Overview
- External ontology
- TOGO:M359 — Deferribacter Abyssi Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M359 Original source: JCM - JCM_M365 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=365
Composition
flowchart LR
CultureMech_009739["deferribacter_abyssi_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009739 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_009739 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009739 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_009739 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_009739 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009739 --> ing5_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing5_MgCl2_6H2O -.-> CHEBI_86345
ing6_Na2S_9H2O["Na2S・9H2O"]
CultureMech_009739 --> ing6_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing6_Na2S_9H2O -.-> CHEBI_76209
ing7_KCl["KCl"]
CultureMech_009739 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_Sodium_acetate["Sodium acetate"]
CultureMech_009739 --> ing8_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing8_Sodium_acetate -.-> CHEBI_32954
ing9_Sulfur["Sulfur"]
CultureMech_009739 --> ing9_Sulfur
CHEBI_26833["CHEBI:26833"]
ing9_Sulfur -.-> CHEBI_26833
ing10_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_009739 --> ing10_Yeast_extract__BD_Difco_
ing11_N2["N2"]
CultureMech_009739 --> ing11_N2
CHEBI_17997["CHEBI:17997"]
ing11_N2 -.-> CHEBI_17997
Ingredients (12)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
30 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.33 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.33 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.33 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Simple component, Defined component, Inorganic compound |
| 6 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.33 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component |
| 7 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
0.5 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Simple component, Inorganic compound, Defined component |
| 8 |
KCl
Cl.K 74.551 g/mol
|
0.33 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 9 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
3 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Simple component, Organic compound, Defined component |
| 10 |
Sulfur
S 32.067 g/mol
|
10 G_PER_L |
CHEBI:26833
sulfur atom
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component |
| 11 | Yeast extract (BD-Difco) | 0.1 G_PER_L | Properties: Undefined component | |
| 12 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
Solutions
Trace minerals (see Medium [M142])
Dose: 10 G_PER_L
Cross-reference to Medium M142
Trace vitamins (see Medium [M190])
Dose: 10 G_PER_L
Cross-reference to Medium M190
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M359_Deferribacter_Abyssi_Medium (CultureMech:009739)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.907052Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M359 |
| 2026-01-28T19:48:36.549331Z | 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 |
| 2026-03-09T08:05:00.941944+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T06:20:08.496985Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009739 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:43.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:27.484474+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Deferribacter Abyssi Medium" to "deferribacter_abyssi_medium" for consistent matching |
| 2026-05-16T09:03:17.396960+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:40.709268+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 7 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:50.407903+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. |
| 2026-08-06T03:05:15.301204+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 58cac0aaf12759faf4d99213554c50af0497b0d6a814481e7dd92dd3262cbc15 |