Overview
- External ontology
- TOGO:M3002 — Geobacter NBAF Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M3002 Original source: JCM - JCM_M1327 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1327
Composition
flowchart LR
CultureMech_009520["geobacter_nbaf_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009520 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_009520 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_NaCl["NaCl"]
CultureMech_009520 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_009520 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_KH2PO4["KH2PO4"]
CultureMech_009520 --> ing4_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing4_KH2PO4 -.-> CHEBI_63036
ing5_NH4Cl["NH4Cl"]
CultureMech_009520 --> ing5_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing5_NH4Cl -.-> CHEBI_31206
ing6_K2HPO4["K2HPO4"]
CultureMech_009520 --> ing6_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing6_K2HPO4 -.-> CHEBI_131527
ing7_KCl["KCl"]
CultureMech_009520 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_Fe2_SO4_3_nH2O["Fe2(SO4)3·nH2O"]
CultureMech_009520 --> ing8_Fe2_SO4_3_nH2O
ing9_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009520 --> ing9_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing9_Carbon_dioxide_gas -.-> CHEBI_16526
ing10_N2["N2"]
CultureMech_009520 --> ing10_N2
CHEBI_17997["CHEBI:17997"]
ing10_N2 -.-> CHEBI_17997
ing11_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_009520 --> ing11_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing11_Na2MoO4_2H2O -.-> CHEBI_75213
ing12_H3BO3["H3BO3"]
CultureMech_009520 --> ing12_H3BO3
CHEBI_33118["CHEBI:33118"]
ing12_H3BO3 -.-> CHEBI_33118
ing13_FeSO4_7H2O["FeSO4·7H2O"]
CultureMech_009520 --> ing13_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing13_FeSO4_7H2O -.-> CHEBI_75836
ing14_MnCl2_4H2O["MnCl2·4H2O"]
CultureMech_009520 --> ing14_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing14_MnCl2_4H2O -.-> CHEBI_86368
ing15_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_009520 --> ing15_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing15_Nitrilotriacetic_acid -.-> CHEBI_44557
ing16_Na2WO4_2H2O["Na2WO4·2H2O"]
CultureMech_009520 --> ing16_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing16_Na2WO4_2H2O -.-> CHEBI_63939
ing17_NiSO4_6H2O["NiSO4·6H2O"]
CultureMech_009520 --> ing17_NiSO4_6H2O
CHEBI_53001["CHEBI:53001"]
ing17_NiSO4_6H2O -.-> CHEBI_53001
ing18_CoCl2_6H2O["CoCl2·6H2O"]
CultureMech_009520 --> ing18_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing18_CoCl2_6H2O -.-> CHEBI_35696
ing19_ZnSO4_7H2O["ZnSO4·7H2O"]
CultureMech_009520 --> ing19_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing19_ZnSO4_7H2O -.-> CHEBI_32312
ing20_CuCl2_2H2O["CuCl2·2H2O"]
CultureMech_009520 --> ing20_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing20_CuCl2_2H2O -.-> CHEBI_86318
ing21_AlK_SO4_2["AlK(SO4)2"]
CultureMech_009520 --> ing21_AlK_SO4_2
CHEBI_86463["CHEBI:86463"]
ing21_AlK_SO4_2 -.-> CHEBI_86463
ing22_NaOH["NaOH"]
CultureMech_009520 --> ing22_NaOH
CHEBI_32145["CHEBI:32145"]
ing22_NaOH -.-> CHEBI_32145
Ingredients (23)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
901.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 900.0, 1.0] |
| 2 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.1 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
NaCl
Cl.Na 58.443 g/mol
|
0.36 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.04 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.42 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.2 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.22 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
KCl
Cl.K 74.551 g/mol
|
0.38 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 | Fe2(SO4)3·nH2O | 0.01 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component | |
| 10 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 11 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 12 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.09 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
H3BO3
H3BO3 61.833 g/mol
|
0.005 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
FeSO4·7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.3 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
MnCl2·4H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.1 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
2.14 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 17 |
Na2WO4·2H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.02 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
NiSO4·6H2O
Ni.O4S 154.756 g/mol
|
0.11 G_PER_L |
CHEBI:53001
nickel sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
CoCl2·6H2O
2Cl.Co 129.839 g/mol
|
variable VARIABLE |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component |
| 20 |
ZnSO4·7H2O
7H2O.O4S.Zn 287.558 g/mol
|
variable VARIABLE |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component |
| 21 |
CuCl2·2H2O
Cl2Cu.2H2O 170.482 g/mol
|
variable VARIABLE |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component |
| 22 |
AlK(SO4)2
Al.K.2O4S 258.206 g/mol
|
variable VARIABLE |
CHEBI:86463
potassium aluminium sulfate
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component |
| 23 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution |
Solutions
0.1% Na2SeO4 solution
Dose: 1 G_PER_L
Role: Mineral source; Properties: Inorganic compound, Defined component, Solution
NB Mineral elixir solution (see below)
Dose: 10 G_PER_L
8% NaHCO3 solution*
Dose: 20 G_PER_L
Role: Buffer; Properties: Inorganic compound, Defined component, Solution
5% Na2CO3 solution*
Dose: 10 G_PER_L
Role: Buffer; Properties: Inorganic compound, Defined component, Solution
1 M Sodium acetate solution
Dose: 15 G_PER_L
Role: Buffer; Properties: Organic compound, Defined component, Solution
1 M Sodium fumarate solution
Dose: 40 G_PER_L
Properties: Defined component, Organic compound, Solution
Trace vitamins (see Medium [M190])
Dose: 15 G_PER_L
Cross-reference to Medium M190
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.808020Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M3002 |
| 2026-01-28T19:48:20.122505Z | 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: N2; Added default concentration for ingredient: CoCl2·6H2O; Added default concentration for ingredient: ZnSO4·7H2O; Added default concentration for ingredient: CuCl2·2H2O; Added default concentration for ingredient: AlK(SO4)2; Added default concentration for ingredient: NaOH |
| 2026-03-09T08:04:33.374500+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 7 solution(s) from ingredients |
| 2026-03-13T03:09:02.794617Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:20:06.548447Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009520 |
| 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 |
| 2026-03-17T06:30:08.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:25.558389+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Geobacter NBAF Medium" to "geobacter_nbaf_medium" for consistent matching |
| 2026-05-16T09:03:16.404016+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:39.667785+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 16 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:29.077756+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. |
| 2026-06-10T07:46:50.054164+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |