Overview
- External ontology
- TOGO:M196 — Pyrodictium Brockii Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M196 Original source: JCM - JCM_M203 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=203 Source discrepancy: TOGO's inherited preparation says H2-CO4, while original JCM203 specifies H2-CO2. Effective preparation follows JCM203; the inconsistent TOGO wording remains quoted as discrepancy evidence. Post-inoculation instruction: Pressurize inoculated vessels to 200kPa H2 -CO2 (80:20, v/v).
Composition
flowchart LR
CultureMech_008551["pyrodictium_brockii_medium"]
ing0_Resazurin["Resazurin"]
CultureMech_008551 --> ing0_Resazurin
CHEBI_8806["CHEBI:8806"]
ing0_Resazurin -.-> CHEBI_8806
ing1_Sulfur__powder_["Sulfur (powder)"]
CultureMech_008551 --> ing1_Sulfur__powder_
CHEBI_33403["CHEBI:33403"]
ing1_Sulfur__powder_ -.-> CHEBI_33403
ing2_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_008551 --> ing2_Yeast_extract__BD_Difco_
ing3_H2SO4["H2SO4"]
CultureMech_008551 --> ing3_H2SO4
CHEBI_26836["CHEBI:26836"]
ing3_H2SO4 -.-> CHEBI_26836
ing4_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008551 --> ing4_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing4_Carbon_dioxide_gas -.-> CHEBI_16526
ing5_N2["N2"]
CultureMech_008551 --> ing5_N2
CHEBI_17997["CHEBI:17997"]
ing5_N2 -.-> CHEBI_17997
ing6_Hydrogen_gas["Hydrogen gas"]
CultureMech_008551 --> ing6_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing6_Hydrogen_gas -.-> CHEBI_18276
Ingredients (7)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Resazurin
C12H7NO4 229.191 g/mol
|
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Defined component, Organic compound, 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 Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.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, Simple component, Defined 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Source batch input: 30 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration.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Source batch input: 2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | ||
| 4 |
H2SO4
H2O4S 98.079 g/mol
|
CHEBI:26836
sulfuric acid
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution Source pH-adjustment reagent with no fixed dose. Removed the unsupported VARIABLE placeholder. | |
| 5 |
Carbon dioxide gas
CO2 44.009 g/mol
|
CHEBI:16526
carbon dioxide
|
Properties: ガス Source atmosphere context, not a fixed gas input or dissolved concentration. Removed the unsupported VARIABLE placeholder. | |
| 6 |
N2
N2 28.014 g/mol
|
CHEBI:17997
dinitrogen
|
Properties: ガス Source atmosphere context, not a fixed gas input or dissolved concentration. Removed the unsupported VARIABLE placeholder. | |
| 7 |
Hydrogen gas
H2 2.016 g/mol
|
CHEBI:18276
dihydrogen
|
Properties: ガス Source atmosphere context, not a fixed gas input or dissolved concentration. Removed the unsupported VARIABLE placeholder. |
Preparation
- Mix components except sulfur, adjust pH to 5.5 with H2SO4 and autoclave under a N2 gas atmosphere.
- Steam sulfur for 3 hr on each of 3 successive days.
- Aseptically distribute the medium and sulfur into culture vessels (e.g., 20 ml of the medium and 0.6 g sulfur in 120 ml serum bottles) under a stream of a H2-CO2 (80:20, v/v) gas mixture and seal with butyl rubber stoppers.
- Prior to inoculation, add per litter the following solution (autoclave and stored under a N2 atmosphere): 5% Na2S·9H2O solution (pH 7.0) 10.0 ml
- Readjust pH to 5.5, if necessary.
Solutions
Salt base solution (see Medium [M142])
Dose: 1 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Source water batch input: 1 L = 1 L. This is not a measured final volume. |
| MgSO4・7H2O | Source batch input: 3.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| NaCl | Source batch input: 13.85 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| KH2PO4 | Source batch input: 0.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| MgCl2・6H2O | Source batch input: 2.75 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| H3BO3 | Source batch input: 15 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| KCl | Source batch input: 0.325 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CaCl2 | Source batch input: 0.75 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| NaBr | Source batch input: 0.05 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| SrCl2・6H2O | Source batch input: 7.5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| KI | Source batch input: 0.05 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| (NH4)2Ni(SO4)2・6H2O | Source batch input: 2 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M142
Source prepared-stock input: 1 L = 1 L per receiving batch, not grams per liter. This input volume does not establish final supplemented-medium volume.
Trace minerals (see Medium [M142])
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. |
| MgSO4・7H2O | Source batch input: 3 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| NaCl | Source batch input: 1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CaCl2・2H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Na2MoO4・2H2O | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| H3BO3 | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| FeSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| ZnSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CuSO4・5H2O | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CoSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Nitrilotriacetic acid | Source batch input: 1.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| MnSO4・xH2O | Source batch input: 0.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| AlK(SO4)2 | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M142
Source prepared-stock input: 10 ml = 0.01 L per receiving batch, not grams per liter. This input volume does not establish final supplemented-medium volume.
KOH solution
Stock pH-adjustment reagent with no fixed dose or numeric strength.
5% Na2S·9H2O solution (pH 7.0)
Dose: 10 ML_PER_L
Role: Reducing agent; Properties: Defined component, Inorganic compound, Solution
Original JCM203 specifies one later 10 ml per-liter addition before inoculation (source spells 'liter' as 'litter'). This is not a fixed final dilution or mass rate. The 5% label has unspecified percentage basis; stock pH is 7.0, not the receiving medium pH. Consolidated the duplicate extracted descriptor and self-reference into this single source-supported addition; no quantities are summed and no self-nested stock is created.
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). |
| 2026-01-27T06:35:54.592827Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M196 |
| 2026-01-28T19:48:29.091872Z | 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: N2; Added default concentration for ingredient: Hydrogen gas; Added default concentration for ingredient: N2 |
| 2026-03-09T08:04:48.235667+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T03:09:19.235898Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:57.950421Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008551 |
| 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 |
| 2026-03-17T06:30:27.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:16.576230+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Pyrodictium Brockii Medium" to "pyrodictium_brockii_medium" for consistent matching |
| 2026-05-16T09:03:11.954816+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:35.097362+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 2 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-10-08T18:08:40.295001+00:00 | codex | RESTORED_PYRODICTIUM_VARIANT_AMOUNTS_AND_STOCK_SCOPES_WITH_EVIDENCE | Restored source-specific stock doses, compositions, preparation, and parent/variant links. Consolidated M196's duplicate sulfide descriptor without summing. Retained explicit child rates separately from unverified inherited final concentrations. Preserved prior history and chemical annotations; no percentage basis or final volume inferred. |