Overview
- External ontology
- TOGO:M2113 — Sulfur-oxidizing bacterium medium
- Applications
-
- Microbial cultivation
- High-metal flag
- True
- Notes
- Source: https://togomedium.org/medium/M2113 Original source: NBRC - NBRC_M1437 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=1437
Composition
flowchart LR
CultureMech_008706["sulfur_oxidizing_bacterium_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008706 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_008706 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008706 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_008706 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_008706 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_KCl["KCl"]
CultureMech_008706 --> ing5_KCl
CHEBI_32588["CHEBI:32588"]
ing5_KCl -.-> CHEBI_32588
ing6_Sodium_acetate["Sodium acetate"]
CultureMech_008706 --> ing6_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing6_Sodium_acetate -.-> CHEBI_32954
ing7_NaNO3["NaNO3"]
CultureMech_008706 --> ing7_NaNO3
CHEBI_63005["CHEBI:63005"]
ing7_NaNO3 -.-> CHEBI_63005
ing8_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008706 --> ing8_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing8_Carbon_dioxide_gas -.-> CHEBI_16526
ing9_Nitrogen_gas["Nitrogen gas"]
CultureMech_008706 --> ing9_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing9_Nitrogen_gas -.-> CHEBI_17997
ing10_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008706 --> ing10_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing10_Na2MoO4_2H2O -.-> CHEBI_75213
ing11_H3BO3["H3BO3"]
CultureMech_008706 --> ing11_H3BO3
CHEBI_33118["CHEBI:33118"]
ing11_H3BO3 -.-> CHEBI_33118
ing12_FeSO4_7H2O["FeSO4·7H2O"]
CultureMech_008706 --> ing12_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing12_FeSO4_7H2O -.-> CHEBI_75836
ing13_MnCl2_4H2O["MnCl2·4H2O"]
CultureMech_008706 --> ing13_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing13_MnCl2_4H2O -.-> CHEBI_86368
ing14_CoCl2_6H2O["CoCl2·6H2O"]
CultureMech_008706 --> ing14_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing14_CoCl2_6H2O -.-> CHEBI_35696
ing15_NiCl2_6H2O["NiCl2·6H2O"]
CultureMech_008706 --> ing15_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing15_NiCl2_6H2O -.-> CHEBI_34887
ing16_ZnSO4_7H2O["ZnSO4·7H2O"]
CultureMech_008706 --> ing16_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing16_ZnSO4_7H2O -.-> CHEBI_32312
ing17_CuCl2_2H2O["CuCl2·2H2O"]
CultureMech_008706 --> ing17_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing17_CuCl2_2H2O -.-> CHEBI_86318
ing18_HCl__25___7_7_M_["HCl (25%; 7.7 M)"]
CultureMech_008706 --> ing18_HCl__25___7_7_M_
ing19_Na2SeO3_5H2O["Na2SeO3·5H2O"]
CultureMech_008706 --> ing19_Na2SeO3_5H2O
CHEBI_131361["CHEBI:131361"]
ing19_Na2SeO3_5H2O -.-> CHEBI_131361
ing20_Na2WO4_2H2O["Na2WO4·2H2O"]
CultureMech_008706 --> ing20_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing20_Na2WO4_2H2O -.-> CHEBI_63939
ing21_NaOH["NaOH"]
CultureMech_008706 --> ing21_NaOH
CHEBI_32145["CHEBI:32145"]
ing21_NaOH -.-> CHEBI_32145
ing22_NaHCO3["NaHCO3"]
CultureMech_008706 --> ing22_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing22_NaHCO3 -.-> CHEBI_32139
ing23_CO2_gas["CO2 gas"]
CultureMech_008706 --> ing23_CO2_gas
ing24_Sodium_phosphate_buffer__10_mM__pH7_1_["Sodium phosphate buffer (10 mM; pH7.1)"]
CultureMech_008706 --> ing24_Sodium_phosphate_buffer__10_mM__pH7_1_
ing25_Biotin["Biotin"]
CultureMech_008706 --> ing25_Biotin
CHEBI_15956["CHEBI:15956"]
ing25_Biotin -.-> CHEBI_15956
ing26_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_008706 --> ing26_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing26_p_Aminobenzoic_acid -.-> CHEBI_30753
ing27_Thiamine_HCl["Thiamine-HCl"]
CultureMech_008706 --> ing27_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing27_Thiamine_HCl -.-> CHEBI_49105
ing28_Ca_pantothenate["Ca-pantothenate"]
CultureMech_008706 --> ing28_Ca_pantothenate
CHEBI_29032["CHEBI:29032"]
ing28_Ca_pantothenate -.-> CHEBI_29032
ing29_Pyridoxine_HCl["Pyridoxine-HCl"]
CultureMech_008706 --> ing29_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing29_Pyridoxine_HCl -.-> CHEBI_30961
CultureMech_008706 --> more["...4 more"]
Ingredients (34)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
2118.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 5 duplicates: 930.0, 987.0, 1.0, 100.0, 100.0] |
| 2 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.5 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.1 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.1 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
KCl
Cl.K 74.551 g/mol
|
0.1 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
0.16 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 8 |
NaNO3
NO3.Na 84.994 g/mol
|
0.85 G_PER_L |
CHEBI:63005
sodium nitrate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 10 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 11 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
36 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
H3BO3
H3BO3 61.833 g/mol
|
30 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
FeSO4·7H2O
Fe.7H2O.O4S 278.013 g/mol
|
2100 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
MnCl2·4H2O
Cl2Mn.4H2O 197.904 g/mol
|
100 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
CoCl2·6H2O
2Cl.Co 129.839 g/mol
|
190 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
NiCl2·6H2O
Cl2Ni 129.599 g/mol
|
24 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
ZnSO4·7H2O
7H2O.O4S.Zn 287.558 g/mol
|
144 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
CuCl2·2H2O
Cl2Cu.2H2O 170.482 g/mol
|
2 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 | HCl (25%; 7.7 M) | 12.5 G_PER_L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component | |
| 20 |
Na2SeO3·5H2O
5H2O.2Na.O3Se 263.012 g/mol
|
6 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
Na2WO4·2H2O
2H2O.2Na.O4W 329.846 g/mol
|
8 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
NaOH
HO.Na 39.997 g/mol
|
0.4 G_PER_L |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Simple component, Inorganic compound |
| 23 |
NaHCO3
CHO3.Na 84.006 g/mol
|
8.4 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 24 | CO2 gas | variable VARIABLE | Properties: ガス | |
| 25 | Sodium phosphate buffer (10 mM; pH7.1) | 100 G_PER_L | Role: Buffer; Properties: Defined component, Inorganic compound, Solution | |
| 26 |
Biotin
C10H16N2O3S 244.316 g/mol
|
1 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 27 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
4 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
Thiamine-HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
10 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 29 |
Ca-pantothenate
C9H16NO5 218.229 g/mol
|
5 G_PER_L |
CHEBI:29032
(R)-pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 30 |
Pyridoxine-HCl
C8H11NO3.HCl 205.641 g/mol
|
15 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 |
Cyanocobalamin
C63H88CoN14O14P 1355.388 g/mol
|
5 G_PER_L |
CHEBI:17439
cyanocob(III)alamin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 32 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
10 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 33 |
Na2S2O3·5H2O
5H2O.2Na.O3S2 248.186 g/mol
|
24.8 G_PER_L |
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Defined component, Inorganic compound, Simple component |
| 34 | N2 gas | variable VARIABLE | Properties: ガス |
Solutions
Trace element mixture*
Dose: 1 G_PER_L
Selenite-tungstate solution**
Dose: 1 G_PER_L
See mediadive_5543_Selenite-tungstate_solution.yaml for composition
Bicarbonate solution***
Dose: 30 G_PER_L
See mediadive_29_Bicarbonate_solution.yaml for composition
Vitamin solution****
Dose: 1 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Thiosulfate solution****
Dose: 20 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:59.085250Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M2113 |
| 2026-01-28T19:48:33.959384Z | 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: Nitrogen gas; Added default concentration for ingredient: CO2 gas; Added default concentration for ingredient: N2 gas |
| 2026-03-09T08:04:56.352801+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 5 solution(s) from ingredients |
| 2026-03-13T03:09:27.910944Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:59.593453Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008706 |
| 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 |
| 2026-03-17T06:30:37.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:18.235082+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Sulfur-oxidizing bacterium medium" to "sulfur_oxidizing_bacterium_medium" for consistent matching |
| 2026-05-16T09:04:32.927408+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:47.603674+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 25 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:50.749695+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. |
| 2026-06-10T06:58:33.470299+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. |
| 2026-06-10T07:47:12.080529+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |