Overview
- External ontology
- TOGO:M562 — Magnetospirillum Medium (A)
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M562 Original source: JCM - JCM_M558 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=558
Composition
flowchart LR
CultureMech_009957["magnetospirillum_medium_a"]
ing0_Distilled_water["Distilled water"]
CultureMech_009957 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_KH2PO4["KH2PO4"]
CultureMech_009957 --> ing1_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing1_KH2PO4 -.-> CHEBI_63036
ing2_NH4Cl["NH4Cl"]
CultureMech_009957 --> ing2_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing2_NH4Cl -.-> CHEBI_31206
ing3_KNO3["KNO3"]
CultureMech_009957 --> ing3_KNO3
CHEBI_63043["CHEBI:63043"]
ing3_KNO3 -.-> CHEBI_63043
ing4_Na2HPO4["Na2HPO4"]
CultureMech_009957 --> ing4_Na2HPO4
CHEBI_34683["CHEBI:34683"]
ing4_Na2HPO4 -.-> CHEBI_34683
ing5_K2SO4["K2SO4"]
CultureMech_009957 --> ing5_K2SO4
CHEBI_32036["CHEBI:32036"]
ing5_K2SO4 -.-> CHEBI_32036
ing6_H3BO3["H3BO3"]
CultureMech_009957 --> ing6_H3BO3
CHEBI_33118["CHEBI:33118"]
ing6_H3BO3 -.-> CHEBI_33118
ing7_CuCl2_2H2O["CuCl2・2H2O"]
CultureMech_009957 --> ing7_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing7_CuCl2_2H2O -.-> CHEBI_86318
ing8_Na2WO4_2H2O["Na2WO4・2H2O"]
CultureMech_009957 --> ing8_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing8_Na2WO4_2H2O -.-> CHEBI_63939
ing9_Na2SeO3["Na2SeO3"]
CultureMech_009957 --> ing9_Na2SeO3
CHEBI_48843["CHEBI:48843"]
ing9_Na2SeO3 -.-> CHEBI_48843
ing10_NaOH["NaOH"]
CultureMech_009957 --> ing10_NaOH
CHEBI_32145["CHEBI:32145"]
ing10_NaOH -.-> CHEBI_32145
ing11_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009957 --> ing11_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing11_CaCl2_2H2O -.-> CHEBI_86158
ing12_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009957 --> ing12_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing12_MgCl2_6H2O -.-> CHEBI_86345
ing13_Sodium_benzoate["Sodium benzoate"]
CultureMech_009957 --> ing13_Sodium_benzoate
CHEBI_113455["CHEBI:113455"]
ing13_Sodium_benzoate -.-> CHEBI_113455
ing14_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_009957 --> ing14_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing14_p__Aminobenzoic_acid -.-> CHEBI_30753
ing15_Thiamine_HCl["Thiamine・HCl"]
CultureMech_009957 --> ing15_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing15_Thiamine_HCl -.-> CHEBI_49105
ing16_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_009957 --> ing16_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing16_Pyridoxine_HCl -.-> CHEBI_30961
ing17_Vitamin_B12["Vitamin B12"]
CultureMech_009957 --> ing17_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing17_Vitamin_B12 -.-> CHEBI_176843
ing18_Nicotinic_acid["Nicotinic acid"]
CultureMech_009957 --> ing18_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing18_Nicotinic_acid -.-> CHEBI_15940
ing19_D__Biotin["D--Biotin"]
CultureMech_009957 --> ing19_D__Biotin
ing20_D__Calcium_pantothenate["D--Calcium pantothenate"]
CultureMech_009957 --> ing20_D__Calcium_pantothenate
ing21_FeSO4_7H2O["FeSO4・7H2O"]
CultureMech_009957 --> ing21_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing21_FeSO4_7H2O -.-> CHEBI_75836
ing22_EDTA_2Na["EDTA・2Na"]
CultureMech_009957 --> ing22_EDTA_2Na
CHEBI_64734["CHEBI:64734"]
ing22_EDTA_2Na -.-> CHEBI_64734
Ingredients (23)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
601.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 7 duplicates: 1.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0] |
| 2 |
KH2PO4
H2O4P.K 136.084 g/mol
|
1 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.5 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
KNO3
K.NO3 101.102 g/mol
|
0.51 G_PER_L |
CHEBI:63043
potassium nitrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
Na2HPO4
HO4P.2Na 141.958 g/mol
|
1.6 G_PER_L |
CHEBI:34683
disodium hydrogenphosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
K2SO4
2K.O4S 174.259 g/mol
|
0.06 G_PER_L |
CHEBI:32036
potassium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
H3BO3
H3BO3 61.833 g/mol
|
6 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
CuCl2・2H2O
Cl2Cu.2H2O 170.482 g/mol
|
2 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Na2WO4・2H2O
2H2O.2Na.O4W 329.846 g/mol
|
0.4 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
Na2SeO3
2Na.O3Se 172.937 g/mol
|
0.2 G_PER_L |
CHEBI:48843
disodium selenite
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
NaOH
HO.Na 39.997 g/mol
|
0.05 G_PER_L |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Simple component |
| 12 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.5 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
2 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
Sodium benzoate
C7H5O2.Na 144.105 g/mol
|
7.2 G_PER_L |
CHEBI:113455
sodium benzoate
|
Properties: Simple component, Organic compound, Defined component |
| 15 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
10 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
10 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
50 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 | Vitamin B12 | 4 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
20 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 20 | D--Biotin | 2 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 21 | D--Calcium pantothenate | 5 G_PER_L | Role: Vitamin; Properties: Defined component | |
| 22 |
FeSO4・7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.05 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
EDTA・2Na
C10H14N2O8.2Na 336.208 g/mol
|
0.5 G_PER_L |
CHEBI:64734
EDTA disodium salt (anhydrous)
|
Properties: Defined component, Organic compound, Simple component |
Solutions
Trace x 10 solution (see below)
Dose: 0.1 G_PER_L
Se/W solution (see below)
Dose: 1 G_PER_L
Mg/Ca solution (see below)
Dose: 5 G_PER_L
Na benzoate solution (see below)
Dose: 2 G_PER_L
7 Vitamins solution (see below)
Dose: 0.5 G_PER_L
FeSO4 solution (see below)
Dose: 3 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.306351Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M562 |
| 2026-01-28T19:48:28.136954Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-03-09T08:04:46.563575+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 6 solution(s) from ingredients |
| 2026-03-13T03:09:17.146521Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 6 duplicate ingredient(s) |
| 2026-03-13T06:20:10.290755Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009957 |
| 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 |
| 2026-03-17T06:30:25.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.220751+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Magnetospirillum Medium (A)" to "magnetospirillum_medium_a" for consistent matching |
| 2026-05-16T09:03:19.114878+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=1 |
| 2026-06-05T07:40:42.566803+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 12 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:34.662713+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 1 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). |
| 2026-06-10T07:46:51.014085+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. |