List and description of Metage2Metabo (M2M) commands.
Command
Action
m2m workflow
Runs the whole m2m workflow
m2m metacom
Runs the workflow with already-reconstructed metabolic networks
m2m recon
Reconstructs metabolic networks using Pathway Tools
m2m iscope
Computes scopes for individual metabolic networks
m2m cscope
Computes the community scope
m2m addedvalue
Computes the cooperation potential
m2m mincom
Selects a minimal community and computes key species
m2m seeds
Creates a SBML file for nutrients
m2m test
Runs m2m workflow on a sample dataset
m2m_analysis
Runs additional analyses on community selection
Table 2
Results of the genome-scale metabolic network (GSMN) reconstruction step and metabolic potential analysis for the three datasets presented in the article (Avg = Average, '±' precedes standard deviation).
Gut dataset
Rumen dataset
Diabetes dataset
Initial data
Draft reference genomes
MAGs
MAGs
Number of genomes
1520
913
778
GSMN reconstruction
All reactions
3932
4418
5554
All metabolites
4001
4466
5386
Avg reactions per GSMN
1144 (±255)
1155 (±199)
1640 (±368)
Avg metabolites per GSMN
1366 (±262)
1422 (±212)
1925 (±361)
Avg genes per mn
596 (±150)
543 (±107)
1658 (±469)
% reactions associated to genes
74.6 (±2.17)
73.8 (±2.61)
79.57 (±1.60)
Avg pathways per mn
163 (±49)
146 (±32)
220 (±58)
Metabolic potential
Number of seeds
93
26
175
Avg scope per mn
286 (±70)
101 (±44)
508 (±83)
Union of individual scopes
828
368
1326
Table 3
Community reduction analysis of the target categories in the gut.
All minimal communities were enumerated, starting from the set of 1520 genome-scale metabolic networks (GSMNs). KS: key species, ES: essential symbionts, AS: alternative symbionts, Firm.: …
Firm.
Bact.
Acti.
Prot.
Fuso.
Total
Aminoacids and derivatives (5 targets)4 bact. per community120,329 communities
KS
142
52
0
27
6
227
ES
0
0
0
0
0
0
AS
142
52
0
27
6
227
Aromatic compounds (11 targets)5 bact. per community950 communities
KS
52
0
0
20
0
72
ES
2
0
0
1
0
3
AS
50
0
0
19
0
69
Carboxyacids (14 targets)9 bact. per community48,412 communities
KS
16
13
0
28
2
59
ES
2
0
0
2
0
4
AS
14
13
0
26
2
55
CoA derivatives (10 targets)5 bact. per community95,256 communities
KS
106
0
50
17
1
174
ES
0
0
0
0
1
1
AS
106
0
50
17
0
173
Lipids (28 targets)7 bact. per community58,520 communities
KS
3
140
22
20
0
185
ES
3
0
0
1
0
4
AS
0
140
22
19
0
181
Sugar derivatives (58 targets)11 bact. per community7,860,528 communities
KS
11
30
78
23
0
142
ES
5
0
0
0
0
5
AS
6
30
78
23
0
137
Appendix 1—table 1
Effect of MAG degradation on genome-scale metabolic network (GSMN) reconstructions.
Numbers are averages. '±' precedes standard deviation values. 'original’: initial MAGs prior degradation, '2pc100’: 2% gene removal in all MAGs, '5pc80’: 5% gene removal in 80% of MAGs, '5pc100’: 5% …