Overview
- External ontology
- TOGO:M625 — Desulfomicrobium Medium
- Applications
-
- Microbial cultivation
- High-metal flag
- True
- Notes
- Source: https://togomedium.org/medium/M625 Original source: JCM - JCM_M616 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=616
Composition
flowchart LR
CultureMech_010025["desulfomicrobium_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010025 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4・7H2O"]
CultureMech_010025 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010025 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_010025 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_010025 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_KCl["KCl"]
CultureMech_010025 --> ing5_KCl
CHEBI_32588["CHEBI:32588"]
ing5_KCl -.-> CHEBI_32588
ing6_Na2SO4["Na2SO4"]
CultureMech_010025 --> ing6_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing6_Na2SO4 -.-> CHEBI_32149
ing7_Sodium_lactate["Sodium lactate"]
CultureMech_010025 --> ing7_Sodium_lactate
CHEBI_75228["CHEBI:75228"]
ing7_Sodium_lactate -.-> CHEBI_75228
ing8_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010025 --> ing8_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing8_Carbon_dioxide_gas -.-> CHEBI_16526
ing9_Nitrogen_gas["Nitrogen gas"]
CultureMech_010025 --> ing9_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing9_Nitrogen_gas -.-> CHEBI_17997
ing10_Na2MoO4_2H2O["Na2MoO4・2H2O"]
CultureMech_010025 --> ing10_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing10_Na2MoO4_2H2O -.-> CHEBI_75213
ing11_H3BO3["H3BO3"]
CultureMech_010025 --> ing11_H3BO3
CHEBI_33118["CHEBI:33118"]
ing11_H3BO3 -.-> CHEBI_33118
ing12_FeSO4_7H2O["FeSO4・7H2O"]
CultureMech_010025 --> ing12_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing12_FeSO4_7H2O -.-> CHEBI_75836
ing13_MnCl4_4H2O["MnCl4・4H2O"]
CultureMech_010025 --> ing13_MnCl4_4H2O
ing14_CoCl2_6H2O["CoCl2・6H2O"]
CultureMech_010025 --> ing14_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing14_CoCl2_6H2O -.-> CHEBI_35696
ing15_NiCl2_6H2O["NiCl2・6H2O"]
CultureMech_010025 --> ing15_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing15_NiCl2_6H2O -.-> CHEBI_34887
ing16_CuCl2_2H2O["CuCl2・2H2O"]
CultureMech_010025 --> ing16_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing16_CuCl2_2H2O -.-> CHEBI_86318
ing17_ZnCl2["ZnCl2"]
CultureMech_010025 --> ing17_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing17_ZnCl2 -.-> CHEBI_49976
ing18_EDTA_2Na["EDTA・2Na"]
CultureMech_010025 --> ing18_EDTA_2Na
CHEBI_64734["CHEBI:64734"]
ing18_EDTA_2Na -.-> CHEBI_64734
ing19_Biotin["Biotin"]
CultureMech_010025 --> ing19_Biotin
CHEBI_15956["CHEBI:15956"]
ing19_Biotin -.-> CHEBI_15956
ing20_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010025 --> ing20_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing20_p__Aminobenzoic_acid -.-> CHEBI_30753
ing21_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010025 --> ing21_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing21_Thiamine_HCl -.-> CHEBI_49105
ing22_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010025 --> ing22_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing22_Pyridoxine_HCl -.-> CHEBI_30961
ing23_Vitamin_B12["Vitamin B12"]
CultureMech_010025 --> ing23_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing23_Vitamin_B12 -.-> CHEBI_176843
ing24_Nicotinic_acid["Nicotinic acid"]
CultureMech_010025 --> ing24_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing24_Nicotinic_acid -.-> CHEBI_15940
ing25_DL__Calcium_pantothenate["DL--Calcium pantothenate"]
CultureMech_010025 --> ing25_DL__Calcium_pantothenate
Ingredients (26)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
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 3 identical duplicates: 1.0, 1.0, 1.0] |
| 2 |
MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.5 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.05 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.25 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
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 |
| 6 |
KCl
Cl.K 74.551 g/mol
|
0.5 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
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 |
| 8 |
Sodium lactate
C3H5O3.Na 112.06 g/mol
|
1.12 G_PER_L |
CHEBI:75228
sodium lactate
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 9 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 10 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 11 |
Na2MoO4・2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
18 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
H3BO3
H3BO3 61.833 g/mol
|
300 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
FeSO4・7H2O
Fe.7H2O.O4S 278.013 g/mol
|
1.1 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 | MnCl4・4H2O | 50 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component | |
| 15 |
CoCl2・6H2O
2Cl.Co 129.839 g/mol
|
190 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
NiCl2・6H2O
Cl2Ni 129.599 g/mol
|
24 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
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 |
| 18 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
42 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
EDTA・2Na
C10H14N2O8.2Na 336.208 g/mol
|
3 G_PER_L |
CHEBI:64734
EDTA disodium salt (anhydrous)
|
Properties: Defined component, Organic compound, Simple component |
| 20 |
Biotin
C10H16N2O3S 244.316 g/mol
|
20 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 21 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
80 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 22 |
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 |
| 23 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
300 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 24 | Vitamin B12 | 100 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 25 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
200 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 26 | DL--Calcium pantothenate | 100 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
Trace element solution SL12B (see below)
Dose: 1 G_PER_L
8% NaHCO3 solution
Dose: 30 G_PER_L
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
5% Na2S・9H2O solution
Dose: 1 G_PER_L
Role: Reducing agent; Properties: Defined component, Solution, Inorganic compound
Vitamin solution (see below)
Dose: 1 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.421950Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M625 |
| 2026-01-28T19:48:19.410283Z | 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 |
| 2026-03-09T08:04:32.151531+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T03:09:01.373084Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:10.790343Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010025 |
| 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 |
| 2026-03-17T06:30:06.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.715755+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Desulfomicrobium Medium" to "desulfomicrobium_medium" for consistent matching |
| 2026-05-16T09:03:19.591296+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:43.073252+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. |
| 2026-06-08T23:19:34.764248+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. |
| 2026-06-10T06:57:31.908150+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. |
| 2026-06-10T07:46:51.180582+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. |
| 2026-09-02T07:37:51.137885+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. |