Overview
- External ontology
- TOGO:M485 — Modified Methanocaldococcus Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M485 Original source: JCM - JCM_M484 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=484
Composition
flowchart LR
CultureMech_009872["modified_methanocaldococcus_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009872 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4・7H2O"]
CultureMech_009872 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_NaCl["NaCl"]
CultureMech_009872 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009872 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_NH4Cl["NH4Cl"]
CultureMech_009872 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_K2HPO4["K2HPO4"]
CultureMech_009872 --> ing5_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing5_K2HPO4 -.-> CHEBI_131527
ing6_Resazurin["Resazurin"]
CultureMech_009872 --> ing6_Resazurin
CHEBI_8806["CHEBI:8806"]
ing6_Resazurin -.-> CHEBI_8806
ing7_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009872 --> ing7_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing7_MgCl2_6H2O -.-> CHEBI_86345
ing8_KCl["KCl"]
CultureMech_009872 --> ing8_KCl
CHEBI_32588["CHEBI:32588"]
ing8_KCl -.-> CHEBI_32588
ing9_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_009872 --> ing9_Yeast_extract__BD_Difco_
ing10_Na2S2O3_5H2O["Na2S2O3・5H2O"]
CultureMech_009872 --> ing10_Na2S2O3_5H2O
CHEBI_32150["CHEBI:32150"]
ing10_Na2S2O3_5H2O -.-> CHEBI_32150
ing11_2__Mercaptoethanol["2--Mercaptoethanol"]
CultureMech_009872 --> ing11_2__Mercaptoethanol
CHEBI_41218["CHEBI:41218"]
ing11_2__Mercaptoethanol -.-> CHEBI_41218
ing12_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009872 --> ing12_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing12_Carbon_dioxide_gas -.-> CHEBI_16526
ing13_N2["N2"]
CultureMech_009872 --> ing13_N2
CHEBI_17997["CHEBI:17997"]
ing13_N2 -.-> CHEBI_17997
ing14_Hydrogen_gas["Hydrogen gas"]
CultureMech_009872 --> ing14_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing14_Hydrogen_gas -.-> CHEBI_18276
ing15_Na2MoO4_2H2O["Na2MoO4・2H2O"]
CultureMech_009872 --> ing15_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing15_Na2MoO4_2H2O -.-> CHEBI_75213
ing16_H3BO3["H3BO3"]
CultureMech_009872 --> ing16_H3BO3
CHEBI_33118["CHEBI:33118"]
ing16_H3BO3 -.-> CHEBI_33118
ing17_FeSO4_7H2O["FeSO4・7H2O"]
CultureMech_009872 --> ing17_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing17_FeSO4_7H2O -.-> CHEBI_75836
ing18_NiCl2_6H2O["NiCl2・6H2O"]
CultureMech_009872 --> ing18_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing18_NiCl2_6H2O -.-> CHEBI_34887
ing19_ZnSO4_7H2O["ZnSO4・7H2O"]
CultureMech_009872 --> ing19_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing19_ZnSO4_7H2O -.-> CHEBI_32312
ing20_CuSO4_5H2O["CuSO4・5H2O"]
CultureMech_009872 --> ing20_CuSO4_5H2O
CHEBI_31440["CHEBI:31440"]
ing20_CuSO4_5H2O -.-> CHEBI_31440
ing21_Na2SeO3_5H2O["Na2SeO3・5H2O"]
CultureMech_009872 --> ing21_Na2SeO3_5H2O
CHEBI_131361["CHEBI:131361"]
ing21_Na2SeO3_5H2O -.-> CHEBI_131361
ing22_CoSO4_7H2O["CoSO4・7H2O"]
CultureMech_009872 --> ing22_CoSO4_7H2O
CHEBI_91244["CHEBI:91244"]
ing22_CoSO4_7H2O -.-> CHEBI_91244
ing23_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_009872 --> ing23_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing23_Nitrilotriacetic_acid -.-> CHEBI_44557
ing24_MnSO4_xH2O["MnSO4・xH2O"]
CultureMech_009872 --> ing24_MnSO4_xH2O
CHEBI_86360["CHEBI:86360"]
ing24_MnSO4_xH2O -.-> CHEBI_86360
ing25_AlK_SO4_2["AlK(SO4)2"]
CultureMech_009872 --> ing25_AlK_SO4_2
CHEBI_86463["CHEBI:86463"]
ing25_AlK_SO4_2 -.-> CHEBI_86463
ing26_KOH["KOH"]
CultureMech_009872 --> ing26_KOH
CHEBI_32035["CHEBI:32035"]
ing26_KOH -.-> CHEBI_32035
Ingredients (27)
| # | 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 2 identical duplicates: 1.0, 1.0] |
| 2 |
MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
|
6.4 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 3.4, 3.0] |
| 3 |
NaCl
Cl.Na 58.443 g/mol
|
31.0 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 30.0, 1.0] |
| 4 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.24000000000000002 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.14, 0.1] |
| 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 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.14 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
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 |
| 8 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
2.7 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
KCl
Cl.K 74.551 g/mol
|
0.33 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 | Yeast extract (BD-Difco) | 2 G_PER_L | Properties: Undefined component | |
| 11 |
Na2S2O3・5H2O
5H2O.2Na.O3S2 248.186 g/mol
|
1 G_PER_L |
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Simple component, Defined component, Inorganic compound |
| 12 |
2--Mercaptoethanol
C2H6OS 78.136 g/mol
|
0.4 G_PER_L |
CHEBI:41218
mercaptoethanol
|
Properties: Defined component, Simple component, Organic compound |
| 13 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 14 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 15 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: ガス |
| 16 |
Na2MoO4・2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.01 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
H3BO3
H3BO3 61.833 g/mol
|
0.01 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
FeSO4・7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.1 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
NiCl2・6H2O
Cl2Ni 129.599 g/mol
|
0.025 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 20 |
ZnSO4・7H2O
7H2O.O4S.Zn 287.558 g/mol
|
0.1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
CuSO4・5H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.01 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
Na2SeO3・5H2O
5H2O.2Na.O3Se 263.012 g/mol
|
0.3 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
CoSO4・7H2O
Co.7H2O.O4S 281.101 g/mol
|
0.1 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
1.5 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 25 |
MnSO4・xH2O
Mn.O4S 151.001 g/mol
|
0.5 G_PER_L |
CHEBI:86360
manganese(II) sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 26 |
AlK(SO4)2
Al.K.2O4S 258.206 g/mol
|
0.01 G_PER_L |
CHEBI:86463
potassium aluminium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 27 |
KOH
HO.K 56.105 g/mol
|
variable VARIABLE |
CHEBI:32035
potassium hydroxide
|
Role: Mineral source; Properties: Defined component, Solution |
Solutions
Iron stock solution (see Medium [M221])
Dose: 5 G_PER_L
Cross-reference to Medium M221
Trace minerals solution (see below)
Dose: 10 G_PER_L
Trace vitamins (see Medium [M190])
Dose: 10 G_PER_L
Cross-reference to Medium M190
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.143982Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M485 |
| 2026-01-28T19:48:25.085897Z | 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; Added default concentration for ingredient: Hydrogen gas; Added default concentration for ingredient: KOH |
| 2026-03-09T08:04:41.495603+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:09:11.500461Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:20:09.557298Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009872 |
| 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 |
| 2026-03-17T06:30:18.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:28.521817+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Modified Methanocaldococcus Medium" to "modified_methanocaldococcus_medium" for consistent matching |
| 2026-05-16T09:03:18.391242+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:41.797102+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 11 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:30.854311+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. |
| 2026-06-10T07:46:50.757791+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. |
| 2026-09-02T07:37:27.880197+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. |