Overview
- External ontology
- TOGO:M2167 — Denitrovibrio Medium
- Applications
-
- Microbial cultivation
- High-metal flag
- True
- Notes
- Source: https://togomedium.org/medium/M2167 Original source: NBRC - NBRC_M1550 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=1550
Composition
flowchart LR
CultureMech_008761["denitrovibrio_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008761 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_008761 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008761 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_008761 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_008761 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_Resazurin["Resazurin"]
CultureMech_008761 --> ing5_Resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Resazurin -.-> CHEBI_8806
ing6_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_008761 --> ing6_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing6_MgCl2_6H2O -.-> CHEBI_86345
ing7_Na2S_9H2O["Na2S·9H2O"]
CultureMech_008761 --> ing7_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing7_Na2S_9H2O -.-> CHEBI_76209
ing8_KCl["KCl"]
CultureMech_008761 --> ing8_KCl
CHEBI_32588["CHEBI:32588"]
ing8_KCl -.-> CHEBI_32588
ing9_Sodium_acetate["Sodium acetate"]
CultureMech_008761 --> ing9_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing9_Sodium_acetate -.-> CHEBI_32954
ing10_Na2CO3["Na2CO3"]
CultureMech_008761 --> ing10_Na2CO3
CHEBI_29377["CHEBI:29377"]
ing10_Na2CO3 -.-> CHEBI_29377
ing11_Na2SO4["Na2SO4"]
CultureMech_008761 --> ing11_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing11_Na2SO4 -.-> CHEBI_32149
ing12_Disodium_fumarate["Disodium fumarate"]
CultureMech_008761 --> ing12_Disodium_fumarate
CHEBI_115156["CHEBI:115156"]
ing12_Disodium_fumarate -.-> CHEBI_115156
ing13_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008761 --> ing13_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing13_Carbon_dioxide_gas -.-> CHEBI_16526
ing14_Nitrogen_gas["Nitrogen gas"]
CultureMech_008761 --> ing14_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing14_Nitrogen_gas -.-> CHEBI_17997
ing15_HCl__35__["HCl (35%)"]
CultureMech_008761 --> ing15_HCl__35__
ing16_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008761 --> ing16_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing16_Na2MoO4_2H2O -.-> CHEBI_75213
ing17_H3BO3["H3BO3"]
CultureMech_008761 --> ing17_H3BO3
CHEBI_33118["CHEBI:33118"]
ing17_H3BO3 -.-> CHEBI_33118
ing18_MnCl2_4H2O["MnCl2·4H2O"]
CultureMech_008761 --> ing18_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing18_MnCl2_4H2O -.-> CHEBI_86368
ing19_CoCl2_6H2O["CoCl2·6H2O"]
CultureMech_008761 --> ing19_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing19_CoCl2_6H2O -.-> CHEBI_35696
ing20_CuCl2_2H2O["CuCl2·2H2O"]
CultureMech_008761 --> ing20_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing20_CuCl2_2H2O -.-> CHEBI_86318
ing21_ZnCl2["ZnCl2"]
CultureMech_008761 --> ing21_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing21_ZnCl2 -.-> CHEBI_49976
ing22_FeCl3_6H2O["FeCl3·6H2O"]
CultureMech_008761 --> ing22_FeCl3_6H2O
CHEBI_86254["CHEBI:86254"]
ing22_FeCl3_6H2O -.-> CHEBI_86254
ing23_Na2WO4["Na2WO4"]
CultureMech_008761 --> ing23_Na2WO4
CHEBI_63940["CHEBI:63940"]
ing23_Na2WO4 -.-> CHEBI_63940
ing24_Na2SeO4["Na2SeO4"]
CultureMech_008761 --> ing24_Na2SeO4
CHEBI_77775["CHEBI:77775"]
ing24_Na2SeO4 -.-> CHEBI_77775
ing25_NiCl2_2H2O["NiCl2·2H2O"]
CultureMech_008761 --> ing25_NiCl2_2H2O
CHEBI_34887["CHEBI:34887"]
ing25_NiCl2_2H2O -.-> CHEBI_34887
ing26_Biotin["Biotin"]
CultureMech_008761 --> ing26_Biotin
CHEBI_15956["CHEBI:15956"]
ing26_Biotin -.-> CHEBI_15956
ing27_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_008761 --> ing27_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing27_p_Aminobenzoic_acid -.-> CHEBI_30753
ing28_Pyridoxine_HCl__Vitamin_B6_["Pyridoxine-HCl (Vitamin B6)"]
CultureMech_008761 --> ing28_Pyridoxine_HCl__Vitamin_B6_
ing29_Folic_acid["Folic acid"]
CultureMech_008761 --> ing29_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing29_Folic_acid -.-> CHEBI_27470
CultureMech_008761 --> more["...7 more"]
Ingredients (37)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
3.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 3 duplicates: 1.0, 1.0, 1.0] |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
20 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.15 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
|
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
|
0.25 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
Resazurin
C12H7NO4 229.191 g/mol
|
0.5 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 7 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
3 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
Na2S·9H2O
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 |
| 9 |
KCl
Cl.K 74.551 g/mol
|
0.5 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
1.64 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 11 |
Na2CO3
CO3.2Na 105.988 g/mol
|
1 G_PER_L |
CHEBI:29377
sodium carbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
Na2SO4
2Na.O4S 142.043 g/mol
|
0.02 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
Disodium fumarate
C4H2O4.2Na 160.036 g/mol
|
6.4 G_PER_L |
CHEBI:115156
disodium fumarate
|
Properties: Defined component, Organic compound, Simple component |
| 14 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 15 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 16 | HCl (35%) | 7 G_PER_L | Role: Solvating media; Properties: Defined component, Inorganic compound, Solution | |
| 17 |
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 |
| 18 |
H3BO3
H3BO3 61.833 g/mol
|
6 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
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 |
| 20 |
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 |
| 21 |
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 |
| 22 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
70 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
FeCl3·6H2O
Cl3Fe.6H2O 270.294 g/mol
|
1.5 G_PER_L |
CHEBI:86254
iron trichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
Na2WO4
2Na.O4W 293.816 g/mol
|
4 G_PER_L |
CHEBI:63940
sodium tungstate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
Na2SeO4
2Na.O4Se 188.936 g/mol
|
4 G_PER_L |
CHEBI:77775
sodium selenate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 26 |
NiCl2·2H2O
Cl2Ni 129.599 g/mol
|
24 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 27 |
Biotin
C10H16N2O3S 244.316 g/mol
|
2 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
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 |
| 29 | Pyridoxine-HCl (Vitamin B6) | 10 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 30 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 | Cyanocobalamin (Vitamin B12) | 0.1 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 32 | Riboflavin (Vitamin B2) | 5 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 33 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 34 | Thiamine-HCl·H2O (Vitamin B1) | 5 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 35 |
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 |
| 36 |
D-Ca-Pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
5 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
Role: Vitamin; Properties: Defined component |
| 37 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution |
Solutions
Trace element solution SL-10*
Dose: 1 G_PER_L
See mediadive_4178_Trace_element_solution_SL-10.yaml for composition
Vitamin solution**
Dose: 10 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M2167_Denitrovibrio_Medium (CultureMech:008761)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:59.193838Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M2167 |
| 2026-01-28T19:48:21.439492Z | 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: NaOH |
| 2026-03-09T08:04:35.838722+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:05.187014Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:00.110083Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008761 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:11.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:18.767776+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Denitrovibrio Medium" to "denitrovibrio_medium" for consistent matching |
| 2026-05-16T09:03:12.424333+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:35.578853+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 26 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:31.802881+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. |
| 2026-06-10T07:46:48.633179+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. |
| 2026-08-06T03:05:10.544945+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint bc5acd4fcb81114205f152ec6fec371d916f74b1728ae26b7de05f1265c3f48c |