modified_d58_medium

CultureMech:008587 bacterial COMPLEX LIQUID
Original name: Modified D58 medium

Overview

External ontology
TOGO:M2000 — Modified D58 medium
Applications
  • Microbial cultivation
Synonyms
  • {'name': 'clostridium_thermocellum_medium_d58_medium', 'source': 'TOGO', 'source_id': 'TOGO:M1766', 'original_category': 'bacterial'}
Notes
Source: https://togomedium.org/medium/M2000 Original source: NBRC - NBRC_M1287 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=1287

Composition

flowchart LR
    CultureMech_008587["modified_d58_medium"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_008587 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_Yeast_extract["Yeast extract"]
    CultureMech_008587 --> ing1_Yeast_extract
    ing2_CaCl2_2H2O["CaCl2·2H2O"]
    CultureMech_008587 --> ing2_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing2_CaCl2_2H2O -.-> CHEBI_86158
    ing3_KH2PO4["KH2PO4"]
    CultureMech_008587 --> ing3_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing3_KH2PO4 -.-> CHEBI_63036
    ing4_Resazurin["Resazurin"]
    CultureMech_008587 --> ing4_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing4_Resazurin -.-> CHEBI_8806
    ing5_MgCl2_6H2O["MgCl2·6H2O"]
    CultureMech_008587 --> ing5_MgCl2_6H2O
    CHEBI_86345["CHEBI:86345"]
    ing5_MgCl2_6H2O -.-> CHEBI_86345
    ing6_FeSO4_7H2O["FeSO4·7H2O"]
    CultureMech_008587 --> ing6_FeSO4_7H2O
    CHEBI_75836["CHEBI:75836"]
    ing6_FeSO4_7H2O -.-> CHEBI_75836
    ing7__NH4_2SO4["(NH4)2SO4"]
    CultureMech_008587 --> ing7__NH4_2SO4
    CHEBI_62946["CHEBI:62946"]
    ing7__NH4_2SO4 -.-> CHEBI_62946
    ing8_K2HPO4_3H2O["K2HPO4·3H2O"]
    CultureMech_008587 --> ing8_K2HPO4_3H2O
    CHEBI_131527["CHEBI:131527"]
    ing8_K2HPO4_3H2O -.-> CHEBI_131527
    ing9_Cellobiose["Cellobiose"]
    CultureMech_008587 --> ing9_Cellobiose
    CHEBI_17057["CHEBI:17057"]
    ing9_Cellobiose -.-> CHEBI_17057
    ing10_Glutathione["Glutathione"]
    CultureMech_008587 --> ing10_Glutathione
    CHEBI_16856["CHEBI:16856"]
    ing10_Glutathione -.-> CHEBI_16856
    ing11_Sodium_glycerophosphate["Sodium glycerophosphate"]
    CultureMech_008587 --> ing11_Sodium_glycerophosphate
    ing12_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_008587 --> ing12_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing12_Carbon_dioxide_gas -.-> CHEBI_16526
    ing13_Nitrogen_gas["Nitrogen gas"]
    CultureMech_008587 --> ing13_Nitrogen_gas
    CHEBI_17997["CHEBI:17997"]
    ing13_Nitrogen_gas -.-> CHEBI_17997

Ingredients (14)

# Ingredient Concentration Ontology Notes
1 Distilled water
H2O 18.015 g/mol
1 G_PER_L CHEBI:15377
water
 Role: Solvating media; Properties: Defined component, Simple component, Inorganic compound
2 Yeast extract 4.5 G_PER_L Role: Nutrient source; Properties: Undefined component
3 CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
0.13 G_PER_L CHEBI:86158
calcium chloride dihydrate
 Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
4 KH2PO4
H2O4P.K 136.084 g/mol
1.43 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
5 Resazurin
C12H7NO4 229.191 g/mol
1 G_PER_L CHEBI:8806
Resazurin
 Role: pH dependent redox indicator; Properties: Defined component, Organic compound, Simple component
6 MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
2.6 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
 Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound
7 FeSO4·7H2O
Fe.7H2O.O4S 278.013 g/mol
1.1 G_PER_L CHEBI:75836
iron(2+) sulfate heptahydrate
 Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
8 (NH4)2SO4
2H4N.O4S 132.141 g/mol
1.3 G_PER_L CHEBI:62946
ammonium sulfate
 Role: Nitrogen source; Properties: Defined component, Simple component, Inorganic compound
9 K2HPO4·3H2O
HO4P.2K 174.174 g/mol
7.2 G_PER_L CHEBI:131527
dipotassium hydrogen phosphate
 Role: Buffer; Properties: Inorganic compound, Simple component, Defined component
10 Cellobiose
C12H22O11 342.297 g/mol
5 G_PER_L CHEBI:17057
cellobiose
 Role: Carbon source; Properties: Simple component, Organic compound, Defined component
11 Glutathione
C10H17N3O6S 307.328 g/mol
0.25 G_PER_L CHEBI:16856
glutathione
 Role: Nitrogen source; Properties: Defined component, Organic compound, Simple component
12 Sodium glycerophosphate 6 G_PER_L Role: Mineral source; Properties: Organic compound, Simple component, Defined component
13 Carbon dioxide gas
CO2 44.009 g/mol
variable VARIABLE CHEBI:16526
carbon dioxide
 Properties: ガス
14 Nitrogen gas
N2 28.014 g/mol
variable VARIABLE CHEBI:17997
dinitrogen
 Properties: ガス

Solutions

Solution A*

Dose: 440 G_PER_L

See mediadive_5342_Solution_A.yaml for composition

Solution B**

Dose: 200 G_PER_L

See mediadive_5343_Solution_B.yaml for composition

Solution C***

Dose: 300 G_PER_L

See mediadive_5312_Solution_C.yaml for composition

Solution D****

Dose: 50 G_PER_L

See mediadive_5313_Solution_D.yaml for composition

Solution E*****

Dose: 10 G_PER_L

See mediadive_4959_Solution_E.yaml for composition

Target organisms

No target organisms are recorded.

Provenance

Merged from 2 source records.

TimestampCuratorActionNotes
2026-01-27T06:35:58.845924Z togo-import Imported from TOGO Medium Source: NBRC, ID: M2000
2026-01-28T19:48:39.182066Z 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: nitrogen gas; Added default concentration for ingredient: nitrogen gas
2026-03-09T08:05:05.835268+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 5 solution(s) from ingredients
2026-03-13T03:09:37.631827Z data-quality-cleanup-v1.0 Data quality fixes Merged 6 duplicate ingredient(s)
2026-03-13T06:19:58.410170Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:008587
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
2026-03-17T06:30:49.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:17.027908+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Modified D58 medium" to "modified_d58_medium" for consistent matching
2026-05-16T09:04:25.277418+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=2
2026-06-05T07:41:36.491403+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.
2026-06-10T07:47:08.612300+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.
2026-08-06T03:05:09.519231+00:00 recipe-merger Merged 2 duplicate recipes into canonical record Sources: TOGO_M1766_Clostridium_thermocellum_Medium_D58_Medium, modified_d58_medium
2026-08-06T03:05:09.519277+00:00 merge_recipes.py MERGED_RECIPES merged 2 source recipe(s) on fingerprint 95e446882aa92a7fffd4a9e02b9990cc9821ccd431bf807248d1e93c34f697a7