2 glucose
4 NAD+
2 ATP
2 ADP
4 NADH
2 oxaloacetate
2 NADH
4 PEP
4 ADP
2 NAPD+
2 NAD+
2 NADPH
4 ATP
2 malate
4 pyruvate
2 CoA
2 H2O
2 fumarate
2 NADH
1 succinate
*
2 NAD+
2 succinate
CoA
2 CO2
+
1 CO2
2 H2
2 Fdox
2 Fdred2-
2 acetyl-CoA
2 Pi
2 CoA
2 acetyl-P
2 ADP
1 succinyl-CoA
2 ATP
2 acetate
1 methylmalonyl-CoA
?
*
1 propionyl-CoA
1 propionate
B1. This assumption is based on values given by Macfarlane & Gibson (1997) for carbohydrate-limited chemostat growth of B. thetaiotaomicron,
B . ovatus and B. fragilis under a CO2 atmosphere. Lactate is reported to be an additional product under a 100% N2 atmosphere. *indicates
energy gain by electron or ion transport (may not operate in all bacteria for methylmalonyl-CoA to propionyl-CoA conversion). Dashed lines
indicate alternative routes for propionate formation (no effect on overall product balance). PEP: phosphoenolpyruvate.
(A)
(B)
1 glucose
2 ADP
2 NAD+
2 ADP
2 NAD+
2 ATP
2 NADH
2 ATP
2 NADH
2 pyruvate
1 ethanol
2 pyruvate
2 H2
4 H2
2 CoA
2 Fdox
2 CoA
2 Fdox
2 CO2
2 Fdred2-
2 CO2
2 Fdred2-
2 acetyl-CoA
2 NAD+
1 glucose
2 NADH
1 Pi
2 Pi
1 CoA
2 CoA
2 acetyl-P
1 acetyl-P
1 acetate
2 acetyl-CoA
1 ADP
2 ADP
1 ATP
2 ATP
2 acetate
B2. Fermentative metabolism of starch-degrading relatives of R. bromii (Moore et al. 1972). Ethanol is produced in addition to acetate in pure
culture, when it provides a hydrogen sink (A). The assumption made for the intact community however is that hydrogen will be consumed by
other microorganisms, especially acetogens and methanogens, resulting in formation of two acetates rather than acetate plus ethanol by R.
bromii (B) (Wolin & Miller, 1983). It is assumed that CO2 rather than formate is produced. The details of electron transfer to hydrogen remain to
be established (dotted line).
1 glucose
2 NAD+
2 NADH
1 ATP
1 ADP
2 PEP
1 oxaloacetate
1 ADP
1 NADH
1
1 ATP
NAD+
1 pyruvate
1 malate
1 Fdox
1 CoA
1 Fdred2-
1 CO2
1 H2O
1 fumarate
1 NADH
1 NAD+
1 acetyl-CoA
1 Pi
*
1 succinate
1 H2
1 CoA
1 acetyl-P
1 ADP
1 ATP
1 acetate
B3. Relatives of R. flavefaciens isolated from the human colon are reported to produce acetate, succinate and ethanol in pure culture (Robert &
Bernalier-Donadille 2003). It has been assumed here that ethanol will be replaced by additional acetate in the mixed community as a result of
interspecies hydrogen transfer (see B2). *indicates energy gain by electron or ion transport. PEP: phosphoenolpyruvate.
6 glucose
6 ATP
6 ADP
3 fructose-6-P + 3 fructose-6-P
3 Pi
3 H2O
3 ADP
3 ATP
3 erythrose-4-P + 3 acetyl-P
6 xylulose-5-P
6 Pi
6 ADP
6 H2O
6 ATP
6 acetate
6 glyceraldehyde-3-P + 6 acetyl-P
12 ADP
6 NAD+
6 NADH
12 ATP
3 acetate
4 NADH 4 NAD+
4 lactate
6 pyruvate
2 Pi
2 ADP
2 formate + 2 acetyl-P
2 ATP
1 acetate
2 NADH
2 NAD+
1 Pi
1 ethanol
B4. Metabolic scheme for bifidobacteria is based on Macfarlane & Gibson (1997). Assumed stoichiometries are based on observations for
Bifidobacterium adolescentis growing on starch (Belenguer et al. 2006). The metabolism of another major group of Actinobacteria, those related
to Collinsella aerofaciens (formerly Eubacterium aerofaciens), has received little study but these organisms also produce lactate, acetate,
formate and ethanol (Moore & Holdeman Moore 1986).
2 glucose
4 ADP
4 NAD+
4 ATP
4 NADH
4 pyruvate
4 CoA
4 Fdox
4 CO2
1 CoA
1 Pi
1 acetyl-P
4 acetyl-CoA
1 ADP
3 CoA
3 acetyl-CoA
3 butyrate
1 ATP
3 acetoacetyl-CoA
2 acetate
3 acetate
3 butyryl-CoA
3 Fdox
6 NADH
6 NAD+
3 NADH
3 NAD+
3 Etf
3 EtfH2
3 3-hydroxybutyryl-CoA
3 crotonyl-CoA
3 H2O
2 H2
2 Fdox
7 Fdred2-
5 NAD+
5 NADH
5 Fdox
cytoplasm
membrane
10 H+
B5. Metabolic scheme for butyrate producers is based on Louis & Flint (2009). For details on redox carriers involved see Louis & Flint (2009).
Assumed stoichiometries are based on observations for Roseburia spp. grown at a pH of 5.5 (Fig. 4 in main manuscript).
6 glucose
12 ADP
8 NAD+
4 NAD+
12 ATP
8 NADH
4 NADH
12 pyruvate
8 CoA
4 lactate
6 Fdox
6 CO2
3 CoA
2 formate
3 Pi
3 acetyl-P
8 acetyl-CoA
3 ADP
5 CoA
5 acetyl-CoA
5 butyrate
3 ATP
5 acetoacetyl-CoA
2 acetate
5 acetate
5 butyryl-CoA
5 Fdox
10 NADH
5 NADH
5 Etf
10 NAD+
5 EtfH2
5 NAD+
5 3-hydroxybutyryl-CoA
5 crotonyl-CoA
5 H2O
4 H2
4 Fdox
11 Fdred2-
7 NAD+
7 NADH
7 Fdox
cytoplasm
membrane
14 H+
B5 Alt. Metabolic scheme for butyrate producers is based on Louis & Flint (2009). Assumed stoichiometries are based observations for multiple
strains of Eubacterium rectale (Duncan & Flint 2008) and Roseburia spp. (Duncan et al 2006) grown at a pH of approximately 6.5. E. rectale in
particular produces significant amounts of lactate in pure culture.
6 glucose
12 ADP
10 NAD+
2 NAD+
12 ATP
10 NADH
2 NADH
12 pyruvate
10 CoA
2 lactate
4 Fdox
4 CO2
3 CoA
6 formate
3 Pi
3 acetyl-P
10 acetyl-CoA
3 ADP
7 CoA
7 acetyl-CoA
7 butyrate
3 ATP
7 acetoacetyl-CoA
4 acetate
7 acetate
7 butyryl-CoA
7 Fdox
14 NADH
7 Etf
14 NAD+
0 Fdox
7 NADH
7 EtfH2
11 Fdred2-
7 NAD+
7 3-hydroxybutyryl-CoA
7 crotonyl-CoA
11 NAD+
11 NADH
7 H2O
11 Fdox
cytoplasm
membrane
22 H+
B6. Metabolic scheme for butyrate producers is based on Louis & Flint (2009). Assumed stoichiometries for Faecalibacterium prausnitzii-related
bacteria are based on observations of Duncan et al (2002) showing formation of formate and lactate but no hydrogen.
(A)
(B)
3 glucose
4 NAD+
4 lactate
6 ADP
6 NAD+
6 ATP
6 NADH
1 NAD+
4 NADH
6 pyruvate
4 CoA
4 lactoyl-CoA
2 Fdox
2 CoA
2 Fdred2-
2 CO2
2 acetyl-CoA
3 lactate
1 pyruvate
2 CoA
2 lactoyl-CoA
2 Pi
4 H2O
4 acryloyl-CoA
2 CoA
2 acetyl-P
1 NADH
1 Fdox
1 CoA
1 Fdred2-
1 CO2
1 acetyl-CoA
1 Pi
2 H2O
2 acryloyl-CoA
1 CoA
1 acetyl-P
4 NADH
2 ADP
2 NADH
1 ADP
4 NAD+
2 ATP
2 NAD+
1 ATP
4 propionyl-CoA
4 CoA
4 propionate
2 acetate
2 propionyl-CoA
1 acetate
2 CoA
2 propionate
B7. Little is known about propionate producers from the human gut utilising the acrylate pathway. This assumption is based on Gottschalk (1979)
and Prins (1977) on glucose (A) and lactate (B) for bacteria related to Megasphaera. The details of electron transfer remain to be established
(dotted line). Bacteria related to Veillonella and Selenomonas produce propionate from glucose or lactate via succinate as shown for group B1,
with additional energy gain from sodium transport from methylmalonyl-CoA to propionyl-CoA (Prins (1977), Seeliger et al (2002)). We assume
the same stoichiometries as generated by the acrylate pathway.
10 glucose
(A)
20 ADP
20 NAD+
20 ATP
20 NADH
20 pyruvate
20 CoA
2 ATP
8 CO2
2 ADP
11 CoA
11 acetyl-P
2 acetate
8 Fdox
12 formate
11 Pi
20 acetyl-CoA
9 ADP
9 CoA
9 acetyl-CoA
9 butyrate
9 ATP
9 acetoacetyl-CoA
4 acetate
9 acetate
9 butyryl-CoA
9 Fdox
18 NADH
18 NAD+
9 NADH
9 Etf
9 EtfH2
9 NAD+
9 3-hydroxybutyryl-CoA
9 crotonyl-CoA
9 H2O
10 H2
10 Fdox
17 Fdred2-
7 NAD+
7 NADH
7 Fdox
cytoplasm
membrane
14 H+
B8(A). Metabolic scheme for butyrate producers is based on Louis & Flint (2009). Assumed stoichiometries for Eubacterium hallii-related
bacteria are based on observations of Duncan et al (2004) for growth on glucose.
(B)
4 NADH
4 NAD+
4 pyruvate
4 CoA
4 lactate
4 Fdox
4 CO2
1 CoA
1 acetyl-P
1 Pi
4 acetyl-CoA
1 ADP
3 CoA
3 acetyl-CoA
3 butyrate
1 ATP
3 acetoacetyl-CoA
2 acetate
3 acetate
3 butyryl-CoA
3 Fdox
6 NADH
6 NAD+
3 NADH
3 NAD+
3 Etf
3 EtfH2
3 3-hydroxybutyryl-CoA
3 crotonyl-CoA
3 H2O
2 H2
2 Fdox
7 Fdred2-
5 NAD+
5 NADH
5 Fdox
cytoplasm
membrane
10 H+
B8(B). Metabolic scheme for butyrate producers is based on Louis & Flint (2009). Assumed stoichiometries for Eubacterium hallii-related
bacteria are based on observations of Duncan et al (2004) for growth on DL-lactate plus acetate.
(A)
(B)
1 glucose
2 ADP
2 NAD+
2 ATP
2 NADH
2 pyruvate
2 CoA
2 acetyl-CoA
CO2 + 2 [H] + CO2 + 2 [H]
formate
2 Pi
formate
2 CoA
ATP
H2O
H2O
ADP
2 acetyl-P
formyl-THF
2 ADP
H2O
2 ATP
methenyl-THF
[CO]
THF
2 [H]
2 acetate
1 acetate
methylene-THF
2 [H]
methyl-THF
E-[Co]
E-[Co]-CH3
CO2 + 2 [H]
+ CO2 + 2 [H]
formate
formate
ATP
H2O
ADP
formyl-THF
H2O
methenyl-THF
2 [H]
1 acetyl-P
CoA
Pi
acetyl-CoA
E-[Co]
2 [H]
methyl-THF
E-[Co]
E-[Co]-CH3
[CO]
THF
methylene-THF
ATP
ADP
H2O
1 acetate
ATP
ADP
1 acetyl-P
CoA
Pi
acetyl-CoA
E-[Co]
B9. Wood-Ljundahl pathway of acetogens is based on Ragsdale and Pierce (2008). Glucose (A) or CO2 plus H2 (B) are converted to acetate
(other C1 units may also be utilised). For simplicity reducing equivalents from H2 are given as [H], as various electron carriers are involved in the
individual reactions. THF: tetrahydrofolate, E-[Co]: enzyme-linked corrinoid. There is experimental evidence for energy gain by ion transport, but
the mechanisms remain unknown (Müller et al 2008).
(A)
(B)
4 formate
CO2 + 2 [H]
CO2 + 2 [H]
H2O
H2O
MF
MF
formyl-MF
formyl-MF
formyl-H4-MPT
formyl-H4-MPT
H2O
H2O
methenyl-H4-MPT
2 [H]
H4-MPT
methenyl-H4-MPT
2 [H]
H4-MPT
methylene-H4-MPT
2 [H]
methylene-H4-MPT
2 [H]
3 CO2
methyl-H4-MPT
methyl-H4-MPT
2 [H]
CoM-SH
CoM-SH
methyl-S-CoM
CoB-SH
methyl-S-CoM
CoB-SH
2 [H]
CoM-S-S-CoB
CH4
CoM-S-S-CoB
CH4
B10. Methanogenic pathways from either CO2 and H2 (A) or from formate (B) are based on Liu and Whitman (2008). For simplicity reducing
equivalents from H2 are given as [H], as various electron carriers are involved in the individual reactions. CoB: coenzyme B, CoM: coenzyme M,
MF: methanofuran, H4-MPT: tetrahydromethanopterin.
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