Overview
- External ontology
- TOGO:M180 — Desulfurococcus Amylolyticus Medium
- Applications
-
- Microbial cultivation
- pH range
- {'min': 6.2, 'max': 6.4}
- High-metal flag
- True
- Notes
- Source: https://togomedium.org/medium/M180 Original source: JCM - JCM_M187 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=187
Composition
flowchart LR
CultureMech_008380["desulfurococcus_amylolyticus_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008380 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_008380 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_008380 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_008380 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_008380 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_Resazurin["Resazurin"]
CultureMech_008380 --> ing5_Resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Resazurin -.-> CHEBI_8806
ing6_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_008380 --> ing6_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing6_MgCl2_6H2O -.-> CHEBI_86345
ing7_KCl["KCl"]
CultureMech_008380 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_Sulfur__powder_["Sulfur (powder)"]
CultureMech_008380 --> ing8_Sulfur__powder_
CHEBI_33403["CHEBI:33403"]
ing8_Sulfur__powder_ -.-> CHEBI_33403
ing9_H2SO4["H2SO4"]
CultureMech_008380 --> ing9_H2SO4
CHEBI_26836["CHEBI:26836"]
ing9_H2SO4 -.-> CHEBI_26836
ing10_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008380 --> ing10_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing10_Carbon_dioxide_gas -.-> CHEBI_16526
ing11_Nitrogen_gas["Nitrogen gas"]
CultureMech_008380 --> ing11_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing11_Nitrogen_gas -.-> CHEBI_17997
Ingredients (12)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
0.99 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 3 duplicates: 990.0, 990.0, 1.0] Source water batch input: 990 ml = 0.99 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record. |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.44 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 6 |
Resazurin
C12H7NO4 229.191 g/mol
|
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component Source batch input: 1 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 7 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.7 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 8 |
KCl
Cl.K 74.551 g/mol
|
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 9 | Sulfur (powder) |
CHEBI:33403
elemental sulfur
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 10 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 10 |
H2SO4
H2O4S 98.079 g/mol
|
CHEBI:26836
sulfuric acid
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution pH-adjustment reagent; no fixed dose is specified. Source reagent strength: 1 N. Normality is not converted to molarity. | |
| 11 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 12 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
Preparation
- Mix ingredients, except yeast extract, peptone, vitamins, sulfur and Na2S・9H2O, and autoclave under a N2--CO2 (80:20) atmosphere. Separately autoclave yeast extract and peptone as 10% solutions and Na2S・9H2O as a 5% solution under a N2 atmosphere. Steam sulfur for 3 hr on each of 3 successive days. Filter--sterilize NaHCO3 as an 8% solution and vitamin solution while gassing with N2. Aseptically and anaerobically add yeast extract, peptone, NaHCO3 and vitamin solutions, and sulfur to the medium under a N2--CO2 (80:20) atmosphere. Prior to inoculation, add the sterile Na2S・9H2O solution, and adjust pH to 6.2--6.4 with sterile 1 N H2SO4.
Solutions
FeCl2 solution (see below)
Dose: 0.001 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 0.99 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 3 duplicates: 990.0, 990.0, 1.0] Source water batch input: 990 ml = 0.99 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record. |
| FeCl2・4H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 1.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. |
Source stock addition: 1 ml = 0.001 L per receiving batch, not grams per liter or a dose per final liter.
HCl reagent (7.7 M)
Dose: 0.01 L
| Ingredient | Concentration | Notes |
|---|---|---|
| 25% HCl (7.7 M) | 7.7 MOLAR | Role: Solvating media; Properties: Defined component, Inorganic compound, Solution Explicit HCl reagent strength 7.7 M, not a final-medium concentration. The 25% basis is unspecified; the enclosing stock holds the 10 ml batch dose. |
Source stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.
Trace element solution (see below)
Dose: 0.001 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 3 duplicates: 990.0, 990.0, 1.0] Source water batch input: 1 L = 1 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record. |
| Na2MoO4・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 36 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| H3BO3 | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 6 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| MnCl2・4H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 100 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CoCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 190 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NiCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 24 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CuCl2・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 2 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| ZnCl2 | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 70 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. |
Source stock addition: 1 ml = 0.001 L per receiving batch, not grams per liter or a dose per final liter.
Trace vitamins (see Medium [M190])
Dose: 0.01 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Source water batch input: 1 L = 1 L. This is not a measured final volume. Prior duplicate-collapse notes describe the superseded flattened record. |
| Biotin | Source batch input: 2 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| p--Aminobenzoic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Thiamine・HCl | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Calcium pantothenate | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Pyridoxine・HCl | Source batch input: 10 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Folic acid | Source batch input: 2 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Vitamin B12 | Source batch input: 0.1 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Riboflavin | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Nicotinic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Lipoic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. |
Cross-reference to Medium M190
Source stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.
Na2S・9H2O separately prepared solution
| Ingredient | Concentration | Notes |
|---|---|---|
| Na2S・9H2O | Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. |
The source specifies a separate percentage-labelled preparation but does not establish percentage basis or its addition volume. No numeric stock strength or dose is asserted. Composition notes record the receiving-batch contribution only.
NaHCO3 separately prepared solution
| Ingredient | Concentration | Notes |
|---|---|---|
| NaHCO3 | Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.8 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. |
The source specifies a separate percentage-labelled preparation but does not establish percentage basis or its addition volume. No numeric stock strength or dose is asserted. Composition notes record the receiving-batch contribution only.
Yeast extract (BD-Difco) separately prepared solution
| Ingredient | Concentration | Notes |
|---|---|---|
| Yeast extract (BD-Difco) | Properties: Undefined component Source batch input: 0.2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. |
The source specifies a separate percentage-labelled preparation but does not establish percentage basis or its addition volume. No numeric stock strength or dose is asserted. Composition notes record the receiving-batch contribution only.
Bacto peptone (BD-Difco) separately prepared solution
| Ingredient | Concentration | Notes |
|---|---|---|
| Bacto peptone (BD-Difco) | Properties: Undefined component Source batch input: 5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. This is the contribution specified for the receiving medium batch, not the mass for preparing an unspecified volume of stock. |
The source specifies a separate percentage-labelled preparation but does not establish percentage basis or its addition volume. No numeric stock strength or dose is asserted. Composition notes record the receiving-batch contribution only.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-06-14T05:58:58.561437+00:00 | idnf-grounding-fix-v1.0 | Fixed ID_NOT_FOUND term groundings | Absent/obsolete CHEBI term ids fixed - 1 re-grounded to the correct CHEBI, 0 de-grounded (mixture or unverifiable). |
| 2026-01-27T06:35:54.563621Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M180 |
| 2026-01-28T19:48:18.159981Z | 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: H2SO4; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas |
| 2026-03-09T08:04:30.099776+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:08:59.028421Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:19:56.301584Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008380 |
| 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 |
| 2026-03-17T06:30:04.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:14.866020+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Desulfurococcus Amylolyticus Medium" to "desulfurococcus_amylolyticus_medium" for consistent matching |
| 2026-05-16T09:03:11.349864+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:34.462038+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 10 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:48.240221+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. |
| 2026-10-08T13:52:57.998884+00:00 | codex | RESTORED_JCM_STOCK_PREPARATION_BOUNDARIES_WITH_EVIDENCE | Restored preparation boundaries and explicit stock-dose bases. Preserved source-specific conflicts, chemical annotations and earlier history. Batch-mass notes do not assert final concentrations; provider-declared stock rates remain qualified. No growth or identity equivalence claim inferred. |