Overview
- External ontology
- TOGO:M355 — Methanocaldococcus Indiensis Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M355 Original source: JCM - JCM_M361 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=361
Composition
flowchart LR
CultureMech_009735["methanocaldococcus_indiensis_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009735 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_009735 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009735 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_009735 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_009735 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_Resazurin["Resazurin"]
CultureMech_009735 --> ing5_Resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Resazurin -.-> CHEBI_8806
ing6_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009735 --> ing6_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing6_MgCl2_6H2O -.-> CHEBI_86345
ing7_Na2S_9H2O["Na2S・9H2O"]
CultureMech_009735 --> ing7_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing7_Na2S_9H2O -.-> CHEBI_76209
ing8_KCl["KCl"]
CultureMech_009735 --> ing8_KCl
CHEBI_32588["CHEBI:32588"]
ing8_KCl -.-> CHEBI_32588
ing9_Vitamin_B12["Vitamin B12"]
CultureMech_009735 --> ing9_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing9_Vitamin_B12 -.-> CHEBI_176843
ing10_Na2SO4["Na2SO4"]
CultureMech_009735 --> ing10_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing10_Na2SO4 -.-> CHEBI_32149
ing11_Na2WO4_2H2O["Na2WO4・2H2O"]
CultureMech_009735 --> ing11_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing11_Na2WO4_2H2O -.-> CHEBI_63939
ing12_PIPES["PIPES"]
CultureMech_009735 --> ing12_PIPES
CHEBI_39033["CHEBI:39033"]
ing12_PIPES -.-> CHEBI_39033
ing13_Na2SeO4["Na2SeO4"]
CultureMech_009735 --> ing13_Na2SeO4
CHEBI_77775["CHEBI:77775"]
ing13_Na2SeO4 -.-> CHEBI_77775
ing14_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_009735 --> ing14_Yeast_extract__BD_Difco_
ing15_HCl["HCl"]
CultureMech_009735 --> ing15_HCl
CHEBI_17883["CHEBI:17883"]
ing15_HCl -.-> CHEBI_17883
ing16_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009735 --> ing16_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing16_Carbon_dioxide_gas -.-> CHEBI_16526
ing17_N2["N2"]
CultureMech_009735 --> ing17_N2
CHEBI_17997["CHEBI:17997"]
ing17_N2 -.-> CHEBI_17997
ing18_Hydrogen_gas["Hydrogen gas"]
CultureMech_009735 --> ing18_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing18_Hydrogen_gas -.-> CHEBI_18276
Ingredients (19)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
30 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
|
0.2 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
|
1 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 | Vitamin B12 | 0.05 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 11 |
Na2SO4
2Na.O4S 142.043 g/mol
|
4 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
Na2WO4・2H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.2 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 | PIPES | 3.46 G_PER_L |
CHEBI:39033
PIPES
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 14 |
Na2SeO4
2Na.O4Se 188.936 g/mol
|
0.05 G_PER_L |
CHEBI:77775
sodium selenate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 | Yeast extract (BD-Difco) | 0.5 G_PER_L | Properties: Undefined component | |
| 16 |
HCl
HCl 36.461 g/mol
|
variable VARIABLE |
CHEBI:17883
hydrogen chloride
|
Role: Solvating media; Properties: Defined component, Solution, Inorganic compound |
| 17 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 18 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 19 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: ガス |
Solutions
Trace element solution (see Medium [M296])
Dose: 1 G_PER_L
Cross-reference to Medium M296
Trace vitamins (see Medium [M190])
Dose: 10 G_PER_L
Cross-reference to Medium M190
Growth stimulating factors (see Medium [M296])
Dose: 1 G_PER_L
Cross-reference to Medium M296
NaHCO3 stock solution
Dose: variable VARIABLE
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.899834Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M355 |
| 2026-01-28T19:48:37.510919Z | 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: NaHCO3 stock solution; Added default concentration for ingredient: HCl; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: Hydrogen gas |
| 2026-03-09T08:05:02.582613+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T06:20:08.464376Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009735 |
| 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 |
| 2026-03-17T06:30:45.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:27.450168+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methanocaldococcus Indiensis Medium" to "methanocaldococcus_indiensis_medium" for consistent matching |
| 2026-05-16T09:03:17.360881+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:40.672171+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. |
| 2026-06-08T23:19:34.137516+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 term reference(s) to the correct CHEBI (see reports/chebi_grounding_audit.md). Label-conditional fixes for pyridoxine/pyridoxamine, glycerol, MnSO4, Ca(NO3)2, selenate; casamino acids de-grounded (mixture, no single CHEBI). |
| 2026-06-10T07:46:50.397268+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. |