Overview
- External ontology
- MEDIADB:322 (source link unavailable) — Complete Chemically-defined Medium
- 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_007222["complete_chemically_defined_medium"]
ing0_Pyridoxamine_HCl["Pyridoxamine HCl"]
CultureMech_007222 --> ing0_Pyridoxamine_HCl
CHEBI_131531["CHEBI:131531"]
ing0_Pyridoxamine_HCl -.-> CHEBI_131531
ing1_Thiamine_HCl["Thiamine HCl"]
CultureMech_007222 --> ing1_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing1_Thiamine_HCl -.-> CHEBI_49105
ing2_Xanthine["Xanthine"]
CultureMech_007222 --> ing2_Xanthine
CHEBI_15318["CHEBI:15318"]
ing2_Xanthine -.-> CHEBI_15318
ing3_Vitamin_B12["Vitamin B12"]
CultureMech_007222 --> ing3_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing3_Vitamin_B12 -.-> CHEBI_176843
ing4_Biotin["Biotin"]
CultureMech_007222 --> ing4_Biotin
CHEBI_15956["CHEBI:15956"]
ing4_Biotin -.-> CHEBI_15956
ing5_Thymidine["Thymidine"]
CultureMech_007222 --> ing5_Thymidine
CHEBI_17748["CHEBI:17748"]
ing5_Thymidine -.-> CHEBI_17748
ing6_Lipoate["Lipoate"]
CultureMech_007222 --> ing6_Lipoate
CHEBI_16494["CHEBI:16494"]
ing6_Lipoate -.-> CHEBI_16494
ing7_Folate["Folate"]
CultureMech_007222 --> ing7_Folate
CHEBI_27470["CHEBI:27470"]
ing7_Folate -.-> CHEBI_27470
ing8_Adenine["Adenine"]
CultureMech_007222 --> ing8_Adenine
ing9_Inosine["Inosine"]
CultureMech_007222 --> ing9_Inosine
CHEBI_17596["CHEBI:17596"]
ing9_Inosine -.-> CHEBI_17596
ing10_Aspartate["Aspartate"]
CultureMech_007222 --> ing10_Aspartate
ing11_Glycine["Glycine"]
CultureMech_007222 --> ing11_Glycine
CHEBI_15428["CHEBI:15428"]
ing11_Glycine -.-> CHEBI_15428
ing12_DL_Tyrosine["DL-Tyrosine"]
CultureMech_007222 --> ing12_DL_Tyrosine
CHEBI_18186["CHEBI:18186"]
ing12_DL_Tyrosine -.-> CHEBI_18186
ing13_Nicotinate["Nicotinate"]
CultureMech_007222 --> ing13_Nicotinate
CHEBI_15940["CHEBI:15940"]
ing13_Nicotinate -.-> CHEBI_15940
ing14_Valine["Valine"]
CultureMech_007222 --> ing14_Valine
CHEBI_16414["CHEBI:16414"]
ing14_Valine -.-> CHEBI_16414
ing15_Leucine["Leucine"]
CultureMech_007222 --> ing15_Leucine
CHEBI_15603["CHEBI:15603"]
ing15_Leucine -.-> CHEBI_15603
ing16_Orotate["Orotate"]
CultureMech_007222 --> ing16_Orotate
ing17_Alanine["Alanine"]
CultureMech_007222 --> ing17_Alanine
CHEBI_16977["CHEBI:16977"]
ing17_Alanine -.-> CHEBI_16977
ing18_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_007222 --> ing18_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing18_Pyridoxine_HCl -.-> CHEBI_30961
ing19_Cysteine["Cysteine"]
CultureMech_007222 --> ing19_Cysteine
CHEBI_15356["CHEBI:15356"]
ing19_Cysteine -.-> CHEBI_15356
ing20_Tryptophan["Tryptophan"]
CultureMech_007222 --> ing20_Tryptophan
CHEBI_27897["CHEBI:27897"]
ing20_Tryptophan -.-> CHEBI_27897
ing21_Histidine["Histidine"]
CultureMech_007222 --> ing21_Histidine
CHEBI_27570["CHEBI:27570"]
ing21_Histidine -.-> CHEBI_27570
ing22_DL_methionine["DL-methionine"]
CultureMech_007222 --> ing22_DL_methionine
CHEBI_16811["CHEBI:16811"]
ing22_DL_methionine -.-> CHEBI_16811
ing23_Magnesium_chloride["Magnesium chloride"]
CultureMech_007222 --> ing23_Magnesium_chloride
CHEBI_86345["CHEBI:86345"]
ing23_Magnesium_chloride -.-> CHEBI_86345
ing24_Cobalt_chloride["Cobalt chloride"]
CultureMech_007222 --> ing24_Cobalt_chloride
CHEBI_35696["CHEBI:35696"]
ing24_Cobalt_chloride -.-> CHEBI_35696
ing25_Phenylalanine["Phenylalanine"]
CultureMech_007222 --> ing25_Phenylalanine
CHEBI_17295["CHEBI:17295"]
ing25_Phenylalanine -.-> CHEBI_17295
ing26_Sodium_acetate["Sodium acetate"]
CultureMech_007222 --> ing26_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing26_Sodium_acetate -.-> CHEBI_32954
ing27_Ferrous_chloride["Ferrous chloride"]
CultureMech_007222 --> ing27_Ferrous_chloride
CHEBI_30812["CHEBI:30812"]
ing27_Ferrous_chloride -.-> CHEBI_30812
ing28_Glutamine["Glutamine"]
CultureMech_007222 --> ing28_Glutamine
ing29_Lysine["Lysine"]
CultureMech_007222 --> ing29_Lysine
CultureMech_007222 --> more["...21 more"]
Ingredients (51)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Pyridoxamine HCl
C8H12N2O2.HCl 204.657 g/mol
|
0.02443 MILLIMOLAR |
CHEBI:131531
pyridoxamine hydrochloride
|
|
| 2 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.002965 MILLIMOLAR |
CHEBI:49105
thiamine hydrochloride
|
|
| 3 |
Xanthine
C5H4N4O2 152.111 g/mol
|
0.06574 MILLIMOLAR |
CHEBI:15318
xanthine
|
Cross-references: KEGG:xan |
| 4 | Vitamin B12 | 0.0007378 MILLIMOLAR |
CHEBI:176843
vitamin B12
|
|
| 5 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.04093 MILLIMOLAR |
CHEBI:15956
biotin
|
Cross-references: KEGG:btn |
| 6 |
Thymidine
C10H14N2O5 242.231 g/mol
|
0.0221 MILLIMOLAR |
CHEBI:17748
thymidine
|
Cross-references: KEGG:thymd |
| 7 |
Lipoate
C8H14O2S2 206.332 g/mol
|
0.01212 MILLIMOLAR |
CHEBI:16494
lipoic acid
|
Cross-references: KEGG:lipoate |
| 8 |
Folate
C19H19N7O6 441.404 g/mol
|
0.002266 MILLIMOLAR |
CHEBI:27470
folic acid
|
Cross-references: KEGG:fol |
| 9 | Adenine | 0.074 MILLIMOLAR | Cross-references: KEGG:ade | |
| 10 |
Inosine
C10H12N4O5 268.229 g/mol
|
0.01864 MILLIMOLAR |
CHEBI:17596
inosine
|
Cross-references: KEGG:ins |
| 11 | Aspartate | 3.456 MILLIMOLAR | ||
| 12 |
Glycine
C2H5NO2 75.067 g/mol
|
2.398 MILLIMOLAR |
CHEBI:15428
glycine
|
Cross-references: KEGG:gly |
| 13 |
DL-Tyrosine
C9H11NO3 181.191 g/mol
|
1.601 MILLIMOLAR |
CHEBI:18186
tyrosine
|
|
| 14 |
Nicotinate
C6H5NO2 123.111 g/mol
|
0.008123 MILLIMOLAR |
CHEBI:15940
nicotinic acid
|
Cross-references: KEGG:nac |
| 15 |
Valine
C5H11NO2 117.148 g/mol
|
2.817 MILLIMOLAR |
CHEBI:16414
L-valine
|
|
| 16 |
Leucine
C6H13NO2 131.175 g/mol
|
3.659 MILLIMOLAR |
CHEBI:15603
L-leucine
|
|
| 17 | Orotate | 0.03203 MILLIMOLAR | Cross-references: KEGG:orot | |
| 18 |
Alanine
C3H7NO2 89.094 g/mol
|
2.694 MILLIMOLAR |
CHEBI:16977
L-alanine
|
|
| 19 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
0.009725 MILLIMOLAR |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 20 |
Cysteine
C3H7NO2S 121.161 g/mol
|
2.063 MILLIMOLAR |
CHEBI:15356
cysteine
|
|
| 21 |
Tryptophan
C11H12N2O2 204.229 g/mol
|
0.2448 MILLIMOLAR |
CHEBI:27897
tryptophan
|
|
| 22 |
Histidine
C6H9N3O2 155.157 g/mol
|
0.9667 MILLIMOLAR |
CHEBI:27570
histidine
|
|
| 23 |
DL-methionine
C5H11NO2S 149.215 g/mol
|
0.8713 MILLIMOLAR |
CHEBI:16811
methionine
|
|
| 24 |
Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
|
0.9838 MILLIMOLAR |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 25 |
Cobalt chloride
2Cl.Co 129.839 g/mol
|
0.01051 MILLIMOLAR |
CHEBI:35696
cobalt dichloride
|
|
| 26 |
Phenylalanine
C9H11NO2 165.192 g/mol
|
1.695 MILLIMOLAR |
CHEBI:17295
L-phenylalanine
|
|
| 27 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
12.19 MILLIMOLAR |
CHEBI:32954
sodium acetate
|
|
| 28 |
Ferrous chloride
Cl2Fe 126.751 g/mol
|
0.2515 MILLIMOLAR |
CHEBI:30812
iron dichloride
|
|
| 29 | Glutamine | 2.668 MILLIMOLAR | ||
| 30 | Lysine | 3.01 MILLIMOLAR | ||
| 31 |
Proline
C5H9NO2 115.132 g/mol
|
5.906 MILLIMOLAR |
CHEBI:26271
proline
|
|
| 32 |
Arginine
C6H14N4O2 174.204 g/mol
|
0.7463 MILLIMOLAR |
CHEBI:29016
arginine
|
|
| 33 | Ammonium citrate | 28.69 MILLIMOLAR | ||
| 34 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.002099 MILLIMOLAR |
CHEBI:31345
Calcium pantothenate
|
|
| 35 |
Guanine
C5H5N5O 151.129 g/mol
|
0.06617 MILLIMOLAR |
CHEBI:16235
guanine
|
Cross-references: KEGG:gua |
| 36 |
4-Aminobenzoate
C7H6NO2 136.13 g/mol
|
0.07292 MILLIMOLAR |
CHEBI:17836
4-aminobenzoate
|
Cross-references: KEGG:4abz |
| 37 | Ascorbate | 2.839 MILLIMOLAR | Cross-references: KEGG:ascb-L | |
| 38 |
Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
|
14.31 MILLIMOLAR |
CHEBI:131527
dipotassium hydrogen phosphate
|
|
| 39 |
Lactose
C12H22O11 342.297 g/mol
|
29.21 MILLIMOLAR |
CHEBI:17716
lactose
|
Cross-references: KEGG:lcts |
| 40 |
Uracil
C4H4N2O2 112.088 g/mol
|
0.08921 MILLIMOLAR |
CHEBI:17568
uracil
|
Cross-references: KEGG:ura |
| 41 |
Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
|
22.04 MILLIMOLAR |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 42 |
L-Glutamate
C5H9NO4 147.13 g/mol
|
2.719 MILLIMOLAR |
CHEBI:16015
L-glutamic acid
|
Cross-references: KEGG:glu-L |
| 43 |
Isoleucine
C6H13NO2 131.175 g/mol
|
1.677 MILLIMOLAR |
CHEBI:17191
L-isoleucine
|
|
| 44 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.3401 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 45 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.002657 MILLIMOLAR |
CHEBI:17015
riboflavin
|
Cross-references: KEGG:ribflv |
| 46 |
Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
|
0.1657 MILLIMOLAR |
CHEBI:86364
manganese(II) sulfate monohydrate
|
|
| 47 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
0.0004005 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
|
| 48 | DL-Serine | 3.235 MILLIMOLAR | ||
| 49 |
Asparagine
C4H8N2O3 132.119 g/mol
|
2.649 MILLIMOLAR |
CHEBI:22653
asparagine
|
|
| 50 | Threonine | 1.931 MILLIMOLAR | ||
| 51 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.1739 MILLIMOLAR |
CHEBI:35176
zinc 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.
- complete_chemically_defined_medium (CultureMech:007222)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:45.531093Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 322, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:16.883359Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:24.179221Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:19:46.986362Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007222 |
| 2026-03-17T06:30:01.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:05.173689+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Complete Chemically-defined Medium" to "complete_chemically_defined_medium" for consistent matching |
| 2026-06-05T07:40:54.741156+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 23 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:36.439953+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 term reference(s) to the correct CHEBI (see reports/chebi_grounding_audit.md). Label-conditional fixes for pyridoxine/pyridoxamine, glycerol, MnSO4, Ca(NO3)2, selenate; casamino acids de-grounded (mixture, no single CHEBI). |
| 2026-08-06T03:05:29.061519+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint d7a4436a65521a7dcbbeb3dacaf146af728c0189310e480bf4eb3926727296b9 |