defined_freshwater_medium_cocl2

CultureMech:007349 bacterial DEFINED LIQUID
Original name: Defined freshwater medium (CoCl2) + 50 mM Iron citrate + 113.2 mM Acetate

Overview

External ontology
MEDIADB:445 (source link unavailable) — Defined freshwater medium (CoCl2) + 50 mM Iron citrate + 113.2 mM Acetate
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_007349["defined_freshwater_medium_cocl2"]
    ing0_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007349 --> ing0_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing0_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing1_Riboflavin["Riboflavin"]
    CultureMech_007349 --> ing1_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing1_Riboflavin -.-> CHEBI_17015
    ing2_Sodium_acetate["Sodium acetate"]
    CultureMech_007349 --> ing2_Sodium_acetate
    CHEBI_32954["CHEBI:32954"]
    ing2_Sodium_acetate -.-> CHEBI_32954
    ing3_Nicotinate["Nicotinate"]
    CultureMech_007349 --> ing3_Nicotinate
    CHEBI_15940["CHEBI:15940"]
    ing3_Nicotinate -.-> CHEBI_15940
    ing4_Vitamin_B12["Vitamin B12"]
    CultureMech_007349 --> ing4_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing4_Vitamin_B12 -.-> CHEBI_176843
    ing5_Folate["Folate"]
    CultureMech_007349 --> ing5_Folate
    CHEBI_27470["CHEBI:27470"]
    ing5_Folate -.-> CHEBI_27470
    ing6_Biotin["Biotin"]
    CultureMech_007349 --> ing6_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing6_Biotin -.-> CHEBI_15956
    ing7_Lipoate["Lipoate"]
    CultureMech_007349 --> ing7_Lipoate
    CHEBI_16494["CHEBI:16494"]
    ing7_Lipoate -.-> CHEBI_16494
    ing8_4_Aminobenzoate["4-Aminobenzoate"]
    CultureMech_007349 --> ing8_4_Aminobenzoate
    CHEBI_17836["CHEBI:17836"]
    ing8_4_Aminobenzoate -.-> CHEBI_17836
    ing9_Fe_III_dicitrate["Fe(III)dicitrate"]
    CultureMech_007349 --> ing9_Fe_III_dicitrate
    ing10_Aluminum_potassium_sulfate["Aluminum potassium sulfate"]
    CultureMech_007349 --> ing10_Aluminum_potassium_sulfate
    CHEBI_86463["CHEBI:86463"]
    ing10_Aluminum_potassium_sulfate -.-> CHEBI_86463
    ing11_Ammonium_chloride["Ammonium chloride"]
    CultureMech_007349 --> ing11_Ammonium_chloride
    CHEBI_31206["CHEBI:31206"]
    ing11_Ammonium_chloride -.-> CHEBI_31206
    ing12_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007349 --> ing12_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing12_Manganese_sulfate -.-> CHEBI_86364
    ing13_Zinc_sulfate["Zinc sulfate"]
    CultureMech_007349 --> ing13_Zinc_sulfate
    CHEBI_35176["CHEBI:35176"]
    ing13_Zinc_sulfate -.-> CHEBI_35176
    ing14_Ferrous_sulfate["Ferrous sulfate"]
    CultureMech_007349 --> ing14_Ferrous_sulfate
    CHEBI_75832["CHEBI:75832"]
    ing14_Ferrous_sulfate -.-> CHEBI_75832
    ing15_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_007349 --> ing15_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing15_Pyridoxine_HCl -.-> CHEBI_30961
    ing16_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_007349 --> ing16_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing16_Calcium_pantothenate -.-> CHEBI_31345
    ing17_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007349 --> ing17_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing17_Magnesium_sulfate -.-> CHEBI_32599
    ing18_Cobalt_chloride["Cobalt chloride"]
    CultureMech_007349 --> ing18_Cobalt_chloride
    CHEBI_35696["CHEBI:35696"]
    ing18_Cobalt_chloride -.-> CHEBI_35696
    ing19_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007349 --> ing19_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing19_Sodium_molybdate -.-> CHEBI_75215
    ing20_Potassium_chloride["Potassium chloride"]
    CultureMech_007349 --> ing20_Potassium_chloride
    CHEBI_32588["CHEBI:32588"]
    ing20_Potassium_chloride -.-> CHEBI_32588
    ing21_Sodium_chloride["Sodium chloride"]
    CultureMech_007349 --> ing21_Sodium_chloride
    CHEBI_26710["CHEBI:26710"]
    ing21_Sodium_chloride -.-> CHEBI_26710
    ing22_Sodium_bicarbonate["Sodium bicarbonate"]
    CultureMech_007349 --> ing22_Sodium_bicarbonate
    CHEBI_32139["CHEBI:32139"]
    ing22_Sodium_bicarbonate -.-> CHEBI_32139
    ing23_Boric_acid["Boric acid"]
    CultureMech_007349 --> ing23_Boric_acid
    CHEBI_33118["CHEBI:33118"]
    ing23_Boric_acid -.-> CHEBI_33118
    ing24_Nickel_chloride["Nickel chloride"]
    CultureMech_007349 --> ing24_Nickel_chloride
    CHEBI_34887["CHEBI:34887"]
    ing24_Nickel_chloride -.-> CHEBI_34887
    ing25_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_007349 --> ing25_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing25_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing26_Thiamine_HCl["Thiamine HCl"]
    CultureMech_007349 --> ing26_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing26_Thiamine_HCl -.-> CHEBI_49105
    ing27_Cupric_sulfate["Cupric sulfate"]
    CultureMech_007349 --> ing27_Cupric_sulfate
    CHEBI_23414["CHEBI:23414"]
    ing27_Cupric_sulfate -.-> CHEBI_23414
    ing28_Sodium_dihydrogen_phosphate_monohydrate["Sodium dihydrogen phosphate monohydrate"]
    CultureMech_007349 --> ing28_Sodium_dihydrogen_phosphate_monohydrate
    CHEBI_114249["CHEBI:114249"]
    ing28_Sodium_dihydrogen_phosphate_monohydrate -.-> CHEBI_114249

Ingredients (29)

# Ingredient Concentration Ontology Notes
1 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.687 MILLIMOLAR CHEBI:3312
calcium dichloride
2 Riboflavin
C17H20N4O6 376.369 g/mol
0.0001329 MILLIMOLAR CHEBI:17015
riboflavin
 Cross-references: KEGG:ribflv
3 Sodium acetate
C2H3O2.Na 82.034 g/mol
6.8 G_PER_L CHEBI:32954
sodium acetate
 Cross-references: KEGG:ac
4 Nicotinate
C6H5NO2 123.111 g/mol
0.0004061 MILLIMOLAR CHEBI:15940
nicotinic acid
 Cross-references: KEGG:nac
5 Vitamin B12 7.378e-07 MILLIMOLAR CHEBI:176843
vitamin B12
6 Folate
C19H19N7O6 441.404 g/mol
4.531e-05 MILLIMOLAR CHEBI:27470
folic acid
 Cross-references: KEGG:fol
7 Biotin
C10H16N2O3S 244.316 g/mol
8.186e-05 MILLIMOLAR CHEBI:15956
biotin
 Cross-references: KEGG:btn
8 Lipoate
C8H14O2S2 206.332 g/mol
0.0002423 MILLIMOLAR CHEBI:16494
lipoic acid
 Cross-references: KEGG:lipoate
9 4-Aminobenzoate
C7H6NO2 136.13 g/mol
0.0003646 MILLIMOLAR CHEBI:17836
4-aminobenzoate
 Cross-references: KEGG:4abz
10 Fe(III)dicitrate 50.0 MILLIMOLAR Cross-references: KEGG:fe3dcit
11 Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
0.0003873 MILLIMOLAR CHEBI:86463
potassium aluminium sulfate
12 Ammonium chloride
Cl.H4N 53.492 g/mol
1.5 G_PER_L CHEBI:31206
ammonium chloride
13 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.02673 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
14 Zinc sulfate
O4S.Zn 161.453 g/mol
0.006194 MILLIMOLAR CHEBI:35176
zinc sulfate
15 Ferrous sulfate
Fe.O4S 151.908 g/mol
0.003597 MILLIMOLAR CHEBI:75832
iron(2+) sulfate (anhydrous)
16 Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
0.0004863 MILLIMOLAR CHEBI:30961
pyridoxine hydrochloride
17 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.0001049 MILLIMOLAR CHEBI:31345
Calcium pantothenate
18 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.1217 MILLIMOLAR CHEBI:32599
magnesium sulfate
19 Cobalt chloride
2Cl.Co 129.839 g/mol
0.007702 MILLIMOLAR CHEBI:35696
cobalt dichloride
20 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.001627 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
21 Potassium chloride
Cl.K 74.551 g/mol
0.1 G_PER_L CHEBI:32588
potassium chloride
22 Sodium chloride
Cl.Na 58.443 g/mol
0.1711 MILLIMOLAR CHEBI:26710
sodium chloride
23 Sodium bicarbonate
CHO3.Na 84.006 g/mol
2.5 G_PER_L CHEBI:32139
sodium hydrogencarbonate
24 Boric acid
H3BO3 61.833 g/mol
0.001617 MILLIMOLAR CHEBI:33118
boric acid
25 Nickel chloride
Cl2Ni 129.599 g/mol
0.00101 MILLIMOLAR CHEBI:34887
nickel dichloride
26 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
0.07848 MILLIMOLAR CHEBI:44557
nitrilotriacetic acid
27 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0001482 MILLIMOLAR CHEBI:49105
thiamine hydrochloride
28 Cupric sulfate
Cu.O4S 159.609 g/mol
0.0004005 MILLIMOLAR CHEBI:23414
copper(II) sulfate
29 Sodium dihydrogen phosphate monohydrate
H2O.H2O4P.Na 137.991 g/mol
0.6 G_PER_L CHEBI:114249
sodium dihydrogenphosphate monohydrate

Preparation

  1. Dissolve all ingredients in distilled water to specified concentrations
  2. Adjust pH if specified in original formulation
  3. Sterilize the medium by autoclaving; the cited Methods does not specify a temperature or duration.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-27T07:21:46.719568Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 445, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:40.721934Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-06T05:10:52.737614Z invalid-chebi-removal Removed 1 invalid CHEBI ID(s) Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data
2026-03-13T06:19:48.143882Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007349
2026-03-17T06:30:52.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:06.471547+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
2026-06-05T07:40:29.035918+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 19 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:29.309997+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.
2026-06-09T01:42:16.138127+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.
2026-08-31T04:05:55.740550+00:00 repair_mediadb_names.py REPAIRED_MEDIADB_TRUNCATED_NAME Restored 1 ingredient name(s) truncated at a parenthesis by the MediaDB SQL parser. Resolved against MEDIADB:445's own compound list in media_database.07Oct2015.sql, requiring a unique prefix match and, where more than one matched, an equal Amount_mM.
2026-08-31T06:17:07.700685+00:00 repair_mediadb_names.py REPAIRED_MEDIADB_TRUNCATED_NAME Restored the medium's own name in media_term.term.label, original_name. The MediaDB SQL parser truncated every value containing a parenthesis at that parenthesis; recovered from media_database.07Oct2015.sql.
2026-10-09T22:13:19.143110+00:00 codex CURATED_GEOBACTER_PRIMARY_BASAL_INPUTS_AND_DONOR_EVIDENCE Only the stated basal inputs, routine acetate input, acetate salt identity, exact single-valued donor amounts and autoclaving are curated. The full formulations are not certified. The four acetate endpoint quantities remain unsupported. Calcium combines basal and possible trace-stock contributions; acceptor-dependent omissions require stage-specific reconstruction, not wholesale deletion. Trace/vitamin final doses, hydrate mismatches, cobalt-source variants, iron basis, citrate stoichiometry and database-selected range endpoints remain unresolved. No organism-growth assertions, new records, classifications or variant links are changed. Historical database names and evidence are retained as source provenance.