defined_freshwater_medium_coso4

CultureMech:007293 bacterial DEFINED LIQUID
Original name: Defined freshwater medium (CoSO4) + Electron Donors/Acceptors

Overview

External ontology
MEDIADB:389 (source link unavailable) — Defined freshwater medium (CoSO4) + 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_007293["defined_freshwater_medium_coso4"]
    ing0_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_007293 --> ing0_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing0_Pyridoxine_HCl -.-> CHEBI_30961
    ing1_4_Aminobenzoate["4-Aminobenzoate"]
    CultureMech_007293 --> ing1_4_Aminobenzoate
    CHEBI_17836["CHEBI:17836"]
    ing1_4_Aminobenzoate -.-> CHEBI_17836
    ing2_D_Mannose["D-Mannose"]
    CultureMech_007293 --> ing2_D_Mannose
    CHEBI_16024["CHEBI:16024"]
    ing2_D_Mannose -.-> CHEBI_16024
    ing3_Fe_III_dicitrate["Fe(III)dicitrate"]
    CultureMech_007293 --> ing3_Fe_III_dicitrate
    ing4_Folate["Folate"]
    CultureMech_007293 --> ing4_Folate
    CHEBI_27470["CHEBI:27470"]
    ing4_Folate -.-> CHEBI_27470
    ing5_Fumarate["Fumarate"]
    CultureMech_007293 --> ing5_Fumarate
    CHEBI_29806["CHEBI:29806"]
    ing5_Fumarate -.-> CHEBI_29806
    ing6_Sucrose["Sucrose"]
    CultureMech_007293 --> ing6_Sucrose
    CHEBI_17992["CHEBI:17992"]
    ing6_Sucrose -.-> CHEBI_17992
    ing7_Nitrate["Nitrate"]
    CultureMech_007293 --> ing7_Nitrate
    CHEBI_17632["CHEBI:17632"]
    ing7_Nitrate -.-> CHEBI_17632
    ing8_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007293 --> ing8_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing8_Magnesium_sulfate -.-> CHEBI_32599
    ing9_Ferric_nitrilotriacetate["Ferric nitrilotriacetate"]
    CultureMech_007293 --> ing9_Ferric_nitrilotriacetate
    ing10_Glycolate["Glycolate"]
    CultureMech_007293 --> ing10_Glycolate
    CHEBI_29805["CHEBI:29805"]
    ing10_Glycolate -.-> CHEBI_29805
    ing11_Lactate["Lactate"]
    CultureMech_007293 --> ing11_Lactate
    CHEBI_24996["CHEBI:24996"]
    ing11_Lactate -.-> CHEBI_24996
    ing12_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_007293 --> ing12_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing12_Calcium_pantothenate -.-> CHEBI_31345
    ing13_Vitamin_B12["Vitamin B12"]
    CultureMech_007293 --> ing13_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing13_Vitamin_B12 -.-> CHEBI_176843
    ing14_Nicotinate["Nicotinate"]
    CultureMech_007293 --> ing14_Nicotinate
    CHEBI_15940["CHEBI:15940"]
    ing14_Nicotinate -.-> CHEBI_15940
    ing15_Acetate["Acetate"]
    CultureMech_007293 --> ing15_Acetate
    CHEBI_30089["CHEBI:30089"]
    ing15_Acetate -.-> CHEBI_30089
    ing16_Citrate["Citrate"]
    CultureMech_007293 --> ing16_Citrate
    CHEBI_16947["CHEBI:16947"]
    ing16_Citrate -.-> CHEBI_16947
    ing17_Cellobiose["Cellobiose"]
    CultureMech_007293 --> ing17_Cellobiose
    CHEBI_17057["CHEBI:17057"]
    ing17_Cellobiose -.-> CHEBI_17057
    ing18_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007293 --> ing18_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing18_Sodium_molybdate -.-> CHEBI_75215
    ing19_Nickel_chloride["Nickel chloride"]
    CultureMech_007293 --> ing19_Nickel_chloride
    CHEBI_34887["CHEBI:34887"]
    ing19_Nickel_chloride -.-> CHEBI_34887
    ing20_Glucose["Glucose"]
    CultureMech_007293 --> ing20_Glucose
    CHEBI_17234["CHEBI:17234"]
    ing20_Glucose -.-> CHEBI_17234
    ing21_Riboflavin["Riboflavin"]
    CultureMech_007293 --> ing21_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing21_Riboflavin -.-> CHEBI_17015
    ing22_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_007293 --> ing22_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing22_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing23_Lipoate["Lipoate"]
    CultureMech_007293 --> ing23_Lipoate
    CHEBI_16494["CHEBI:16494"]
    ing23_Lipoate -.-> CHEBI_16494
    ing24_Sodium_chloride["Sodium chloride"]
    CultureMech_007293 --> ing24_Sodium_chloride
    CHEBI_26710["CHEBI:26710"]
    ing24_Sodium_chloride -.-> CHEBI_26710
    ing25_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007293 --> ing25_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing25_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing26_Potassium_chloride["Potassium chloride"]
    CultureMech_007293 --> ing26_Potassium_chloride
    CHEBI_32588["CHEBI:32588"]
    ing26_Potassium_chloride -.-> CHEBI_32588
    ing27_Ammonium_chloride["Ammonium chloride"]
    CultureMech_007293 --> ing27_Ammonium_chloride
    CHEBI_31206["CHEBI:31206"]
    ing27_Ammonium_chloride -.-> CHEBI_31206
    ing28_Sodium_dihydrogen_phosphate["Sodium dihydrogen phosphate"]
    CultureMech_007293 --> ing28_Sodium_dihydrogen_phosphate
    CHEBI_37585["CHEBI:37585"]
    ing28_Sodium_dihydrogen_phosphate -.-> CHEBI_37585
    ing29_Zinc_sulfate["Zinc sulfate"]
    CultureMech_007293 --> ing29_Zinc_sulfate
    CHEBI_35176["CHEBI:35176"]
    ing29_Zinc_sulfate -.-> CHEBI_35176
    CultureMech_007293 --> more["...9 more"]

Ingredients (39)

# Ingredient Concentration Ontology Notes
1 Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
0.0004863 MILLIMOLAR CHEBI:30961
pyridoxine hydrochloride
2 4-Aminobenzoate
C7H6NO2 136.13 g/mol
0.0003646 MILLIMOLAR CHEBI:17836
4-aminobenzoate
 Cross-references: KEGG:4abz
3 D-Mannose
C6H12O6 180.156 g/mol
5.551 MILLIMOLAR CHEBI:16024
D-mannose
 Cross-references: KEGG:man
4 Fe(III)dicitrate 56.0 MILLIMOLAR Cross-references: KEGG:fe3dcit
5 Folate
C19H19N7O6 441.404 g/mol
4.531e-05 MILLIMOLAR CHEBI:27470
folic acid
 Cross-references: KEGG:fol
6 Fumarate
C4H2O4 114.056 g/mol
30.0 MILLIMOLAR CHEBI:29806
fumarate(2-)
 Cross-references: KEGG:fum
7 Sucrose
C12H22O11 342.297 g/mol
2.921 MILLIMOLAR CHEBI:17992
sucrose
 Cross-references: KEGG:sucr
8 Nitrate
NO3 62.004 g/mol
20.0 MILLIMOLAR CHEBI:17632
nitrate
 Cross-references: KEGG:no3
9 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.1217 MILLIMOLAR CHEBI:32599
magnesium sulfate
10 Ferric nitrilotriacetate 5.0 MILLIMOLAR
11 Glycolate
C2H3O3 75.043 g/mol
10.0 MILLIMOLAR CHEBI:29805
glycolate
 Cross-references: KEGG:glyclt
12 Lactate
C3H5O3 89.07 g/mol
11.1 MILLIMOLAR CHEBI:24996
lactate
13 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.0001049 MILLIMOLAR CHEBI:31345
Calcium pantothenate
14 Vitamin B12 7.378e-07 MILLIMOLAR CHEBI:176843
vitamin B12
15 Nicotinate
C6H5NO2 123.111 g/mol
0.0004061 MILLIMOLAR CHEBI:15940
nicotinic acid
 Cross-references: KEGG:nac
16 Acetate
C2H3O2 59.044 g/mol
10.0 MILLIMOLAR CHEBI:30089
acetate
 Cross-references: KEGG:ac
17 Citrate
C6H5O7 189.099 g/mol
10.0 MILLIMOLAR CHEBI:16947
citrate(3-)
 Cross-references: KEGG:cit
18 Cellobiose
C12H22O11 342.297 g/mol
2.921 MILLIMOLAR CHEBI:17057
cellobiose
19 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.00162722 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
20 Nickel chloride
Cl2Ni 129.599 g/mol
0.00101 MILLIMOLAR CHEBI:34887
nickel dichloride
21 Glucose
C6H12O6 180.156 g/mol
5.551 MILLIMOLAR CHEBI:17234
glucose
22 Riboflavin
C17H20N4O6 376.369 g/mol
0.0001329 MILLIMOLAR CHEBI:17015
riboflavin
 Cross-references: KEGG:ribflv
23 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
0.07848 MILLIMOLAR CHEBI:44557
nitrilotriacetic acid
24 Lipoate
C8H14O2S2 206.332 g/mol
0.0002423 MILLIMOLAR CHEBI:16494
lipoic acid
 Cross-references: KEGG:lipoate
25 Sodium chloride
Cl.Na 58.443 g/mol
0.1711 MILLIMOLAR CHEBI:26710
sodium chloride
26 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.687 MILLIMOLAR CHEBI:3312
calcium dichloride
27 Potassium chloride
Cl.K 74.551 g/mol
1.341 MILLIMOLAR CHEBI:32588
potassium chloride
28 Ammonium chloride
Cl.H4N 53.492 g/mol
28.04 MILLIMOLAR CHEBI:31206
ammonium chloride
29 Sodium dihydrogen phosphate
H2O4P.Na 119.976 g/mol
4.348 MILLIMOLAR CHEBI:37585
sodium dihydrogenphosphate
30 Zinc sulfate
O4S.Zn 161.453 g/mol
0.006194 MILLIMOLAR CHEBI:35176
zinc sulfate
31 Boric acid
H3BO3 61.833 g/mol
0.001617 MILLIMOLAR CHEBI:33118
boric acid
32 Ferrous sulfate
Fe.O4S 151.908 g/mol
0.003597 MILLIMOLAR CHEBI:75832
iron(2+) sulfate (anhydrous)
33 Cobaltous sulfate
Co.O4S 154.996 g/mol
0.006494 MILLIMOLAR CHEBI:53470
cobalt(2+) sulfate
34 Cupric sulfate
Cu.O4S 159.609 g/mol
0.0004005 MILLIMOLAR CHEBI:23414
copper(II) sulfate
35 Biotin
C10H16N2O3S 244.316 g/mol
8.186e-05 MILLIMOLAR CHEBI:15956
biotin
 Cross-references: KEGG:btn
36 Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
0.0003873 MILLIMOLAR CHEBI:86463
potassium aluminium sulfate
37 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.02673 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
38 Sodium bicarbonate
CHO3.Na 84.006 g/mol
29.76 MILLIMOLAR CHEBI:32139
sodium hydrogencarbonate
39 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0001482 MILLIMOLAR CHEBI:49105
thiamine hydrochloride

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
2026-01-27T07:21:46.143405Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 389, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:25.619661Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-06T05:10:34.444556Z invalid-chebi-removal Removed 1 invalid CHEBI ID(s) Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data
2026-03-13T06:19:47.476696Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007293
2026-03-17T06:30:19.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:05.707342+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "'Defined freshwater medium (CoSO4" to "defined_freshwater_medium_coso4" for consistent matching
2026-06-05T07:40:55.520371+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.
2026-06-08T23:19:36.543806+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.
2026-06-09T01:42:18.587818+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.
2026-08-20T19:01:38.800040+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).
2026-08-31T04:06:13.219304+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:389's own compound list in media_database.07Oct2015.sql, requiring a unique prefix match and, where more than one matched, an equal Amount_mM.
2026-08-31T06:17:25.158277+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.