Table 3 Identified genera in animal manure samples and their predicted metabolic contributions to biogas production.

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

^62,63,64

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

^66,67,68

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

^62,63,64

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

^62,63,64

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}