignocellulosic material saccharification, amino acid metabolism	^{59, 71}
Jaetgalicoccus	Horse < pig < cow	Members of the genus are capable of producing terminal alkenes inferring its production of functional enzymes in complex hydrocarbon degradation. It produces enzymes involved the one-step fatty acid decarboxylation reaction employing OleTJE cytochrome P450. KEGG pathway describes thiamine metabolism in Jeotgalicoccus sp. ATCC 8456	^{72, 73}
Bacteria genera in consortia likely playing roles in pathways with direct relation to acidogenesis and acetogenesis
Escherichia	Horse < cow < pig	Facultatively anaerobic with wide spectrum capability for several organic carbon sources necessary for heterotrophic growth, also known to be involved in acidogenesis. Mostly harmless but some species and strains are pathogenic	^{57, 74}
Jaetgalicoccus	Horse < pig < cow	Members of the genus are capable of producing terminal alkenes inferring its production of functional enzymes in complex hydrocarbon degradation. It produces enzymes involved the one-step fatty acid decarboxylation reaction employing OleTJE cytochrome P450. KEGG pathway describes thiamine metabolism in Jeotgalicoccus sp. ATCC 8456	^{72, 73}
Aerococcus	Horse < cow < pig	Members of the genus produce acids from a variety of carbohydrates and are directly involved in acidogenesis The KEGG pathway shows involvement of A. urinae in anaerobic energy and selenocompound metabolism. Some species are considered pathogenic	^62–64
Enterococcus	Horse < pig < cow	Members of the genus employ fermentative metabolism for the conversion of a variety of carbohydrates to lactic acid. They are strict anaerobes as they lack apparatus for implementing Kreb’s cycle reactions. However, they utilise each of the three possible routes of intermediary carbohydrate metabolism – the Embden-Meyerhof-Parnas (glycolysis), Entner-Doudoroff, and pentose phosphate (phosphogluconate) pathways	^{75, 76}
Staphylococcus	Horse < pig < cow	Some members of the genus Staphylococcus are facultatively aerobe and in aerobic conditions can synthesize enzymes such as lactate dehydrogenases and alcohol dehydrogenases with an accumulation of lactic acid and acetic acid. In hypoxic conditions they associate and form biofilms for protection	^{77, 78}
Lactobacillus	Horse = pig < cow	Lactobacilli ferment hexose sugars to produce lactic acid using the phosphoketolase pathway to produce lactate, CO₂ and acetate or ethanol as major end products. They are also capable of acidogenesis biosyntheses of amino acids, purine/pyrimidines, and cofactors	^{79, 80}
Corynebacterium	Horse < cow = pig	Corynebacteria demonstrate fermentative metabolism of various carbohydrates to lactic acid under certain conditions. They are fastidious slow-growing organisms that are also able to produce glutamic acid, lysine and threonine. The KEGG pathway describes nitrogen metabolism in C. glutamicum R	⁸¹
Prevotella	Pig = cow	Members of this genus utilise glucose in anaerobic growth using the Embden-Meyerhof-Parnas pathway and the usual enzymes involved except that phosphofructokinase was pyrophosphate-dependent. The cells use available glucose to produce acetate, formate and succinate	^{82, 83}
Terrisporobacter	Pig = cow	Members of the genus are able to ferment glucose to produce acetates	^{84, 85}
Streptococcus	Horse < cow = pig	Species of Streptococcus utilise carbohydrate metabolism to generate energy for growth generating acids in the process. They are mostly pathogenic	^{86, 87}
Clostridium	Cow < Pig < horse	Most members of these species are pathogenic to animals. They are capable of converting various carbohydrates to succinate and acetate	^{70, 88}
Sporobacter	Horse = pig	Members of the genus are capable of using organic compounds in metabolism yielding acetates	^{89, 90}
Bacteria genera in consortia that are likely pathogenic
Asaccharospora	Horse	One identified species Asaccharospora irregularis resembling in characteristics Clostridium irregularis described as pathogenic	⁷⁰
Aerococcus	Horse < cow < pig	Members of the genus produce acids from a variety of carbohydrates and are directly involved in acidogenesis The KEGG pathway shows involvement of A. urinae in anaerobic energy and selenocompound metabolism. Some species are considered pathogenic	^62–64
Acinetobacter	Horse = pig < cow	Most members of this genus are pathogenic and possess virulence factors but enzymes produced are also involved in amino acid, carbohydrate and lipid transport and metabolism	⁹¹
Pseudomonas	Horse = pig < cow	Pseudomonas spp. perform anaerobic energy metabolism, carbon-sources versatility observed in the free-living bacteria allowing it to selectively assimilate a preferred carbon-source from mixtures in a process known as carbon catabolite repression using regulatory mechanisms. Some species have multiple virulence factors	^{92, 93}
Streptococcus	Horse < cow = pig	Species of Streptococcus utilise carbohydrate metabolism to generate energy for growth generating acids in the process. They are mostly pathogenic	^{86, 87}
Clostridium	Cow < Pig < horse	Most members of these species are pathogenic to animals. They are capable of converting various carbohydrates to succinate and acetate	^{70, 88}
Treponema	Cow	Members of the genus are pathogenic	^{94, 95}