defined_freshwater_medium_cocl2

CultureMech:007372 bacterial DEFINED LIQUID
Original name: 'Defined freshwater medium (CoCl2

Overview

External ontology
MEDIADB:466 (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/

Composition

flowchart LR
    CultureMech_007372["defined_freshwater_medium_cocl2"]
    ing0_Sodium_bicarbonate["Sodium bicarbonate"]
    CultureMech_007372 --> ing0_Sodium_bicarbonate
    CHEBI_32139["CHEBI:32139"]
    ing0_Sodium_bicarbonate -.-> CHEBI_32139
    ing1_Folate["Folate"]
    CultureMech_007372 --> ing1_Folate
    CHEBI_27470["CHEBI:27470"]
    ing1_Folate -.-> CHEBI_27470
    ing2_Biotin["Biotin"]
    CultureMech_007372 --> ing2_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing2_Biotin -.-> CHEBI_15956
    ing3_Riboflavin["Riboflavin"]
    CultureMech_007372 --> ing3_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing3_Riboflavin -.-> CHEBI_17015
    ing4_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007372 --> ing4_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing4_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing5_4_Aminobenzoate["4-Aminobenzoate"]
    CultureMech_007372 --> ing5_4_Aminobenzoate
    CHEBI_17836["CHEBI:17836"]
    ing5_4_Aminobenzoate -.-> CHEBI_17836
    ing6_Nicotinate["Nicotinate"]
    CultureMech_007372 --> ing6_Nicotinate
    CHEBI_15940["CHEBI:15940"]
    ing6_Nicotinate -.-> CHEBI_15940
    ing7_Vitamin_B12["Vitamin B12"]
    CultureMech_007372 --> ing7_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing7_Vitamin_B12 -.-> CHEBI_176843
    ing8_Lipoate["Lipoate"]
    CultureMech_007372 --> ing8_Lipoate
    CHEBI_16494["CHEBI:16494"]
    ing8_Lipoate -.-> CHEBI_16494
    ing9_Boric_acid["Boric acid"]
    CultureMech_007372 --> ing9_Boric_acid
    CHEBI_33118["CHEBI:33118"]
    ing9_Boric_acid -.-> CHEBI_33118
    ing10_Ferric_oxide["Ferric oxide"]
    CultureMech_007372 --> ing10_Ferric_oxide
    ing11_Ferrous_sulfate["Ferrous sulfate"]
    CultureMech_007372 --> ing11_Ferrous_sulfate
    CHEBI_75832["CHEBI:75832"]
    ing11_Ferrous_sulfate -.-> CHEBI_75832
    ing12_Ammonium_chloride["Ammonium chloride"]
    CultureMech_007372 --> ing12_Ammonium_chloride
    CHEBI_31206["CHEBI:31206"]
    ing12_Ammonium_chloride -.-> CHEBI_31206
    ing13_Sodium_dihydrogen_phosphate["Sodium dihydrogen phosphate"]
    CultureMech_007372 --> ing13_Sodium_dihydrogen_phosphate
    CHEBI_37585["CHEBI:37585"]
    ing13_Sodium_dihydrogen_phosphate -.-> CHEBI_37585
    ing14_Zinc_sulfate["Zinc sulfate"]
    CultureMech_007372 --> ing14_Zinc_sulfate
    CHEBI_35176["CHEBI:35176"]
    ing14_Zinc_sulfate -.-> CHEBI_35176
    ing15_Thiamine_HCl["Thiamine HCl"]
    CultureMech_007372 --> ing15_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing15_Thiamine_HCl -.-> CHEBI_49105
    ing16_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_007372 --> ing16_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing16_Pyridoxine_HCl -.-> CHEBI_30961
    ing17_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007372 --> ing17_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing17_Manganese_sulfate -.-> CHEBI_86364
    ing18_Sodium_chloride["Sodium chloride"]
    CultureMech_007372 --> ing18_Sodium_chloride
    CHEBI_26710["CHEBI:26710"]
    ing18_Sodium_chloride -.-> CHEBI_26710
    ing19_p_Hydroxybenzyl_alcohol["p-Hydroxybenzyl alcohol"]
    CultureMech_007372 --> ing19_p_Hydroxybenzyl_alcohol
    ing20_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_007372 --> ing20_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing20_Calcium_pantothenate -.-> CHEBI_31345
    ing21_Potassium_chloride["Potassium chloride"]
    CultureMech_007372 --> ing21_Potassium_chloride
    CHEBI_32588["CHEBI:32588"]
    ing21_Potassium_chloride -.-> CHEBI_32588
    ing22_Nickel_chloride["Nickel chloride"]
    CultureMech_007372 --> ing22_Nickel_chloride
    CHEBI_34887["CHEBI:34887"]
    ing22_Nickel_chloride -.-> CHEBI_34887
    ing23_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_007372 --> ing23_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing23_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing24_Cobalt_chloride["Cobalt chloride"]
    CultureMech_007372 --> ing24_Cobalt_chloride
    CHEBI_35696["CHEBI:35696"]
    ing24_Cobalt_chloride -.-> CHEBI_35696
    ing25_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007372 --> ing25_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing25_Sodium_molybdate -.-> CHEBI_75215
    ing26_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007372 --> ing26_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing26_Magnesium_sulfate -.-> CHEBI_32599
    ing27_Aluminum_potassium_sulfate["Aluminum potassium sulfate"]
    CultureMech_007372 --> ing27_Aluminum_potassium_sulfate
    CHEBI_86463["CHEBI:86463"]
    ing27_Aluminum_potassium_sulfate -.-> CHEBI_86463
    ing28_Cupric_sulfate["Cupric sulfate"]
    CultureMech_007372 --> ing28_Cupric_sulfate
    CHEBI_23414["CHEBI:23414"]
    ing28_Cupric_sulfate -.-> CHEBI_23414

Ingredients (29)

# Ingredient Concentration Ontology Notes
1 Sodium bicarbonate
CHO3.Na 84.006 g/mol
29.76 MILLIMOLAR CHEBI:32139
sodium hydrogencarbonate
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 Boric acid
H3BO3 61.833 g/mol
0.001617 MILLIMOLAR CHEBI:33118
boric acid
11 Ferric oxide 100.0 MILLIMOLAR
12 Ferrous sulfate
Fe.O4S 151.908 g/mol
0.003597 MILLIMOLAR CHEBI:75832
iron(2+) sulfate (anhydrous)
13 Ammonium chloride
Cl.H4N 53.492 g/mol
28.04 MILLIMOLAR CHEBI:31206
ammonium chloride
14 Sodium dihydrogen phosphate
H2O4P.Na 119.976 g/mol
4.348 MILLIMOLAR CHEBI:37585
sodium dihydrogenphosphate
15 Zinc sulfate
O4S.Zn 161.453 g/mol
0.006194 MILLIMOLAR CHEBI:35176
zinc sulfate
16 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0001482 MILLIMOLAR CHEBI:49105
thiamine hydrochloride
17 Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
0.0004863 MILLIMOLAR CHEBI:30961
pyridoxine hydrochloride
18 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.02673 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
19 Sodium chloride
Cl.Na 58.443 g/mol
0.1711 MILLIMOLAR CHEBI:26710
sodium chloride
20 p-Hydroxybenzyl alcohol 0.5 MILLIMOLAR
21 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.0001049 MILLIMOLAR CHEBI:31345
Calcium pantothenate
22 Potassium chloride
Cl.K 74.551 g/mol
1.341 MILLIMOLAR CHEBI:32588
potassium chloride
23 Nickel chloride
Cl2Ni 129.599 g/mol
0.00101 MILLIMOLAR CHEBI:34887
nickel dichloride
24 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
0.07848 MILLIMOLAR CHEBI:44557
nitrilotriacetic acid
25 Cobalt chloride
2Cl.Co 129.839 g/mol
0.007702 MILLIMOLAR CHEBI:35696
cobalt dichloride
26 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.001627 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
27 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.1217 MILLIMOLAR CHEBI:32599
magnesium sulfate
28 Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
0.0003873 MILLIMOLAR CHEBI:86463
potassium aluminium sulfate
29 Cupric sulfate
Cu.O4S 159.609 g/mol
0.0004005 MILLIMOLAR CHEBI:23414
copper(II) sulfate

Preparation

  1. Dissolve all ingredients in distilled water to specified concentrations
  2. Adjust pH if specified in original formulation
  3. Sterilize by filtration (0.22 μm) to preserve heat-sensitive components

Target organisms

No target organisms are recorded.

Provenance

Merged from 1 source record.

TimestampCuratorActionNotes
2026-01-27T07:21:46.944074Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 466, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:12.560660Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-06T05:10:19.006313Z invalid-chebi-removal Removed 1 invalid CHEBI ID(s) Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data
2026-03-13T06:19:48.431949Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007372
2026-03-17T06:29:52.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:06.772343+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
2026-06-05T07:40:29.370089+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.
2026-06-08T23:19:29.654494+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.
2026-06-09T01:42:16.467580+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.
2026-08-06T03:05:04.406623+00:00 merge_recipes.py MERGED_RECIPES merged 1 source recipe(s) on fingerprint e7c7e61b33508fa3d8922ad52c5b0b1df2c0fcf59058349fb3403cb6b6f9f4f5