Overview
- External ontology
- TOGO:M2658 — Methanosphaera (MCB-3) Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M2658 Original URL: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium322.pdf
Composition
flowchart LR
CultureMech_009213["methanosphaera_mcb_3_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009213 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
CultureMech_009213 --> ing1_MgSO4_x_7_H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_x_7_H2O -.-> CHEBI_31795
ing2_Yeast_extract["Yeast extract"]
CultureMech_009213 --> ing2_Yeast_extract
ing3_NaCl["NaCl"]
CultureMech_009213 --> ing3_NaCl
CHEBI_26710["CHEBI:26710"]
ing3_NaCl -.-> CHEBI_26710
ing4_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_009213 --> ing4_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing4_CaCl2_x_2_H2O -.-> CHEBI_86158
ing5_KH2PO4["KH2PO4"]
CultureMech_009213 --> ing5_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing5_KH2PO4 -.-> CHEBI_63036
ing6_NH4Cl["NH4Cl"]
CultureMech_009213 --> ing6_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing6_NH4Cl -.-> CHEBI_31206
ing7_K2HPO4["K2HPO4"]
CultureMech_009213 --> ing7_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing7_K2HPO4 -.-> CHEBI_131527
ing8_Na2S_x_9_H2O["Na2S x 9 H2O"]
CultureMech_009213 --> ing8_Na2S_x_9_H2O
CHEBI_76209["CHEBI:76209"]
ing8_Na2S_x_9_H2O -.-> CHEBI_76209
ing9_NaHCO3["NaHCO3"]
CultureMech_009213 --> ing9_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing9_NaHCO3 -.-> CHEBI_32139
ing10__NH4_2SO4["(NH4)2SO4"]
CultureMech_009213 --> ing10__NH4_2SO4
CHEBI_62946["CHEBI:62946"]
ing10__NH4_2SO4 -.-> CHEBI_62946
ing11_Na_acetate["Na-acetate"]
CultureMech_009213 --> ing11_Na_acetate
CHEBI_32954["CHEBI:32954"]
ing11_Na_acetate -.-> CHEBI_32954
ing12_Methanol["Methanol"]
CultureMech_009213 --> ing12_Methanol
CHEBI_17790["CHEBI:17790"]
ing12_Methanol -.-> CHEBI_17790
ing13_Rumen_fluid__clarified["Rumen fluid, clarified"]
CultureMech_009213 --> ing13_Rumen_fluid__clarified
ing14_Trypticase_peptone__BD_BBL_["Trypticase peptone (BD BBL)"]
CultureMech_009213 --> ing14_Trypticase_peptone__BD_BBL_
ing15_Na_formate["Na-formate"]
CultureMech_009213 --> ing15_Na_formate
CHEBI_62965["CHEBI:62965"]
ing15_Na_formate -.-> CHEBI_62965
ing16_L_Cysteine_HCl_x_H2O["L-Cysteine-HCl x H2O"]
CultureMech_009213 --> ing16_L_Cysteine_HCl_x_H2O
CHEBI_91248["CHEBI:91248"]
ing16_L_Cysteine_HCl_x_H2O -.-> CHEBI_91248
ing17_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009213 --> ing17_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing17_Carbon_dioxide_gas -.-> CHEBI_16526
ing18_Hydrogen_gas["Hydrogen gas"]
CultureMech_009213 --> ing18_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing18_Hydrogen_gas -.-> CHEBI_18276
ing19_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
CultureMech_009213 --> ing19_Na2MoO4_x_2_H2O
CHEBI_75213["CHEBI:75213"]
ing19_Na2MoO4_x_2_H2O -.-> CHEBI_75213
ing20_H3BO3["H3BO3"]
CultureMech_009213 --> ing20_H3BO3
CHEBI_33118["CHEBI:33118"]
ing20_H3BO3 -.-> CHEBI_33118
ing21_FeSO4_x_7_H2O["FeSO4 x 7 H2O"]
CultureMech_009213 --> ing21_FeSO4_x_7_H2O
CHEBI_75836["CHEBI:75836"]
ing21_FeSO4_x_7_H2O -.-> CHEBI_75836
ing22_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
CultureMech_009213 --> ing22_NiCl2_x_6_H2O
CHEBI_34887["CHEBI:34887"]
ing22_NiCl2_x_6_H2O -.-> CHEBI_34887
ing23_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
CultureMech_009213 --> ing23_ZnSO4_x_7_H2O
CHEBI_32312["CHEBI:32312"]
ing23_ZnSO4_x_7_H2O -.-> CHEBI_32312
ing24_CuSO4_x_5_H2O["CuSO4 x 5 H2O"]
CultureMech_009213 --> ing24_CuSO4_x_5_H2O
CHEBI_31440["CHEBI:31440"]
ing24_CuSO4_x_5_H2O -.-> CHEBI_31440
ing25_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
CultureMech_009213 --> ing25_Na2SeO3_x_5_H2O
CHEBI_131361["CHEBI:131361"]
ing25_Na2SeO3_x_5_H2O -.-> CHEBI_131361
ing26_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
CultureMech_009213 --> ing26_CoSO4_x_7_H2O
CHEBI_91244["CHEBI:91244"]
ing26_CoSO4_x_7_H2O -.-> CHEBI_91244
ing27_KAl_SO4_2_x_12_H2O["KAl(SO4)2 x 12 H2O"]
CultureMech_009213 --> ing27_KAl_SO4_2_x_12_H2O
CHEBI_86465["CHEBI:86465"]
ing27_KAl_SO4_2_x_12_H2O -.-> CHEBI_86465
ing28_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_009213 --> ing28_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing28_Nitrilotriacetic_acid -.-> CHEBI_44557
ing29_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
CultureMech_009213 --> ing29_Na2WO4_x_2_H2O
CHEBI_63939["CHEBI:63939"]
ing29_Na2WO4_x_2_H2O -.-> CHEBI_63939
CultureMech_009213 --> more["...12 more"]
Ingredients (42)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
2900.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 3 duplicates: 900.0, 1000.0, 1000.0] |
| 2 |
MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
|
3.15 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.15, 3.0] |
| 3 | Yeast extract | 2 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 4 |
NaCl
Cl.Na 58.443 g/mol
|
1.6 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.6, 1.0] |
| 5 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.18 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.08, 0.1] |
| 6 |
KH2PO4
H2O4P.K 136.084 g/mol
|
2.8 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
NH4Cl
Cl.H4N 53.492 g/mol
|
1 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.6 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Na2S x 9 H2O
9H2O.2Na.S 240.182 g/mol
|
0.5 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
NaHCO3
CHO3.Na 84.006 g/mol
|
4 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
(NH4)2SO4
2H4N.O4S 132.141 g/mol
|
0.3 G_PER_L |
CHEBI:62946
ammonium sulfate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
Na-acetate
C2H3O2.Na 82.034 g/mol
|
0.5 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 13 |
Methanol
CH4O 32.042 g/mol
|
5 G_PER_L |
CHEBI:17790
methanol
|
Role: Solvating media; Properties: Organic compound, Defined component, Simple component |
| 14 | Rumen fluid, clarified | 100 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 15 | Trypticase peptone (BD BBL) | 2 G_PER_L | Properties: Undefined component | |
| 16 |
Na-formate
CHO2.Na 68.007 g/mol
|
0.5 G_PER_L |
CHEBI:62965
sodium formate
|
Properties: Simple component, Defined component, Inorganic compound |
| 17 |
L-Cysteine-HCl x H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
|
0.5 G_PER_L |
CHEBI:91248
L-cysteine hydrochloride hydrate
|
Properties: Defined component, Simple component, Organic compound |
| 18 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 19 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: ガス |
| 20 |
Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.01 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
H3BO3
H3BO3 61.833 g/mol
|
0.01 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
FeSO4 x 7 H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.1 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
|
0.03 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
|
0.18 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
CuSO4 x 5 H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.01 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 26 |
Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
|
0.3 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 27 |
CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
|
0.18 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 28 |
KAl(SO4)2 x 12 H2O
Al.12H2O.K.2O4S 474.386 g/mol
|
0.02 G_PER_L |
CHEBI:86465
potassium aluminium sulfate dodecahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 29 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
1.5 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 30 |
Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.4 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 31 |
MnSO4 x H2O
H2O.Mn.O4S 169.016 g/mol
|
0.5 G_PER_L |
CHEBI:86364
manganese(II) sulfate monohydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 32 |
Biotin
C10H16N2O3S 244.316 g/mol
|
2 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 33 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
5 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 34 |
Thiamine-HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
5 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 35 |
Pyridoxine-HCl
C8H11NO3.HCl 205.641 g/mol
|
10 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 36 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 37 | Vitamin B12 | 0.1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 38 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 39 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 40 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
5 G_PER_L |
CHEBI:16494
lipoic acid
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 41 |
D-Ca-pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
5 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
Role: Vitamin; Properties: Defined component |
| 42 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
Solutions
Na-resazurin solution (0.1% w/v)
Dose: 0.5 G_PER_L
Role: pH dependent redox indicator; Properties: Defined component, Solution
Na2SeO4 solution (0.1% w/v)
Dose: 1.9 G_PER_L
Role: Mineral source; Properties: Inorganic compound, Solution, Defined component
NiCl2 x 6 H2O solution (0.1% w/v)
Dose: 0.7 G_PER_L
Role: Mineral source; Properties: Defined component, Solution
FeSO4 x 7 H2O solution (0.1% w/v in 0.1 N H2SO4)
Dose: 3 G_PER_L
Role: Mineral source; Properties: Inorganic compound, Defined component, Solution
Trace element solution
Dose: 10 G_PER_L
See mediadive_6187_Trace_element_solution.yaml for composition
Vitamin solution
Dose: 20 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
KOH solution
Dose: variable VARIABLE
Role: Mineral source; Properties: Defined component, Solution
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:56.964821Z | togo-import | Imported from TOGO Medium | Source: TOGO, ID: M2658 |
| 2026-01-28T19:48:23.960836Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Hydrogen gas; Added default concentration for ingredient: KOH solution; Added default concentration for ingredient: N2 |
| 2026-03-09T08:04:39.604353+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 7 solution(s) from ingredients |
| 2026-03-13T03:09:09.480388Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 5 duplicate ingredient(s) |
| 2026-03-13T06:20:04.155314Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009213 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:16.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:22.880958+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methanosphaera (MCB-3) Medium" to "methanosphaera_mcb_3_medium" for consistent matching |
| 2026-05-16T09:04:22.655570+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:32.589738+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 35 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:47.936875+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24) | Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md. |
| 2026-06-10T06:58:23.415200+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:47:07.363442+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 7 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |