Overview
- External ontology
- TOGO:M599 — Alicycliphilus Denitrificans Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M599 Original source: JCM - JCM_M594 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=594
Composition
flowchart LR
CultureMech_009996["alicycliphilus_denitrificans_medium"]
ing0_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009996 --> ing0_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing0_Carbon_dioxide_gas -.-> CHEBI_16526
ing1_N2["N2"]
CultureMech_009996 --> ing1_N2
CHEBI_17997["CHEBI:17997"]
ing1_N2 -.-> CHEBI_17997
ing2_Distilled_water["Distilled water"]
CultureMech_009996 --> ing2_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing2_Distilled_water -.-> CHEBI_15377
ing3_KH2PO4["KH2PO4"]
CultureMech_009996 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NaNO3["NaNO3"]
CultureMech_009996 --> ing4_NaNO3
CHEBI_63005["CHEBI:63005"]
ing4_NaNO3 -.-> CHEBI_63005
ing5_Na2HPO4_2H2O["Na2HPO4・2H2O"]
CultureMech_009996 --> ing5_Na2HPO4_2H2O
CHEBI_34683["CHEBI:34683"]
ing5_Na2HPO4_2H2O -.-> CHEBI_34683
ing6_Sodium_acetate_3H2O["Sodium acetate・3H2O"]
CultureMech_009996 --> ing6_Sodium_acetate_3H2O
CHEBI_32954["CHEBI:32954"]
ing6_Sodium_acetate_3H2O -.-> CHEBI_32954
ing7_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_009996 --> ing7_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing7_CaCl2_x_2_H2O -.-> CHEBI_86158
ing8_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009996 --> ing8_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing8_MgCl2_6H2O -.-> CHEBI_86345
ing9_NaHCO3["NaHCO3"]
CultureMech_009996 --> ing9_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing9_NaHCO3 -.-> CHEBI_32139
ing10_Na2SO4["Na2SO4"]
CultureMech_009996 --> ing10_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing10_Na2SO4 -.-> CHEBI_32149
ing11_NH4HCO3["NH4HCO3"]
CultureMech_009996 --> ing11_NH4HCO3
CHEBI_184335["CHEBI:184335"]
ing11_NH4HCO3 -.-> CHEBI_184335
Ingredients (12)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 2 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 3 |
Distilled water
H2O 18.015 g/mol
|
1000.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Simple component, Defined component [Merged 3 duplicates: 900.0, 50.0, 50.0] |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.41 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Simple component, Defined component |
| 5 |
NaNO3
NO3.Na 84.994 g/mol
|
0.85 G_PER_L |
CHEBI:63005
sodium nitrate
|
Role: Nitrogen source; Properties: Defined component, Simple component, Inorganic compound |
| 6 |
Na2HPO4・2H2O
HO4P.2Na 141.958 g/mol
|
0.53 G_PER_L |
CHEBI:34683
disodium hydrogenphosphate
|
Role: Buffer; Properties: Defined component, Inorganic compound, Simple component |
| 7 |
Sodium acetate・3H2O
C2H3O2.Na 82.034 g/mol
|
0.136 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Simple component, Defined component |
| 8 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.11 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.1 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component |
| 10 |
NaHCO3
CHO3.Na 84.006 g/mol
|
3.73 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component |
| 11 |
Na2SO4
2Na.O4S 142.043 g/mol
|
0.2 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 12 |
NH4HCO3
CHO3.H4N 79.055 g/mol
|
0.44 G_PER_L |
CHEBI:184335
Ammonium bicarbonate
|
Role: Nitrogen source; Properties: Inorganic compound, Simple component, Defined component |
Solutions
Solution A
Dose: 903 G_PER_L
See mediadive_5342_Solution_A.yaml for composition
Solution B
Dose: 50 G_PER_L
See mediadive_5343_Solution_B.yaml for composition
Solution C
Dose: 50 G_PER_L
See mediadive_5312_Solution_C.yaml for composition
FeCl2 solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Trace element solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Selenite--tungstate solution (see Medium [M431])
Dose: 1 G_PER_L
Cross-reference to Medium M431
1.0 M Sodium acetate solution
Dose: 10 G_PER_L
Role: Buffer; Properties: Defined component, Organic compound, Solution
Vitamin solution (see Medium [M401])
Dose: 1 G_PER_L
Cross-reference to Medium M401
Thiamine solution (see Medium [M401])
Dose: 1 G_PER_L
Cross-reference to Medium M401
Vitamin B12 solution (see Medium [M401])
Dose: 1 G_PER_L
Cross-reference to Medium M401
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M599_Alicycliphilus_Denitrificans_Medium (CultureMech:009996)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.375239Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M599 |
| 2026-01-28T19:48:08.194929Z | 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 |
| 2026-03-09T08:04:13.185712+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 10 solution(s) from ingredients |
| 2026-03-13T03:08:40.143463Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:10.595966Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009996 |
| 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; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:29:42.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.522485+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Alicycliphilus Denitrificans Medium" to "alicycliphilus_denitrificans_medium" for consistent matching |
| 2026-05-16T09:03:19.420891+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:42.874207+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 7 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:51.117209+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-06T03:05:17.664676+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint ebb1d386864d5dc9721d66657ef01f48ef92b3b4e3b2d10109736579ac148d2b |