Overview
- External ontology
- TOGO:M609 — Desulfovibrio Magnus Medium
- Applications
-
- Microbial cultivation
- High-metal flag
- True
- Notes
- Source: https://togomedium.org/medium/M609 Original source: JCM - JCM_M602 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=602
Composition
flowchart LR
CultureMech_010008["desulfovibrio_magnus_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010008 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_010008 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_KH2PO4["KH2PO4"]
CultureMech_010008 --> ing2_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing2_KH2PO4 -.-> CHEBI_63036
ing3_NH4Cl["NH4Cl"]
CultureMech_010008 --> ing3_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing3_NH4Cl -.-> CHEBI_31206
ing4_Na2SO4["Na2SO4"]
CultureMech_010008 --> ing4_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing4_Na2SO4 -.-> CHEBI_32149
ing5_Sodium_lactate["Sodium lactate"]
CultureMech_010008 --> ing5_Sodium_lactate
CHEBI_75228["CHEBI:75228"]
ing5_Sodium_lactate -.-> CHEBI_75228
ing6_Na2HPO4_2H2O["Na2HPO4・2H2O"]
CultureMech_010008 --> ing6_Na2HPO4_2H2O
CHEBI_34683["CHEBI:34683"]
ing6_Na2HPO4_2H2O -.-> CHEBI_34683
ing7_N2["N2"]
CultureMech_010008 --> ing7_N2
CHEBI_17997["CHEBI:17997"]
ing7_N2 -.-> CHEBI_17997
ing8_6_N_HCl["6 N HCl"]
CultureMech_010008 --> ing8_6_N_HCl
ing9_H3BO3["H3BO3"]
CultureMech_010008 --> ing9_H3BO3
CHEBI_33118["CHEBI:33118"]
ing9_H3BO3 -.-> CHEBI_33118
ing10_MnCl2_4H2O["MnCl2・4H2O"]
CultureMech_010008 --> ing10_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing10_MnCl2_4H2O -.-> CHEBI_86368
ing11_CoCl2_6H2O["CoCl2・6H2O"]
CultureMech_010008 --> ing11_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing11_CoCl2_6H2O -.-> CHEBI_35696
ing12_NiCl2_6H2O["NiCl2・6H2O"]
CultureMech_010008 --> ing12_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing12_NiCl2_6H2O -.-> CHEBI_34887
ing13_ZnCl2["ZnCl2"]
CultureMech_010008 --> ing13_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing13_ZnCl2 -.-> CHEBI_49976
ing14_FeCl2_4H2O["FeCl2・4H2O"]
CultureMech_010008 --> ing14_FeCl2_4H2O
CHEBI_86249["CHEBI:86249"]
ing14_FeCl2_4H2O -.-> CHEBI_86249
ing15_Na2MoO4_2H2O["Na2MoO4・2H2O"]
CultureMech_010008 --> ing15_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing15_Na2MoO4_2H2O -.-> CHEBI_75213
ing16_Na2SeO3_5H2O["Na2SeO3・5H2O"]
CultureMech_010008 --> ing16_Na2SeO3_5H2O
CHEBI_131361["CHEBI:131361"]
ing16_Na2SeO3_5H2O -.-> CHEBI_131361
ing17_Na2WO4_2H2O["Na2WO4・2H2O"]
CultureMech_010008 --> ing17_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing17_Na2WO4_2H2O -.-> CHEBI_63939
ing18_NaOH["NaOH"]
CultureMech_010008 --> ing18_NaOH
CHEBI_32145["CHEBI:32145"]
ing18_NaOH -.-> CHEBI_32145
ing19_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010008 --> ing19_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing19_CaCl2_2H2O -.-> CHEBI_86158
ing20_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_010008 --> ing20_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing20_MgCl2_6H2O -.-> CHEBI_86345
ing21_NaHCO3["NaHCO3"]
CultureMech_010008 --> ing21_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing21_NaHCO3 -.-> CHEBI_32139
ing22_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010008 --> ing22_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing22_Carbon_dioxide_gas -.-> CHEBI_16526
ing23_Biotin["Biotin"]
CultureMech_010008 --> ing23_Biotin
CHEBI_15956["CHEBI:15956"]
ing23_Biotin -.-> CHEBI_15956
ing24_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010008 --> ing24_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing24_p__Aminobenzoic_acid -.-> CHEBI_30753
ing25_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010008 --> ing25_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing25_Thiamine_HCl -.-> CHEBI_49105
ing26_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010008 --> ing26_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing26_Pyridoxine_HCl -.-> CHEBI_30961
ing27_Vitamin_B12["Vitamin B12"]
CultureMech_010008 --> ing27_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing27_Vitamin_B12 -.-> CHEBI_176843
ing28_Riboflavin["Riboflavin"]
CultureMech_010008 --> ing28_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing28_Riboflavin -.-> CHEBI_17015
ing29_Nicotinic_acid["Nicotinic acid"]
CultureMech_010008 --> ing29_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing29_Nicotinic_acid -.-> CHEBI_15940
CultureMech_010008 --> more["...1 more"]
Ingredients (31)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1003.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 6 duplicates: 900.0, 1.0, 1.0, 50.0, 50.0, 1.0] |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
0.3 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.41 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.3 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
Na2SO4
2Na.O4S 142.043 g/mol
|
1.42 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
Sodium lactate
C3H5O3.Na 112.06 g/mol
|
2.24 G_PER_L |
CHEBI:75228
sodium lactate
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 7 |
Na2HPO4・2H2O
HO4P.2Na 141.958 g/mol
|
0.53 G_PER_L |
CHEBI:34683
disodium hydrogenphosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 9 | 6 N HCl | 10 G_PER_L | Role: Solvating media; Properties: Defined component, Inorganic compound, Solution | |
| 10 |
H3BO3
H3BO3 61.833 g/mol
|
61.8 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
MnCl2・4H2O
Cl2Mn.4H2O 197.904 g/mol
|
61.25 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
CoCl2・6H2O
2Cl.Co 129.839 g/mol
|
64.5 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
NiCl2・6H2O
Cl2Ni 129.599 g/mol
|
12.86 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
67.7 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
FeCl2・4H2O
Cl2Fe.4H2O 198.811 g/mol
|
943.5 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
Na2MoO4・2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
20.5 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
Na2SeO3・5H2O
5H2O.2Na.O3Se 263.012 g/mol
|
17.3 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
Na2WO4・2H2O
2H2O.2Na.O4W 329.846 g/mol
|
29.4 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
NaOH
HO.Na 39.997 g/mol
|
400 G_PER_L |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Simple component |
| 20 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.11 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.1 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
NaHCO3
CHO3.Na 84.006 g/mol
|
2 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 24 |
Biotin
C10H16N2O3S 244.316 g/mol
|
20 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 25 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
100 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 26 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
200 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 27 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
500 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 | Vitamin B12 | 100 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 29 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
100 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 30 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
200 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 | DL--Calcium pantothenate | 100 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
Solution A
Dose: 900 G_PER_L
See mediadive_5342_Solution_A.yaml for composition
Solution B
Dose: 50 G_PER_L
See mediadive_5343_Solution_B.yaml for composition
Solution C
Dose: 50 G_PER_L
See mediadive_5312_Solution_C.yaml for composition
Vitamin solution
Dose: 1 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Acid trace element solution (see below)
Dose: 1 G_PER_L
Alkaline trace element solution (see below)
Dose: 1 G_PER_L
Na2S・9H2O solution
Dose: variable VARIABLE
Role: Reducing agent; Properties: Defined component, Inorganic compound, Solution
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.396760Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M609 |
| 2026-01-28T19:48:29.768694Z | 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: N2; Added default concentration for ingredient: Na2S・9H2O solution; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: N2 |
| 2026-03-09T08:04:49.461595+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 7 solution(s) from ingredients |
| 2026-03-13T03:09:20.612944Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 7 duplicate ingredient(s) |
| 2026-03-13T06:20:10.679782Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010008 |
| 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; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:28.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.608126+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Desulfovibrio Magnus Medium" to "desulfovibrio_magnus_medium" for consistent matching |
| 2026-05-16T09:03:19.498804+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:42.964531+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 15 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:34.740778+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24) | Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md. |
| 2026-06-10T07:46:51.143017+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |