Overview
- External ontology
- TOGO:M142 — Pyrococcus Medium
- Applications
-
- Microbial cultivation
- pH
- 6.5
- Notes
- Source: https://togomedium.org/medium/M142 Original source: JCM - JCM_M151 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=151
Composition
flowchart LR
CultureMech_007968["pyrococcus_medium"]
ing0_Resazurin["Resazurin"]
CultureMech_007968 --> ing0_Resazurin
CHEBI_8806["CHEBI:8806"]
ing0_Resazurin -.-> CHEBI_8806
ing1_Sulfur__powder_["Sulfur (powder)"]
CultureMech_007968 --> ing1_Sulfur__powder_
CHEBI_33403["CHEBI:33403"]
ing1_Sulfur__powder_ -.-> CHEBI_33403
ing2_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_007968 --> ing2_Yeast_extract__BD_Difco_
ing3_Bacto_peptone__BD_Difco_["Bacto peptone (BD-Difco)"]
CultureMech_007968 --> ing3_Bacto_peptone__BD_Difco_
ing4_Citric_acid["Citric acid"]
CultureMech_007968 --> ing4_Citric_acid
CHEBI_30769["CHEBI:30769"]
ing4_Citric_acid -.-> CHEBI_30769
ing5_H2SO4["H2SO4"]
CultureMech_007968 --> ing5_H2SO4
CHEBI_26836["CHEBI:26836"]
ing5_H2SO4 -.-> CHEBI_26836
ing6_N2["N2"]
CultureMech_007968 --> ing6_N2
CHEBI_17997["CHEBI:17997"]
ing6_N2 -.-> CHEBI_17997
Ingredients (7)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
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 Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 2 | Sulfur (powder) |
CHEBI:33403
elemental sulfur
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 30 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 3 | Yeast extract (BD-Difco) | Properties: Undefined component Source batch input: 1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | ||
| 4 | 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Source batch input: 5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | ||
| 5 |
Citric acid
C6H8O7 192.123 g/mol
|
CHEBI:30769
citric acid
|
Properties: Defined component, Simple component, Organic compound 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. | |
| 6 |
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. Normality is not converted to molarity. | |
| 7 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
Preparation
- Mix ingredients, except sulfur and Na2S・9H2O, and adjust pH to 6.5 with H2SO4. Sterilize by filtration under a N2 atmosphere. Steam sulfur for 3 hr on each of 3 successive days. Neutralize Na2S・9H2O as a 5% solution, and autoclave under a N2 atmosphere. Aseptically and anaerobically add sterile sulfur to the medium. Prior to inoculation, add the sterile Na2S・9H2O solution, and readjust pH to 6.5, if necessary.
Solutions
Salt base solution (see below)
Dose: 1 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 2 identical duplicates: 1.0, 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. |
| MgSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 3.5, 3.0] Source batch input: 3.5 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NaCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 13.85, 1.0] Source batch input: 13.85 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| KH2PO4 | Role: Buffer; 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. | |
| MgCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 2.75 g. 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 [Merged 2 duplicates: 15.0, 0.01] Source batch input: 15 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| KCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.325 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CaCl2 | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.75 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NaBr | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.05 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| SrCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 7.5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| KI | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.05 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| (NH4)2Ni(SO4)2・6H2O | 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. |
Source stock addition: 1 L = 1 L per receiving batch, not grams per liter or a dose per final liter.
Trace minerals (see below)
Dose: 0.01 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 2 identical duplicates: 1.0, 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. |
| MgSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 3.5, 3.0] Source batch input: 3 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NaCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 13.85, 1.0] Source batch input: 1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CaCl2・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Na2MoO4・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.01 g. 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 [Merged 2 duplicates: 15.0, 0.01] Source batch input: 0.01 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| FeSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| ZnSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CuSO4・5H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.01 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CoSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Nitrilotriacetic acid | Role: Mineral source; Properties: Organic 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. | |
| MnSO4・xH2O | 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. | |
| AlK(SO4)2 | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.01 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: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.
KOH solution
Role: Mineral source; Properties: Defined component, Solution
pH-adjustment reagent; no fixed dose is specified. Normality is not converted to molarity.
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.
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). |
| 2026-01-27T06:35:54.508138Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M142 |
| 2026-01-28T19:48:08.502913Z | 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: N2; Added default concentration for ingredient: KOH solution |
| 2026-03-09T08:04:13.749841+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:08:40.744112Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:52.768156Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007968 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:29:42.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:11.243886+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Pyrococcus Medium" to "pyrococcus_medium" for consistent matching |
| 2026-05-16T09:03:10.052766+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:33.074309+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 13 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:23.285040+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. |
| 2026-06-10T07:46:47.816216+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. |
| 2026-09-02T07:37:25.855263+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. |
| 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. |
| 2026-10-08T14:34:18.972918+00:00 | codex | RESTORED_JCM261_VARIANT_FORMULATION_WITH_EVIDENCE | Source-defined variant overrides and reciprocal links restored. Parent formulations and prior history preserved. Batch amounts and stock composition are not final-medium concentrations. Unknown percentage basis/dose remains unresolved; chemical annotations preserved, not recertified. |