Overview
- External ontology
- TOGO:M1038 — Methanomethylovorans Uponensis Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1038 Original source: JCM - JCM_M985 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=985
Composition
flowchart LR
CultureMech_007553["methanomethylovorans_uponensis_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_007553 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_007553 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_007553 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_007553 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_007553 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_Resazurin["Resazurin"]
CultureMech_007553 --> ing5_Resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Resazurin -.-> CHEBI_8806
ing6_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_007553 --> ing6_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing6_MgCl2_6H2O -.-> CHEBI_86345
ing7_KCl["KCl"]
CultureMech_007553 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_007553 --> ing8_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing8_Carbon_dioxide_gas -.-> CHEBI_16526
ing9_Nitrogen_gas["Nitrogen gas"]
CultureMech_007553 --> ing9_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing9_Nitrogen_gas -.-> CHEBI_17997
Ingredients (10)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
0.96 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component Water input: 960 ml / 1000 ml per L = 0.96 L per batch, not final-medium volume. |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component Source batch amount: 1 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 3 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component Source batch amount: 0.1 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component Source batch amount: 0.2 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component Source batch amount: 0.5 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 6 |
Resazurin
C12H7NO4 229.191 g/mol
|
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component Source batch amount: 1 mg. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 7 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component Source batch amount: 0.4 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 8 |
KCl
Cl.K 74.551 g/mol
|
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component Source batch amount: 0.5 g. Withdraw unsupported G_PER_L encoding; final-medium volume is unreported. This evidence supports the batch-mass note only. | |
| 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 |
Preparation
- Mix components thoroughly and autoclave under a N2-CO2 (80:20, v/v) gas atmosphere. After cooling, add the following solutions (autoclaved or *filter-sterilized):
- Aseptically and anaerobically distribute the medium into culture vessels under a N2-CO2 (80:20, v/v) gas mixture and seal with butyl rubber stoppers. Finally, add per liter the following solution from an anaerobic stock (autoclaved and stored under a N2 atmosphere):
Solutions
8% NaHCO3 solution*
Dose: 0.02 L
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
Source stock input: 20 ml / 1000 ml per L = 0.02 L per recipe batch, not a dose per final liter. The source label says 8%, but the percentage basis is unspecified; no numeric stock strength or dilution is asserted. Stock composition and final-medium concentrations remain unresolved.
3% Trimethylamine·HCl solution*
Dose: 0.01 L
Role: Nutrient source; Properties: Solution, Defined component, Complex component
Source stock input: 10 ml / 1000 ml per L = 0.01 L per recipe batch, not a dose per final liter. The source label says 3%, but the percentage basis is unspecified; no numeric stock strength or dilution is asserted. Stock composition and final-medium concentrations remain unresolved.
TOGO M1038 labels this stock 3%, whereas MediaDive J985 labels it 30%. Preserve the TOGO label and the disagreement; neither a common stock strength nor a variant is inferred. Both transcriptions specify a 10 ml addition. Original JCM985 returned Nothing found.
Trace vitamins (see Medium [M190])
Dose: 0.01 L
Cross-reference to Medium M190
Source stock input: 10 ml / 1000 ml per L = 0.01 L per recipe batch, not a dose per final liter. Stock composition and final-medium concentrations remain unresolved.
FeCl2 solution (see Medium [M180])
Dose: 0.001 L
Cross-reference to Medium M180
Source stock input: 1 ml / 1000 ml per L = 0.001 L per recipe batch, not a dose per final liter. Stock composition and final-medium concentrations remain unresolved.
Trace element solution (see Medium [M180])
Dose: 0.001 L
Cross-reference to Medium M180
Source stock input: 1 ml / 1000 ml per L = 0.001 L per recipe batch, not a dose per final liter. Stock composition and final-medium concentrations remain unresolved.
Selenite--tungstate solution (see Medium [M431])
Dose: 0.001 L
Cross-reference to Medium M431
Source stock input: 1 ml / 1000 ml per L = 0.001 L per recipe batch, not a dose per final liter. Stock composition and final-medium concentrations remain unresolved.
5% Na2S·9H2O solution
Dose: 8 ML_PER_L
Role: Reducing agent; Properties: Inorganic compound, Solution, Defined component
Source explicitly says add per liter: 8 ml/L stock working dose, not an 8 ml batch input. The source label says 5%, but the percentage basis is unspecified; no numeric stock strength or dilution is asserted. Stock composition and final-medium concentrations remain unresolved.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:53.804270Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M1038 |
| 2026-01-28T19:48:39.578643Z | 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: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas |
| 2026-03-09T08:05:06.566579+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 7 solution(s) from ingredients |
| 2026-03-13T03:09:38.305357Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:19:49.619145Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007553 |
| 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 |
| 2026-03-17T06:30:50.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:07.966330+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methanomethylovorans Uponensis Medium" to "methanomethylovorans_uponensis_medium" for consistent matching |
| 2026-05-16T09:03:07.087851+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:29.913545+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. |
| 2026-06-10T07:46:46.761561+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. |
| 2026-10-08T10:47:19.502771+00:00 | codex | REPAIRED_METHANOGEN_STOCK_DOSES_AND_BASE_REFERENCE_WITH_EVIDENCE | Corrected recipe-specific quantities and provenance; preserved stock-strength conflicts and unresolved final-volume/base-composition claims. Existing history, conditions and organism claims unchanged. |