Overview
- External ontology
- TOGO:M208 — Pyrobaculum Aerophilum Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M208 Original source: JCM - JCM_M215 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=215 Original post-inoculation instruction: Pressurize inoculated bottles to 200 kPa N2-CO2-O2 (80:20:1).
Composition
flowchart LR
CultureMech_008680["pyrobaculum_aerophilum_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008680 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_KH2PO4["KH2PO4"]
CultureMech_008680 --> ing1_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing1_KH2PO4 -.-> CHEBI_63036
ing2_NH4Cl["NH4Cl"]
CultureMech_008680 --> ing2_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing2_NH4Cl -.-> CHEBI_31206
ing3_NaHCO3["NaHCO3"]
CultureMech_008680 --> ing3_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing3_NaHCO3 -.-> CHEBI_32139
ing4_NaWO4_2H2O["NaWO4・2H2O"]
CultureMech_008680 --> ing4_NaWO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing4_NaWO4_2H2O -.-> CHEBI_63939
ing5_Fe_NH4_2_SO4_2_6H2O["Fe(NH4)2(SO4)2・6H2O"]
CultureMech_008680 --> ing5_Fe_NH4_2_SO4_2_6H2O
CHEBI_76181["CHEBI:76181"]
ing5_Fe_NH4_2_SO4_2_6H2O -.-> CHEBI_76181
ing6__NH4_2Ni_SO4_2_6H2O["(NH4)2Ni(SO4)2・6H2O"]
CultureMech_008680 --> ing6__NH4_2Ni_SO4_2_6H2O
CHEBI_86149["CHEBI:86149"]
ing6__NH4_2Ni_SO4_2_6H2O -.-> CHEBI_86149
ing7_Na2SeO4["Na2SeO4"]
CultureMech_008680 --> ing7_Na2SeO4
CHEBI_77775["CHEBI:77775"]
ing7_Na2SeO4 -.-> CHEBI_77775
ing8_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_008680 --> ing8_Yeast_extract__BD_Difco_
ing9_Na2S2O3_5H2O["Na2S2O3・5H2O"]
CultureMech_008680 --> ing9_Na2S2O3_5H2O
CHEBI_32150["CHEBI:32150"]
ing9_Na2S2O3_5H2O -.-> CHEBI_32150
ing10_H2SO4["H2SO4"]
CultureMech_008680 --> ing10_H2SO4
CHEBI_26836["CHEBI:26836"]
ing10_H2SO4 -.-> CHEBI_26836
ing11_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008680 --> ing11_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing11_Carbon_dioxide_gas -.-> CHEBI_16526
ing12_Nitrogen_gas["Nitrogen gas"]
CultureMech_008680 --> ing12_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing12_Nitrogen_gas -.-> CHEBI_17997
ing13_Oxygen_gas["Oxygen gas"]
CultureMech_008680 --> ing13_Oxygen_gas
Ingredients (14)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
0.865 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 865.0, 1.0] Source water batch input: 865 ml = 0.865 L. This is not a measured final volume. The earlier duplicate-summing note is superseded: it combined separate preparation scopes and source units. This node carries only the batch input at the cited source row; other occurrences are separate scoped ingredients. |
| 2 |
KH2PO4
H2O4P.K 136.084 g/mol
|
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.07 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 3 |
NH4Cl
Cl.H4N 53.492 g/mol
|
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.25 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 4 |
NaHCO3
CHO3.Na 84.006 g/mol
|
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 2.2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 5 |
NaWO4・2H2O
2H2O.2Na.O4W 329.846 g/mol
|
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component 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. Both TOGO and original JCM215 print NaWO4. The legacy sodium-tungstate grounding is retained, not recertified; the formula discrepancy is unresolved. No formula normalization or molar conversion is performed. | |
| 6 |
Fe(NH4)2(SO4)2・6H2O
Fe.6H2O.2H4N.2O4S 392.139 g/mol
|
CHEBI:76181
ferrous ammonium sulfate hexahydrate
|
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. | |
| 7 |
(NH4)2Ni(SO4)2・6H2O
6H2O.2H4N.Ni.2O4S 394.987 g/mol
|
CHEBI:86149
ammonium nickel sulfate hexahydrate
|
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. | |
| 8 |
Na2SeO4
2Na.O4Se 188.936 g/mol
|
CHEBI:77775
sodium selenate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component 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. | |
| 9 | Yeast extract (BD-Difco) | Properties: Undefined 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. | ||
| 10 |
Na2S2O3・5H2O
5H2O.2Na.O3S2 248.186 g/mol
|
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Defined component, Simple component, Inorganic compound 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. | |
| 11 |
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. Original JCM215 specifies 1 N H2SO4 reagent; normality is not converted to molarity or a receiving-medium dose. | |
| 12 |
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. The 80:20:1 gas ratio is retained as written, not normalized to percentages. | |
| 13 |
Nitrogen gas
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. The 80:20:1 gas ratio is retained as written, not normalized to percentages. | |
| 14 | Oxygen gas | Properties: ガス Source atmosphere context, not a fixed gas input or dissolved concentration. Removed the unsupported VARIABLE placeholder. The 80:20:1 gas ratio is retained as written, not normalized to percentages. |
Preparation
- Adjust pH to 7.0 with 1 N H2SO4, and sterilize by filtration.
- Dispense the medium into bottles under a N2-CO2-O2 (80:20:1) atmosphere.
Solutions
Marine medium/Synthetic seawater mix solution (see below)
Dose: 0.125 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 865.0, 1.0] Source water batch input: 1 L = 1 L. This is not a measured final volume. The earlier duplicate-summing note is superseded: it combined separate preparation scopes and source units. This node carries only the batch input at the cited source row; other occurrences are separate scoped ingredients. |
| MgSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 7 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 Source batch input: 47.15 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: 3.13 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: 18.1 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 Source batch input: 52 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Na2CO3 | Role: Buffer; 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. | |
| Na2SO4 | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 3.24 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Na2HPO4 | Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 8.1 mg. 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: 0.1 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: 72 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. | |
| NaF | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 2.4 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| KBr | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 80 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| Sodium silicate | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.4 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: 125 ml = 0.125 L per receiving batch, not grams per liter or a dose per final liter.
Expand only this named stock table, not the complete referenced medium or its other stocks/preparation instructions. Stock water is an input, not an established final stock 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 stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter.
Expand only this named stock table, not the complete referenced medium or its other stocks/preparation instructions. Stock water is an input, not an established final stock volume.
KOH solution
Stock pH-adjustment reagent with no fixed dose or numeric strength.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.616955Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M208 |
| 2026-01-28T19:48:21.253481Z | 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; Added default concentration for ingredient: Oxygen gas |
| 2026-03-09T08:04:35.414824+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:04.765509Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:59.327625Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008680 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:10.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:17.964144+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Pyrobaculum Aerophilum Medium" to "pyrobaculum_aerophilum_medium" for consistent matching |
| 2026-05-16T09:03:12.281989+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:35.440815+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 16 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:31.705862+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). |
| 2026-06-10T06:57:25.451107+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. |
| 2026-06-10T07:46:48.586026+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 9 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-10-08T19:08:27.997542+00:00 | codex | RESTORED_MARINE_STOCK_SCOPES_AND_BATCH_AMOUNTS_WITH_EVIDENCE | Separated collapsed main/stock water, restored named stock compositions and batch-volume inputs, and removed unsupported final-rate and VARIABLE assertions. Preserved exact batch masses, preparation, annotations and history with evidence. No final volume, percentage basis or molar conversion inferred. |