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Table 3 Prediction of bacterial fermentation pathways as deduced from genome sequence information

From: Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Pathway analyzed Predicted product after fermentation Clostridium cellulosi DG5 Clostridium sp. N3C Clostridium bornimense M2/40T Clostridium thermocellum BC1 Proteiniborus sp. DW1 Sporanaerobacter sp. PP17-6a Herbinix hemicellulosilytica T3/55T Herbinix luporum SD1DT
GP EPa GP EP GP EPb GP EP GP EP GP EP GP EPc GP EPd
Propionic acid fermentationg                  
 Acrylyl-CoA pathway Propionic acid ND NA NC (D) NA + NA NA NC (D) N
 Methylmalonyl-CoA pathway +
Ethanol fermentation Ethanol + D + + D + + + + D + D
Formic acid fermentation              
 2,3-Butanediol fermentation 2,3-Butanediol ND ND ND ND
Formic acid + + D + + + +
CO2 and H2 + D +
 Mixed-acid fermentation Ethanol + D + + D + + + + D + D
Acetate + + + ND + + + + +
Lactate + ND + + D + + + ND + ND
Succinate + + ND + +
Butyric acid fermentation Butyrate + + D + + + D + D
Homoacetogenesis Acetate + D + + ND + + + + +
Lactic acid fermentation              
 Homolactic acid fermentation Lactate + ND + + D + + + ND + ND
 Heterolactic acid fermentation Lactate D
Acetate + D + ND + + + + D + D
Ethanol + + D + + + + +
Pathway analyzed Predicted product after fermentation Peptoniphilaceae bacterium str. ING2-D1G Propionispora sp. 2/2-37 Bacillus thermoamylovorans 1A1 Proteiniphilum saccharofermentans M3/6T Fermentimonas caenicola ING2-E5BT Petrimonas mucosa ING2-E5AT Defluviitoga tunisiensis L3   
GP EPa GP EPa GP EPa GP EPe GP EPe GP EPe GP EPf   
Propionic acid fermentationg                  
 Acrylyl-CoA pathway Propionic acid ND D ND D D D ND   
 Methylmalonyl-CoA pathway + + + + +   
Ethanol fermentation Ethanol + + D + ND + ND + ND +   
Formic acid fermentation             
 2,3-Butanediol fermentation 2,3-Butanediol + ND + ND   
Formic acid + + + + +   
CO2 and H2 +   
 Mixed-acid fermentation Ethanol + D + D + + +   
Acetate + D + + + D + D + D + D   
Lactate + ND + ND + ND + ND + ND + ND + ND   
Succinate + + + + +   
Butyric acid fermentation Butyrate + D + D + + + + D +   
Homoacetogenesis Acetate + D + + D + D + D + + D   
Lactic acid fermentation                  
 Homolactic acid fermentation Lactate + ND + ND + ND + ND + ND + ND + ND   
 Heterolactic acid fermentation Lactate    
Acetate + D + D + D + D + D + D +   
Ethanol + ND + + + + + ND +   
  1. Genomic loci encoding enzymatic functions participating to the corresponding fermentation type for each bacterial strain analyzed are listed in Additional file 2
  2. +, synthesis of the corresponding fermentation end-product is predicted; −, pathway incomplete or misses key enzymes, the synthesis of the corresponding fermentation end-product is doubtful; EP, experimental proof; D, the corresponding fermentation product has been experimentally detected; GP, genes predicted applying metabolic reconstruction within the GenDB 2.0 system [39]; NA; not analyzed; NC, not confirmed; ND, fermentation product has been experimentally not detected
  3. aUnpublished data
  4. bData published in [20]
  5. cData published in [54]
  6. dData published in [55]
  7. eData published in [26]
  8. fData published in [27]
  9. gPathways for propionic acid synthesis via succinate decarboxylation or amino acid degradation were not included