Overview
- External ontology
- TOGO:M655 — NCDC-99X Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M655 Original source: JCM - JCM_M641 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=641
Composition
flowchart LR
CultureMech_010057["ncdc_99x_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010057 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Yeast_extract["Yeast extract"]
CultureMech_010057 --> ing1_Yeast_extract
ing2_Resazurin["Resazurin"]
CultureMech_010057 --> ing2_Resazurin
CHEBI_8806["CHEBI:8806"]
ing2_Resazurin -.-> CHEBI_8806
ing3_Na2CO3["Na2CO3"]
CultureMech_010057 --> ing3_Na2CO3
CHEBI_29377["CHEBI:29377"]
ing3_Na2CO3 -.-> CHEBI_29377
ing4_Histidine["Histidine"]
CultureMech_010057 --> ing4_Histidine
CHEBI_27570["CHEBI:27570"]
ing4_Histidine -.-> CHEBI_27570
ing5_Arginine["Arginine"]
CultureMech_010057 --> ing5_Arginine
CHEBI_32696["CHEBI:32696"]
ing5_Arginine -.-> CHEBI_32696
ing6_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
CultureMech_010057 --> ing6_L__Cysteine_HCl_H2O
CHEBI_91248["CHEBI:91248"]
ing6_L__Cysteine_HCl_H2O -.-> CHEBI_91248
ing7_Phytone_peptone__BD_BBL_["Phytone peptone (BD-BBL)"]
CultureMech_010057 --> ing7_Phytone_peptone__BD_BBL_
ing8_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010057 --> ing8_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing8_Carbon_dioxide_gas -.-> CHEBI_16526
ing9_Nitrogen_gas["Nitrogen gas"]
CultureMech_010057 --> ing9_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing9_Nitrogen_gas -.-> CHEBI_17997
ing10_K2HPO4["K2HPO4"]
CultureMech_010057 --> ing10_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing10_K2HPO4 -.-> CHEBI_131527
ing11_MgSO4_7H2O["MgSO4・7H2O"]
CultureMech_010057 --> ing11_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing11_MgSO4_7H2O -.-> CHEBI_31795
ing12_NaCl["NaCl"]
CultureMech_010057 --> ing12_NaCl
CHEBI_26710["CHEBI:26710"]
ing12_NaCl -.-> CHEBI_26710
ing13_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010057 --> ing13_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing13_CaCl2_2H2O -.-> CHEBI_86158
ing14_KH2PO4["KH2PO4"]
CultureMech_010057 --> ing14_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing14_KH2PO4 -.-> CHEBI_63036
ing15__NH4_2SO4["(NH4)2SO4"]
CultureMech_010057 --> ing15__NH4_2SO4
CHEBI_62946["CHEBI:62946"]
ing15__NH4_2SO4 -.-> CHEBI_62946
Ingredients (16)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 3 identical duplicates: 1.0, 1.0, 1.0] |
| 2 | Yeast extract | 1 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 3 |
Resazurin
C12H7NO4 229.191 g/mol
|
1 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 4 |
Na2CO3
CO3.2Na 105.988 g/mol
|
4 G_PER_L |
CHEBI:29377
sodium carbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
Histidine
C6H9N3O2 155.157 g/mol
|
1.55 G_PER_L |
CHEBI:27570
histidine
|
Role: Nitrogen source; Properties: Organic compound, Defined component, Simple component |
| 6 |
Arginine
C6H15N4O2 175.212 g/mol
|
2.11 G_PER_L |
CHEBI:32696
argininium(1+)
|
Role: Nitrogen source; Properties: Organic compound, Defined component, Simple component |
| 7 |
L--Cysteine・HCl・H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
|
0.5 G_PER_L |
CHEBI:91248
L-cysteine hydrochloride hydrate
|
Properties: Defined component, Organic compound, Simple component |
| 8 | Phytone peptone (BD-BBL) | 2 G_PER_L | Properties: Undefined 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 |
K2HPO4
HO4P.2K 174.174 g/mol
|
6 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
|
1.2 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
NaCl
Cl.Na 58.443 g/mol
|
12 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
1.2 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
KH2PO4
H2O4P.K 136.084 g/mol
|
6 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
(NH4)2SO4
2H4N.O4S 132.141 g/mol
|
12 G_PER_L |
CHEBI:62946
ammonium sulfate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
Solutions
Mineral solution 1 (see below)
Dose: 37.5 G_PER_L
Mineral solution 2 (see below)
Dose: 37.5 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.476428Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M655 |
| 2026-01-28T19:48:33.204958Z | 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 |
| 2026-03-09T08:04:55.013011+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:26.512801Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:11.022174Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010057 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:35.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.949811+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "NCDC-99X Medium" to "ncdc_99x_medium" for consistent matching |
| 2026-05-16T09:03:19.824475+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:43.319182+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 8 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:32.122925+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. |
| 2026-06-10T07:46:51.264174+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. |
| 2026-09-02T07:37:51.402876+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |