Overview
- External ontology
- TOGO:M1586 — Pyrococcus Medium 2
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1586 Original source: NBRC - NBRC_M394 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=394
Composition
flowchart LR
CultureMech_008136["pyrococcus_medium_2"]
ing0_Resazurin["Resazurin"]
CultureMech_008136 --> ing0_Resazurin
CHEBI_8806["CHEBI:8806"]
ing0_Resazurin -.-> CHEBI_8806
ing1_Na2S_9H2O["Na2S·9H2O"]
CultureMech_008136 --> ing1_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing1_Na2S_9H2O -.-> CHEBI_76209
ing2_Bacto_Yeast_Extract__Difco_["Bacto Yeast Extract (Difco)"]
CultureMech_008136 --> ing2_Bacto_Yeast_Extract__Difco_
ing3_Bacto_Peptone__Difco_["Bacto Peptone (Difco)"]
CultureMech_008136 --> ing3_Bacto_Peptone__Difco_
ing4_Citric_acid["Citric acid"]
CultureMech_008136 --> ing4_Citric_acid
CHEBI_30769["CHEBI:30769"]
ing4_Citric_acid -.-> CHEBI_30769
ing5_H2SO4["H2SO4"]
CultureMech_008136 --> ing5_H2SO4
CHEBI_26836["CHEBI:26836"]
ing5_H2SO4 -.-> CHEBI_26836
ing6_N2["N2"]
CultureMech_008136 --> ing6_N2
CHEBI_17997["CHEBI:17997"]
ing6_N2 -.-> CHEBI_17997
ing7_Distilled_water["Distilled water"]
CultureMech_008136 --> ing7_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing7_Distilled_water -.-> CHEBI_15377
ing8_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_008136 --> ing8_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing8_MgSO4_7H2O -.-> CHEBI_31795
ing9_NaCl["NaCl"]
CultureMech_008136 --> ing9_NaCl
CHEBI_26710["CHEBI:26710"]
ing9_NaCl -.-> CHEBI_26710
ing10_KH2PO4["KH2PO4"]
CultureMech_008136 --> ing10_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing10_KH2PO4 -.-> CHEBI_63036
ing11_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_008136 --> ing11_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing11_MgCl2_6H2O -.-> CHEBI_86345
ing12_H3BO3["H3BO3"]
CultureMech_008136 --> ing12_H3BO3
CHEBI_33118["CHEBI:33118"]
ing12_H3BO3 -.-> CHEBI_33118
ing13_KCl["KCl"]
CultureMech_008136 --> ing13_KCl
CHEBI_32588["CHEBI:32588"]
ing13_KCl -.-> CHEBI_32588
ing14_CaCl2["CaCl2"]
CultureMech_008136 --> ing14_CaCl2
CHEBI_3312["CHEBI:3312"]
ing14_CaCl2 -.-> CHEBI_3312
ing15_NaBr["NaBr"]
CultureMech_008136 --> ing15_NaBr
CHEBI_63004["CHEBI:63004"]
ing15_NaBr -.-> CHEBI_63004
ing16_SrCl2_6H2O["SrCl2·6H2O"]
CultureMech_008136 --> ing16_SrCl2_6H2O
CHEBI_36385["CHEBI:36385"]
ing16_SrCl2_6H2O -.-> CHEBI_36385
ing17_KI["KI"]
CultureMech_008136 --> ing17_KI
CHEBI_8346["CHEBI:8346"]
ing17_KI -.-> CHEBI_8346
ing18__NH4_2Ni_SO4_2_6H2O["(NH4)2Ni(SO4)2·6H2O"]
CultureMech_008136 --> ing18__NH4_2Ni_SO4_2_6H2O
CHEBI_86149["CHEBI:86149"]
ing18__NH4_2Ni_SO4_2_6H2O -.-> CHEBI_86149
ing19_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008136 --> ing19_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing19_CaCl2_2H2O -.-> CHEBI_86158
ing20_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008136 --> ing20_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing20_Na2MoO4_2H2O -.-> CHEBI_75213
ing21_FeSO4_7H2O["FeSO4·7H2O"]
CultureMech_008136 --> ing21_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing21_FeSO4_7H2O -.-> CHEBI_75836
ing22_ZnSO4_7H2O["ZnSO4·7H2O"]
CultureMech_008136 --> ing22_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing22_ZnSO4_7H2O -.-> CHEBI_32312
ing23_CuSO4_5H2O["CuSO4·5H2O"]
CultureMech_008136 --> ing23_CuSO4_5H2O
CHEBI_31440["CHEBI:31440"]
ing23_CuSO4_5H2O -.-> CHEBI_31440
ing24_CoSO4_7H2O["CoSO4·7H2O"]
CultureMech_008136 --> ing24_CoSO4_7H2O
CHEBI_91244["CHEBI:91244"]
ing24_CoSO4_7H2O -.-> CHEBI_91244
ing25_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_008136 --> ing25_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing25_Nitrilotriacetic_acid -.-> CHEBI_44557
ing26_MnSO4_xH2O["MnSO4·xH2O"]
CultureMech_008136 --> ing26_MnSO4_xH2O
ing27_AlK_SO4_2["AlK(SO4)2"]
CultureMech_008136 --> ing27_AlK_SO4_2
CHEBI_86463["CHEBI:86463"]
ing27_AlK_SO4_2 -.-> CHEBI_86463
Ingredients (28)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Resazurin
C12H7NO4 229.191 g/mol
|
1 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 2 |
Na2S·9H2O
9H2O.2Na.S 240.182 g/mol
|
0.5 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 3 | Bacto Yeast Extract (Difco) | 1 G_PER_L | Properties: Undefined component | |
| 4 | Bacto Peptone (Difco) | 5 G_PER_L | Properties: Undefined component | |
| 5 |
Citric acid
C6H8O7 192.123 g/mol
|
5 G_PER_L |
CHEBI:30769
citric acid
|
Properties: Defined component, Simple component, Organic compound |
| 6 |
H2SO4
H2O4S 98.079 g/mol
|
variable VARIABLE |
CHEBI:26836
sulfuric acid
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution |
| 7 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 8 |
Distilled water
H2O 18.015 g/mol
|
1.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 2 identical duplicates: 1.0, 1.0] |
| 9 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
6.5 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 3.5, 3.0] |
| 10 |
NaCl
Cl.Na 58.443 g/mol
|
14.85 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 13.85, 1.0] |
| 11 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.5 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
2.75 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
H3BO3
H3BO3 61.833 g/mol
|
15.01 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 15.0, 0.01] |
| 14 |
KCl
Cl.K 74.551 g/mol
|
0.325 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
CaCl2
Ca.2Cl 110.984 g/mol
|
0.75 G_PER_L |
CHEBI:3312
calcium dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
NaBr
Br.Na 102.894 g/mol
|
0.05 G_PER_L |
CHEBI:63004
sodium bromide
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
SrCl2·6H2O
Cl2Sr.6H2O 266.616 g/mol
|
7.5 G_PER_L |
CHEBI:36385
strontium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
KI
I.K 166.002 g/mol
|
0.05 G_PER_L |
CHEBI:8346
potassium iodide
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
(NH4)2Ni(SO4)2·6H2O
6H2O.2H4N.Ni.2O4S 394.987 g/mol
|
2 G_PER_L |
CHEBI:86149
ammonium nickel sulfate hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 20 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.01 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
FeSO4·7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.1 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
ZnSO4·7H2O
7H2O.O4S.Zn 287.558 g/mol
|
0.1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
CuSO4·5H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.01 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
CoSO4·7H2O
Co.7H2O.O4S 281.101 g/mol
|
0.1 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 26 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
1.5 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 27 | MnSO4·xH2O | 0.5 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component | |
| 28 |
AlK(SO4)2
Al.K.2O4S 258.206 g/mol
|
0.01 G_PER_L |
CHEBI:86463
potassium aluminium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
Solutions
Sulfur (powder)***
Dose: 30 G_PER_L
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
Salt base solution*
Dose: 1 G_PER_L
See mediadive_4598_Salt_base_solution.yaml for composition
Trace minerals**
Dose: 10 G_PER_L
See mediadive_5363_Trace_minerals.yaml for composition
KOH solution
Dose: variable VARIABLE
Role: Mineral source; Properties: Defined component, Solution
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:57.896301Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1586 |
| 2026-01-28T19:48:40.560688Z | 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 |
| 2026-03-09T08:05:08.372527+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T03:09:40.106926Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:53.817972Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008136 |
| 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 |
| 2026-03-17T06:30:52.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:12.366550+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Pyrococcus Medium 2" to "pyrococcus_medium_2" for consistent matching |
| 2026-05-16T09:04:29.970167+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:43.293471+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 22 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:58:30.468112+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. |
| 2026-06-10T07:47:10.662665+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. |
| 2026-09-02T07:37:31.697112+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. |