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

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

Pathway analyzed	Predicted product after fermentation	Clostridium cellulosi DG5		Clostridium sp. N3C		Clostridium bornimense M2/40^T		Clostridium thermocellum BC1		Proteiniborus sp. DW1		Sporanaerobacter sp. PP17-6a		Herbinix hemicellulosilytica T3/55^T		Herbinix luporum SD1D^T
Pathway analyzed	Predicted product after fermentation	GP	EP^a	GP	EP	GP	EP^b	GP	EP	GP	EP	GP	EP	GP	EP^c	GP	EP^d
Propionic acid fermentation^g
Acrylyl-CoA pathway	Propionic acid	−	ND	−	NA	−	NC (D)	−	NA	+	NA	−	NA	−	NC (D)	−	N
Methylmalonyl-CoA pathway	Propionic acid	−	ND	−		−	NC (D)	−		−		+		−	NC (D)	−	N
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	+	D	+		+	ND	+		+		+		+	D	+	D
	Lactate	+	ND	+		+	D	+		+		−		+	ND	+	ND
	Succinate	−		+		+	ND	+		−		−		−	ND	+	ND
Butyric acid fermentation	Butyrate	−		+		+	D	−		+		+		+	D	+	D
Homoacetogenesis	Acetate	+	D	+		+	ND	+		+		+		+	D	+	D
Lactic acid fermentation
Homolactic acid fermentation	Lactate	+	ND	+		+	D	+		+		−		+	ND	+	ND
Heterolactic acid fermentation	Lactate	−	ND	−		−	D	−		−		−		−	ND	−	ND
	Acetate	+	D			+	ND	+		+		+		+	D	+	D
	Ethanol	+	D			+	D	+		+		+		+	D	+	D

Pathway analyzed	Predicted product after fermentation	Peptoniphilaceae bacterium str. ING2-D1G		Propionispora sp. 2/2-37		Bacillus thermoamylovorans 1A1		Proteiniphilum saccharofermentans M3/6^T		Fermentimonas caenicola ING2-E5B^T		Petrimonas mucosa ING2-E5A^T		Defluviitoga tunisiensis L3
Pathway analyzed	Predicted product after fermentation	GP	EP^a	GP	EP^a	GP	EP^a	GP	EP^e	GP	EP^e	GP	EP^e	GP	EP^f
Propionic acid fermentation^g
Acrylyl-CoA pathway	Propionic acid	−	ND	−	D	−	ND	−	D	−	D	−	D	−	ND
Methylmalonyl-CoA pathway	Propionic acid	−		+		+	ND	+	D	+	D	+	D	−
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	+	D	+	D
	Lactate	+	ND	+	ND	+	ND	+	ND	+	ND	+	ND	+	ND
	Succinate	−	ND	−	ND	+		+		+		+	ND	+
Butyric acid fermentation	Butyrate	+	D	+	D	+		+		+		+	D	+
Homoacetogenesis	Acetate	+	D	+	D	+	D	+	D	+	D	+	D	+	D
Lactic acid fermentation
Homolactic acid fermentation	Lactate	+	ND	+	ND	+	ND	+	ND	+	ND	+	ND	+	ND
Heterolactic acid fermentation	Lactate		ND	−	ND	−	ND	−	ND	−	ND	−	ND	−
	Acetate	+	D	+	D	+	D	+	D	+	D	+	D	+
	Ethanol	+	ND	+	D	+	D	+	D	+	D	+	ND	+

Genomic loci encoding enzymatic functions participating to the corresponding fermentation type for each bacterial strain analyzed are listed in Additional file 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
^aUnpublished data
^bData published in [20]
^cData published in [54]
^dData published in [55]
^eData published in [26]
^fData published in [27]
^gPathways for propionic acid synthesis via succinate decarboxylation or amino acid degradation were not included

ISSN: 2731-3654