Overview
- External ontology
- MEDIADB:460 (source link unavailable) — 'Defined freshwater medium (CoCl2
- Applications
-
- Cultivation of genome-sequenced organisms
- Metabolic modeling
- Systems biology research
- Notes
- Source: MediaDB (Chemically-defined media for genome-sequenced organisms) Reference: https://mediadb.systemsbiology.net/ Commercial Product: LB Medium (Luria-Bertani, Miller formulation) Supplier: Multiple suppliers (Difco, Sigma, etc.) Catalog: Multiple (L3522 Sigma, 244520 BD) Source: https://www.laboratorynotes.com/preparation-of-luria-bertani-lb-miller-broth/ Accessed: 2026-03-28 Constituent composition researched from product specification.
Composition
flowchart LR
CultureMech_007366["defined_freshwater_medium_cocl2"]
ing0_Boric_acid["Boric acid"]
CultureMech_007366 --> ing0_Boric_acid
CHEBI_33118["CHEBI:33118"]
ing0_Boric_acid -.-> CHEBI_33118
ing1_Folate["Folate"]
CultureMech_007366 --> ing1_Folate
CHEBI_27470["CHEBI:27470"]
ing1_Folate -.-> CHEBI_27470
ing2_Biotin["Biotin"]
CultureMech_007366 --> ing2_Biotin
CHEBI_15956["CHEBI:15956"]
ing2_Biotin -.-> CHEBI_15956
ing3_Riboflavin["Riboflavin"]
CultureMech_007366 --> ing3_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing3_Riboflavin -.-> CHEBI_17015
ing4_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
CultureMech_007366 --> ing4_Calcium_chloride_anhydrous
CHEBI_3312["CHEBI:3312"]
ing4_Calcium_chloride_anhydrous -.-> CHEBI_3312
ing5_4_Aminobenzoate["4-Aminobenzoate"]
CultureMech_007366 --> ing5_4_Aminobenzoate
CHEBI_17836["CHEBI:17836"]
ing5_4_Aminobenzoate -.-> CHEBI_17836
ing6_Nicotinate["Nicotinate"]
CultureMech_007366 --> ing6_Nicotinate
CHEBI_15940["CHEBI:15940"]
ing6_Nicotinate -.-> CHEBI_15940
ing7_Vitamin_B12["Vitamin B12"]
CultureMech_007366 --> ing7_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing7_Vitamin_B12 -.-> CHEBI_176843
ing8_Lipoate["Lipoate"]
CultureMech_007366 --> ing8_Lipoate
CHEBI_16494["CHEBI:16494"]
ing8_Lipoate -.-> CHEBI_16494
ing9_Tryptone["Tryptone"]
CultureMech_007366 --> ing9_Tryptone
ing10_Yeast_extract["Yeast extract"]
CultureMech_007366 --> ing10_Yeast_extract
ing11_Sodium_chloride["Sodium chloride"]
CultureMech_007366 --> ing11_Sodium_chloride
CHEBI_26710["CHEBI:26710"]
ing11_Sodium_chloride -.-> CHEBI_26710
ing12_Ferric_oxide["Ferric oxide"]
CultureMech_007366 --> ing12_Ferric_oxide
ing13_Ferrous_sulfate["Ferrous sulfate"]
CultureMech_007366 --> ing13_Ferrous_sulfate
CHEBI_75832["CHEBI:75832"]
ing13_Ferrous_sulfate -.-> CHEBI_75832
ing14_Ammonium_chloride["Ammonium chloride"]
CultureMech_007366 --> ing14_Ammonium_chloride
CHEBI_31206["CHEBI:31206"]
ing14_Ammonium_chloride -.-> CHEBI_31206
ing15_Sodium_dihydrogen_phosphate["Sodium dihydrogen phosphate"]
CultureMech_007366 --> ing15_Sodium_dihydrogen_phosphate
CHEBI_37585["CHEBI:37585"]
ing15_Sodium_dihydrogen_phosphate -.-> CHEBI_37585
ing16_Zinc_sulfate["Zinc sulfate"]
CultureMech_007366 --> ing16_Zinc_sulfate
CHEBI_35176["CHEBI:35176"]
ing16_Zinc_sulfate -.-> CHEBI_35176
ing17_Thiamine_HCl["Thiamine HCl"]
CultureMech_007366 --> ing17_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing17_Thiamine_HCl -.-> CHEBI_49105
ing18_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_007366 --> ing18_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing18_Pyridoxine_HCl -.-> CHEBI_30961
ing19_Manganese_sulfate["Manganese sulfate"]
CultureMech_007366 --> ing19_Manganese_sulfate
CHEBI_86364["CHEBI:86364"]
ing19_Manganese_sulfate -.-> CHEBI_86364
ing20_Sodium_chloride["Sodium chloride"]
CultureMech_007366 --> ing20_Sodium_chloride
ing20_Sodium_chloride -.-> CHEBI_26710
ing21_Cobalt_chloride["Cobalt chloride"]
CultureMech_007366 --> ing21_Cobalt_chloride
CHEBI_35696["CHEBI:35696"]
ing21_Cobalt_chloride -.-> CHEBI_35696
ing22_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_007366 --> ing22_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing22_Calcium_pantothenate -.-> CHEBI_31345
ing23_Potassium_chloride["Potassium chloride"]
CultureMech_007366 --> ing23_Potassium_chloride
CHEBI_32588["CHEBI:32588"]
ing23_Potassium_chloride -.-> CHEBI_32588
ing24_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_007366 --> ing24_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing24_Nitrilotriacetic_acid -.-> CHEBI_44557
ing25_Sodium_bicarbonate["Sodium bicarbonate"]
CultureMech_007366 --> ing25_Sodium_bicarbonate
CHEBI_32139["CHEBI:32139"]
ing25_Sodium_bicarbonate -.-> CHEBI_32139
ing26_Sodium_molybdate["Sodium molybdate"]
CultureMech_007366 --> ing26_Sodium_molybdate
CHEBI_75215["CHEBI:75215"]
ing26_Sodium_molybdate -.-> CHEBI_75215
ing27_Nickel_chloride["Nickel chloride"]
CultureMech_007366 --> ing27_Nickel_chloride
CHEBI_34887["CHEBI:34887"]
ing27_Nickel_chloride -.-> CHEBI_34887
ing28_Magnesium_sulfate["Magnesium sulfate"]
CultureMech_007366 --> ing28_Magnesium_sulfate
CHEBI_32599["CHEBI:32599"]
ing28_Magnesium_sulfate -.-> CHEBI_32599
ing29_Aluminum_potassium_sulfate["Aluminum potassium sulfate"]
CultureMech_007366 --> ing29_Aluminum_potassium_sulfate
CHEBI_86463["CHEBI:86463"]
ing29_Aluminum_potassium_sulfate -.-> CHEBI_86463
CultureMech_007366 --> more["...1 more"]
Ingredients (31)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Boric acid
H3BO3 61.833 g/mol
|
0.001617 MILLIMOLAR |
CHEBI:33118
boric acid
|
|
| 2 |
Folate
C19H19N7O6 441.404 g/mol
|
4.531e-05 MILLIMOLAR |
CHEBI:27470
folic acid
|
Cross-references: KEGG:fol |
| 3 |
Biotin
C10H16N2O3S 244.316 g/mol
|
8.186e-05 MILLIMOLAR |
CHEBI:15956
biotin
|
Cross-references: KEGG:btn |
| 4 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.0001329 MILLIMOLAR |
CHEBI:17015
riboflavin
|
Cross-references: KEGG:ribflv |
| 5 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.687 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 6 |
4-Aminobenzoate
C7H6NO2 136.13 g/mol
|
0.0003646 MILLIMOLAR |
CHEBI:17836
4-aminobenzoate
|
Cross-references: KEGG:4abz |
| 7 |
Nicotinate
C6H5NO2 123.111 g/mol
|
0.0004061 MILLIMOLAR |
CHEBI:15940
nicotinic acid
|
Cross-references: KEGG:nac |
| 8 | Vitamin B12 | 7.378e-07 MILLIMOLAR |
CHEBI:176843
vitamin B12
|
|
| 9 |
Lipoate
C8H14O2S2 206.332 g/mol
|
0.0002423 MILLIMOLAR |
CHEBI:16494
lipoic acid
|
Cross-references: KEGG:lipoate |
| 10 |
Tryptone
Multiple suppliers (Difco, Sigma, etc.) LB Medium (Luria-Bertani, Miller formulation) Multiple (L3522 Sigma, 244520 BD)
|
10.0 G_PER_L |
MICRO:0000182 (source link unavailable)
tryptone
|
Pancreatic digest of casein providing amino acids, peptides, and nitrogen; Constituent of LB Medium (Luria-Bertani, Miller formulation) commercial product |
| 11 |
Yeast extract
Multiple suppliers (Difco, Sigma, etc.) LB Medium (Luria-Bertani, Miller formulation) Multiple (L3522 Sigma, 244520 BD)
|
5.0 G_PER_L |
FOODON:03315426
yeast extract
|
Autodigest of Saccharomyces cerevisiae providing vitamins, amino acids, and trace elements; Constituent of LB Medium (Luria-Bertani, Miller formulation) commercial product |
| 12 |
Sodium chloride
Cl.Na 58.443 g/mol
Multiple suppliers (Difco, Sigma, etc.) LB Medium (Luria-Bertani, Miller formulation) Multiple (L3522 Sigma, 244520 BD)
|
10.0 G_PER_L |
CHEBI:26710
sodium chloride
|
Maintains osmotic equilibrium (Miller formulation); Constituent of LB Medium (Luria-Bertani, Miller formulation) commercial product |
| 13 | Ferric oxide | 100.0 MILLIMOLAR | ||
| 14 |
Ferrous sulfate
Fe.O4S 151.908 g/mol
|
0.003597 MILLIMOLAR |
CHEBI:75832
iron(2+) sulfate (anhydrous)
|
|
| 15 |
Ammonium chloride
Cl.H4N 53.492 g/mol
|
28.04 MILLIMOLAR |
CHEBI:31206
ammonium chloride
|
|
| 16 |
Sodium dihydrogen phosphate
H2O4P.Na 119.976 g/mol
|
4.348 MILLIMOLAR |
CHEBI:37585
sodium dihydrogenphosphate
|
|
| 17 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.006194 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 18 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.0001482 MILLIMOLAR |
CHEBI:49105
thiamine hydrochloride
|
|
| 19 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
0.0004863 MILLIMOLAR |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 20 |
Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
|
0.02673 MILLIMOLAR |
CHEBI:86364
manganese(II) sulfate monohydrate
|
|
| 21 |
Sodium chloride
Cl.Na 58.443 g/mol
|
0.1711 MILLIMOLAR |
CHEBI:26710
sodium chloride
|
|
| 22 |
Cobalt chloride
2Cl.Co 129.839 g/mol
|
0.007702 MILLIMOLAR |
CHEBI:35696
cobalt dichloride
|
|
| 23 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.0001049 MILLIMOLAR |
CHEBI:31345
Calcium pantothenate
|
|
| 24 |
Potassium chloride
Cl.K 74.551 g/mol
|
1.341 MILLIMOLAR |
CHEBI:32588
potassium chloride
|
|
| 25 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
0.07848 MILLIMOLAR |
CHEBI:44557
nitrilotriacetic acid
|
|
| 26 |
Sodium bicarbonate
CHO3.Na 84.006 g/mol
|
29.76 MILLIMOLAR |
CHEBI:32139
sodium hydrogencarbonate
|
|
| 27 |
Sodium molybdate
MoO4.2Na 205.916 g/mol
|
0.001627 MILLIMOLAR |
CHEBI:75215
sodium molybdate (anhydrous)
|
|
| 28 |
Nickel chloride
Cl2Ni 129.599 g/mol
|
0.00101 MILLIMOLAR |
CHEBI:34887
nickel dichloride
|
|
| 29 |
Magnesium sulfate
Mg.O4S 120.368 g/mol
|
0.1217 MILLIMOLAR |
CHEBI:32599
magnesium sulfate
|
|
| 30 |
Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
|
0.0003873 MILLIMOLAR |
CHEBI:86463
potassium aluminium sulfate
|
|
| 31 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
0.0004005 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
Preparation
- Dissolve all ingredients in distilled water to specified concentrations
- Adjust pH if specified in original formulation
- Sterilize by filtration (0.22 μm) to preserve heat-sensitive components
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- MEDIADB_460_Defined_freshwater_medium_CoCl2 (CultureMech:007366)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:46.880626Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 460, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:07.493253Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:12.784525Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:19:48.357709Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007366 |
| 2026-03-17T06:29:40.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:06.693500+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "'Defined freshwater medium (CoCl2" to "defined_freshwater_medium_cocl2" for consistent matching |
| 2026-06-05T07:40:29.278531+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 18 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:29.557683+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. |
| 2026-06-09T01:42:16.374012+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. |
| 2026-08-06T03:05:04.315483+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 840efe348eab84ef470d799694f5bec40e4c0991e6466e5d725d4a969a72242f |