defined_freshwater_medium_cocl2

CultureMech:007294 bacterial DEFINED LIQUID
Original name: Defined freshwater medium (CoCl2) + Electron Donors/Acceptors

Overview

External ontology
MEDIADB:390 (source link unavailable) — Defined freshwater medium (CoCl2) + Electron Donors/Acceptors
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_007294["defined_freshwater_medium_cocl2"]
    ing0_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007294 --> ing0_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing0_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing1_Boric_acid["Boric acid"]
    CultureMech_007294 --> ing1_Boric_acid
    CHEBI_33118["CHEBI:33118"]
    ing1_Boric_acid -.-> CHEBI_33118
    ing2_4_Aminobenzoate["4-Aminobenzoate"]
    CultureMech_007294 --> ing2_4_Aminobenzoate
    CHEBI_17836["CHEBI:17836"]
    ing2_4_Aminobenzoate -.-> CHEBI_17836
    ing3_Vitamin_B12["Vitamin B12"]
    CultureMech_007294 --> ing3_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing3_Vitamin_B12 -.-> CHEBI_176843
    ing4_Fe_III_dicitrate["Fe(III)dicitrate"]
    CultureMech_007294 --> ing4_Fe_III_dicitrate
    ing5_Lipoate["Lipoate"]
    CultureMech_007294 --> ing5_Lipoate
    CHEBI_16494["CHEBI:16494"]
    ing5_Lipoate -.-> CHEBI_16494
    ing6_Folate["Folate"]
    CultureMech_007294 --> ing6_Folate
    CHEBI_27470["CHEBI:27470"]
    ing6_Folate -.-> CHEBI_27470
    ing7_Riboflavin["Riboflavin"]
    CultureMech_007294 --> ing7_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing7_Riboflavin -.-> CHEBI_17015
    ing8_Glucose["Glucose"]
    CultureMech_007294 --> ing8_Glucose
    CHEBI_17234["CHEBI:17234"]
    ing8_Glucose -.-> CHEBI_17234
    ing9_Aluminum_potassium_sulfate["Aluminum potassium sulfate"]
    CultureMech_007294 --> ing9_Aluminum_potassium_sulfate
    CHEBI_86463["CHEBI:86463"]
    ing9_Aluminum_potassium_sulfate -.-> CHEBI_86463
    ing10_Ferrous_sulfate["Ferrous sulfate"]
    CultureMech_007294 --> ing10_Ferrous_sulfate
    CHEBI_75832["CHEBI:75832"]
    ing10_Ferrous_sulfate -.-> CHEBI_75832
    ing11_Ferric_nitrilotriacetate["Ferric nitrilotriacetate"]
    CultureMech_007294 --> ing11_Ferric_nitrilotriacetate
    ing12_Cupric_sulfate["Cupric sulfate"]
    CultureMech_007294 --> ing12_Cupric_sulfate
    CHEBI_23414["CHEBI:23414"]
    ing12_Cupric_sulfate -.-> CHEBI_23414
    ing13_Zinc_sulfate["Zinc sulfate"]
    CultureMech_007294 --> ing13_Zinc_sulfate
    CHEBI_35176["CHEBI:35176"]
    ing13_Zinc_sulfate -.-> CHEBI_35176
    ing14_Cobalt_chloride["Cobalt chloride"]
    CultureMech_007294 --> ing14_Cobalt_chloride
    CHEBI_35696["CHEBI:35696"]
    ing14_Cobalt_chloride -.-> CHEBI_35696
    ing15_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007294 --> ing15_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing15_Manganese_sulfate -.-> CHEBI_86364
    ing16_Sodium_dihydrogen_phosphate["Sodium dihydrogen phosphate"]
    CultureMech_007294 --> ing16_Sodium_dihydrogen_phosphate
    CHEBI_37585["CHEBI:37585"]
    ing16_Sodium_dihydrogen_phosphate -.-> CHEBI_37585
    ing17_Biotin["Biotin"]
    CultureMech_007294 --> ing17_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing17_Biotin -.-> CHEBI_15956
    ing18_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_007294 --> ing18_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing18_Calcium_pantothenate -.-> CHEBI_31345
    ing19_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_007294 --> ing19_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing19_Pyridoxine_HCl -.-> CHEBI_30961
    ing20_Lactate["Lactate"]
    CultureMech_007294 --> ing20_Lactate
    CHEBI_24996["CHEBI:24996"]
    ing20_Lactate -.-> CHEBI_24996
    ing21_Ammonium_chloride["Ammonium chloride"]
    CultureMech_007294 --> ing21_Ammonium_chloride
    CHEBI_31206["CHEBI:31206"]
    ing21_Ammonium_chloride -.-> CHEBI_31206
    ing22_Thiamine_HCl["Thiamine HCl"]
    CultureMech_007294 --> ing22_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing22_Thiamine_HCl -.-> CHEBI_49105
    ing23_Sodium_bicarbonate["Sodium bicarbonate"]
    CultureMech_007294 --> ing23_Sodium_bicarbonate
    CHEBI_32139["CHEBI:32139"]
    ing23_Sodium_bicarbonate -.-> CHEBI_32139
    ing24_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_007294 --> ing24_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing24_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing25_Nickel_chloride["Nickel chloride"]
    CultureMech_007294 --> ing25_Nickel_chloride
    CHEBI_34887["CHEBI:34887"]
    ing25_Nickel_chloride -.-> CHEBI_34887
    ing26_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007294 --> ing26_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing26_Sodium_molybdate -.-> CHEBI_75215
    ing27_Sodium_chloride["Sodium chloride"]
    CultureMech_007294 --> ing27_Sodium_chloride
    CHEBI_26710["CHEBI:26710"]
    ing27_Sodium_chloride -.-> CHEBI_26710
    ing28_Potassium_chloride["Potassium chloride"]
    CultureMech_007294 --> ing28_Potassium_chloride
    CHEBI_32588["CHEBI:32588"]
    ing28_Potassium_chloride -.-> CHEBI_32588
    ing29_Cellobiose["Cellobiose"]
    CultureMech_007294 --> ing29_Cellobiose
    CHEBI_17057["CHEBI:17057"]
    ing29_Cellobiose -.-> CHEBI_17057
    CultureMech_007294 --> more["...9 more"]

Ingredients (39)

# Ingredient Concentration Ontology Notes
1 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.687 MILLIMOLAR CHEBI:3312
calcium dichloride
2 Boric acid
H3BO3 61.833 g/mol
0.001617 MILLIMOLAR CHEBI:33118
boric acid
3 4-Aminobenzoate
C7H6NO2 136.13 g/mol
0.0003646 MILLIMOLAR CHEBI:17836
4-aminobenzoate
 Cross-references: KEGG:4abz
4 Vitamin B12 7.378e-07 MILLIMOLAR CHEBI:176843
vitamin B12
5 Fe(III)dicitrate 56.0 MILLIMOLAR Cross-references: KEGG:fe3dcit
6 Lipoate
C8H14O2S2 206.332 g/mol
0.0002423 MILLIMOLAR CHEBI:16494
lipoic acid
 Cross-references: KEGG:lipoate
7 Folate
C19H19N7O6 441.404 g/mol
4.531e-05 MILLIMOLAR CHEBI:27470
folic acid
 Cross-references: KEGG:fol
8 Riboflavin
C17H20N4O6 376.369 g/mol
0.0001329 MILLIMOLAR CHEBI:17015
riboflavin
 Cross-references: KEGG:ribflv
9 Glucose
C6H12O6 180.156 g/mol
5.551 MILLIMOLAR CHEBI:17234
glucose
10 Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
0.0003873 MILLIMOLAR CHEBI:86463
potassium aluminium sulfate
11 Ferrous sulfate
Fe.O4S 151.908 g/mol
0.003597 MILLIMOLAR CHEBI:75832
iron(2+) sulfate (anhydrous)
12 Ferric nitrilotriacetate 5.0 MILLIMOLAR
13 Cupric sulfate
Cu.O4S 159.609 g/mol
0.0004005 MILLIMOLAR CHEBI:23414
copper(II) sulfate
14 Zinc sulfate
O4S.Zn 161.453 g/mol
0.006194 MILLIMOLAR CHEBI:35176
zinc sulfate
15 Cobalt chloride
2Cl.Co 129.839 g/mol
0.007702 MILLIMOLAR CHEBI:35696
cobalt dichloride
16 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.02673 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
17 Sodium dihydrogen phosphate
H2O4P.Na 119.976 g/mol
4.348 MILLIMOLAR CHEBI:37585
sodium dihydrogenphosphate
18 Biotin
C10H16N2O3S 244.316 g/mol
8.186e-05 MILLIMOLAR CHEBI:15956
biotin
 Cross-references: KEGG:btn
19 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.0001049 MILLIMOLAR CHEBI:31345
Calcium pantothenate
20 Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
0.0004863 MILLIMOLAR CHEBI:30961
pyridoxine hydrochloride
21 Lactate
C3H5O3 89.07 g/mol
11.1 MILLIMOLAR CHEBI:24996
lactate
22 Ammonium chloride
Cl.H4N 53.492 g/mol
28.04 MILLIMOLAR CHEBI:31206
ammonium chloride
23 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0001482 MILLIMOLAR CHEBI:49105
thiamine hydrochloride
24 Sodium bicarbonate
CHO3.Na 84.006 g/mol
29.76 MILLIMOLAR CHEBI:32139
sodium hydrogencarbonate
25 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
0.07848 MILLIMOLAR CHEBI:44557
nitrilotriacetic acid
26 Nickel chloride
Cl2Ni 129.599 g/mol
0.00101 MILLIMOLAR CHEBI:34887
nickel dichloride
27 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.00162722 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
28 Sodium chloride
Cl.Na 58.443 g/mol
0.1711 MILLIMOLAR CHEBI:26710
sodium chloride
29 Potassium chloride
Cl.K 74.551 g/mol
1.341 MILLIMOLAR CHEBI:32588
potassium chloride
30 Cellobiose
C12H22O11 342.297 g/mol
2.921 MILLIMOLAR CHEBI:17057
cellobiose
31 Citrate
C6H5O7 189.099 g/mol
10.0 MILLIMOLAR CHEBI:16947
citrate(3-)
 Cross-references: KEGG:cit
32 D-Mannose
C6H12O6 180.156 g/mol
5.551 MILLIMOLAR CHEBI:16024
D-mannose
 Cross-references: KEGG:man
33 Nitrate
NO3 62.004 g/mol
20.0 MILLIMOLAR CHEBI:17632
nitrate
 Cross-references: KEGG:no3
34 Fumarate
C4H2O4 114.056 g/mol
30.0 MILLIMOLAR CHEBI:29806
fumarate(2-)
 Cross-references: KEGG:fum
35 Acetate
C2H3O2 59.044 g/mol
10.0 MILLIMOLAR CHEBI:30089
acetate
 Cross-references: KEGG:ac
36 Sucrose
C12H22O11 342.297 g/mol
2.921 MILLIMOLAR CHEBI:17992
sucrose
 Cross-references: KEGG:sucr
37 Glycolate
C2H3O3 75.043 g/mol
10.0 MILLIMOLAR CHEBI:29805
glycolate
 Cross-references: KEGG:glyclt
38 Nicotinate
C6H5NO2 123.111 g/mol
0.0004061 MILLIMOLAR CHEBI:15940
nicotinic acid
 Cross-references: KEGG:nac
39 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.1217 MILLIMOLAR CHEBI:32599
magnesium 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

TimestampCuratorActionNotes
2026-01-27T07:21:46.154785Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 390, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:16.250532Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-06T05:10:23.423381Z invalid-chebi-removal Removed 1 invalid CHEBI ID(s) Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data
2026-03-13T06:19:47.492651Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007294
2026-03-17T06:29:59.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:05.727038+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
2026-06-05T07:40:55.499900+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 24 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:36.524051+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.
2026-06-09T01:42:18.568061+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.
2026-08-20T19:01:38.779752+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 3 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-08-31T04:06:13.196655+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:390's own compound list in media_database.07Oct2015.sql, requiring a unique prefix match and, where more than one matched, an equal Amount_mM.
2026-08-31T06:17:25.136498+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.