Overview
- External ontology
- TOGO:M641 — Freshwater Iron-Oxidizing Bacteria Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M641 Original source: JCM - JCM_M628 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=628
Composition
flowchart LR
CultureMech_010042["freshwater_iron_oxidizing_bacteria_medium"]
ing0_Bottom_layer["Bottom layer"]
CultureMech_010042 --> ing0_Bottom_layer
ing1_Top_layer["Top layer"]
CultureMech_010042 --> ing1_Top_layer
ing2_Agarose["Agarose"]
CultureMech_010042 --> ing2_Agarose
CHEBI_2511["CHEBI:2511"]
ing2_Agarose -.-> CHEBI_2511
ing3_NaHCO3["NaHCO3"]
CultureMech_010042 --> ing3_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing3_NaHCO3 -.-> CHEBI_32139
ing4_MES["MES"]
CultureMech_010042 --> ing4_MES
CHEBI_39010["CHEBI:39010"]
ing4_MES -.-> CHEBI_39010
ing5_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010042 --> ing5_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing5_Carbon_dioxide_gas -.-> CHEBI_16526
ing6_Nitrogen_gas["Nitrogen gas"]
CultureMech_010042 --> ing6_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing6_Nitrogen_gas -.-> CHEBI_17997
ing7_Oxygen_gas["Oxygen gas"]
CultureMech_010042 --> ing7_Oxygen_gas
ing8_Distilled_water["Distilled water"]
CultureMech_010042 --> ing8_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing8_Distilled_water -.-> CHEBI_15377
ing9_Na2S_9H2O["Na2S・9H2O"]
CultureMech_010042 --> ing9_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing9_Na2S_9H2O -.-> CHEBI_76209
ing10_FeSO4_7H2O["FeSO4・7H2O"]
CultureMech_010042 --> ing10_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing10_FeSO4_7H2O -.-> CHEBI_75836
ing11_MgSO4_7H2O["MgSO4・7H2O"]
CultureMech_010042 --> ing11_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing11_MgSO4_7H2O -.-> CHEBI_31795
ing12_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010042 --> ing12_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing12_CaCl2_2H2O -.-> CHEBI_86158
ing13_KH2PO4["KH2PO4"]
CultureMech_010042 --> ing13_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing13_KH2PO4 -.-> CHEBI_63036
ing14_NH4Cl["NH4Cl"]
CultureMech_010042 --> ing14_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing14_NH4Cl -.-> CHEBI_31206
Ingredients (15)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | Bottom layer | 100 G_PER_L | ||
| 2 | Top layer | 101 G_PER_L | ||
| 3 |
Agarose
(C12H18O9)n.C12H20O10 630.549 g/mol
|
1.15 G_PER_L |
CHEBI:2511
agarose
|
Role: Solidifying component [Merged 2 duplicates: 1.0, 0.15] |
| 4 |
NaHCO3
CHO3.Na 84.006 g/mol
|
0.042 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component |
| 5 | MES | 0.195 G_PER_L |
CHEBI:39010
MES
|
Role: Buffer; Properties: Defined component, Organic compound, Simple component |
| 6 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 7 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 8 | Oxygen gas | variable VARIABLE | Properties: ガス | |
| 9 |
Distilled water
H2O 18.015 g/mol
|
301.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Defined component, Simple component, Inorganic compound [Merged 2 duplicates: 300.0, 1.0] |
| 10 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
39.6 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Defined component, Inorganic compound, Simple component |
| 11 |
FeSO4・7H2O
Fe.7H2O.O4S 278.013 g/mol
|
46.2 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component |
| 12 |
MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.2 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 13 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 14 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.05 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Defined component, Simple component, Inorganic compound |
| 15 |
NH4Cl
Cl.H4N 53.492 g/mol
|
1 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
Solutions
FeS solution (see below)
Dose: 50 G_PER_L
Modified Wolfe's solution (see below)
Dose: 50 G_PER_L
Modified Wolfe's solution (see below)
Dose: 100 G_PER_L
Trace mineral solution (see Medium [M190])
Dose: 1 G_PER_L
Cross-reference to Medium M190
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.449758Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M641 |
| 2026-01-28T19:48:15.785368Z | 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: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: Oxygen gas |
| 2026-03-09T08:04:26.030731+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T03:08:54.563688Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:10.900795Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010042 |
| 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 |
| 2026-03-17T06:29:58.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.828751+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Freshwater Iron-Oxidizing Bacteria Medium" to "freshwater_iron_oxidizing_bacteria_medium" for consistent matching |
| 2026-05-16T09:03:19.701472+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:43.193344+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 6 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:32.012038+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. |
| 2026-06-10T07:46:51.214600+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |