Overview
- External ontology
- MEDIADB:407 (source link unavailable) — MCD 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_007307["mcd_medium"]
ing0_Glycine["Glycine"]
CultureMech_007307 --> ing0_Glycine
CHEBI_15428["CHEBI:15428"]
ing0_Glycine -.-> CHEBI_15428
ing1_Glutamine["Glutamine"]
CultureMech_007307 --> ing1_Glutamine
ing2_Cysteine["Cysteine"]
CultureMech_007307 --> ing2_Cysteine
CHEBI_15356["CHEBI:15356"]
ing2_Cysteine -.-> CHEBI_15356
ing3_Asparagine["Asparagine"]
CultureMech_007307 --> ing3_Asparagine
CHEBI_22653["CHEBI:22653"]
ing3_Asparagine -.-> CHEBI_22653
ing4_Lysine_HCl["Lysine-HCl"]
CultureMech_007307 --> ing4_Lysine_HCl
ing5_Leucine["Leucine"]
CultureMech_007307 --> ing5_Leucine
CHEBI_15603["CHEBI:15603"]
ing5_Leucine -.-> CHEBI_15603
ing6_Isoleucine["Isoleucine"]
CultureMech_007307 --> ing6_Isoleucine
CHEBI_17191["CHEBI:17191"]
ing6_Isoleucine -.-> CHEBI_17191
ing7_Histidine["Histidine"]
CultureMech_007307 --> ing7_Histidine
CHEBI_27570["CHEBI:27570"]
ing7_Histidine -.-> CHEBI_27570
ing8_Arginine["Arginine"]
CultureMech_007307 --> ing8_Arginine
CHEBI_29016["CHEBI:29016"]
ing8_Arginine -.-> CHEBI_29016
ing9_Alanine["Alanine"]
CultureMech_007307 --> ing9_Alanine
CHEBI_16977["CHEBI:16977"]
ing9_Alanine -.-> CHEBI_16977
ing10_Sodium_acetate["Sodium acetate"]
CultureMech_007307 --> ing10_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing10_Sodium_acetate -.-> CHEBI_32954
ing11_Ammonium_citrate["Ammonium citrate"]
CultureMech_007307 --> ing11_Ammonium_citrate
ing12_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
CultureMech_007307 --> ing12_Potassium_dihydrogen_phosphate
CHEBI_63036["CHEBI:63036"]
ing12_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
ing13_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
CultureMech_007307 --> ing13_Potassium_dibasic_phosphate
CHEBI_131527["CHEBI:131527"]
ing13_Potassium_dibasic_phosphate -.-> CHEBI_131527
ing14_Adenine["Adenine"]
CultureMech_007307 --> ing14_Adenine
CHEBI_16708["CHEBI:16708"]
ing14_Adenine -.-> CHEBI_16708
ing15_Guanine["Guanine"]
CultureMech_007307 --> ing15_Guanine
CHEBI_16235["CHEBI:16235"]
ing15_Guanine -.-> CHEBI_16235
ing16_Uracil["Uracil"]
CultureMech_007307 --> ing16_Uracil
CHEBI_17568["CHEBI:17568"]
ing16_Uracil -.-> CHEBI_17568
ing17_Vitamin_B12["Vitamin B12"]
CultureMech_007307 --> ing17_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing17_Vitamin_B12 -.-> CHEBI_176843
ing18_Xanthine["Xanthine"]
CultureMech_007307 --> ing18_Xanthine
CHEBI_15318["CHEBI:15318"]
ing18_Xanthine -.-> CHEBI_15318
ing19_4_Aminobenzoate["4-Aminobenzoate"]
CultureMech_007307 --> ing19_4_Aminobenzoate
CHEBI_17836["CHEBI:17836"]
ing19_4_Aminobenzoate -.-> CHEBI_17836
ing20_Pyridoxamine["Pyridoxamine"]
CultureMech_007307 --> ing20_Pyridoxamine
CHEBI_16410["CHEBI:16410"]
ing20_Pyridoxamine -.-> CHEBI_16410
ing21_Folate["Folate"]
CultureMech_007307 --> ing21_Folate
CHEBI_27470["CHEBI:27470"]
ing21_Folate -.-> CHEBI_27470
ing22_Biotin["Biotin"]
CultureMech_007307 --> ing22_Biotin
CHEBI_15956["CHEBI:15956"]
ing22_Biotin -.-> CHEBI_15956
ing23_Thymidine["Thymidine"]
CultureMech_007307 --> ing23_Thymidine
CHEBI_17748["CHEBI:17748"]
ing23_Thymidine -.-> CHEBI_17748
ing24_Orotate["Orotate"]
CultureMech_007307 --> ing24_Orotate
ing25_Lipoate["Lipoate"]
CultureMech_007307 --> ing25_Lipoate
CHEBI_16494["CHEBI:16494"]
ing25_Lipoate -.-> CHEBI_16494
ing26_Inosine["Inosine"]
CultureMech_007307 --> ing26_Inosine
CHEBI_17596["CHEBI:17596"]
ing26_Inosine -.-> CHEBI_17596
ing27_Valine["Valine"]
CultureMech_007307 --> ing27_Valine
CHEBI_16414["CHEBI:16414"]
ing27_Valine -.-> CHEBI_16414
ing28_DL_Tyrosine["DL-Tyrosine"]
CultureMech_007307 --> ing28_DL_Tyrosine
CHEBI_18186["CHEBI:18186"]
ing28_DL_Tyrosine -.-> CHEBI_18186
ing29_Glucose["Glucose"]
CultureMech_007307 --> ing29_Glucose
CHEBI_17234["CHEBI:17234"]
ing29_Glucose -.-> CHEBI_17234
CultureMech_007307 --> more["...16 more"]
Ingredients (46)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Glycine
C2H5NO2 75.067 g/mol
|
2.265 MILLIMOLAR |
CHEBI:15428
glycine
|
Cross-references: KEGG:gly |
| 2 | Glutamine | 3.49 MILLIMOLAR | ||
| 3 |
Cysteine
C3H7NO2S 121.161 g/mol
|
1.403 MILLIMOLAR |
CHEBI:15356
cysteine
|
|
| 4 |
Asparagine
C4H8N2O3 132.119 g/mol
|
2.573 MILLIMOLAR |
CHEBI:22653
asparagine
|
|
| 5 | Lysine-HCl | 1.916 MILLIMOLAR | ||
| 6 |
Leucine
C6H13NO2 131.175 g/mol
|
3.583 MILLIMOLAR |
CHEBI:15603
L-leucine
|
|
| 7 |
Isoleucine
C6H13NO2 131.175 g/mol
|
1.525 MILLIMOLAR |
CHEBI:17191
L-isoleucine
|
|
| 8 |
Histidine
C6H9N3O2 155.157 g/mol
|
0.7089 MILLIMOLAR |
CHEBI:27570
histidine
|
|
| 9 |
Arginine
C6H14N4O2 174.204 g/mol
|
0.6889 MILLIMOLAR |
CHEBI:29016
arginine
|
|
| 10 |
Alanine
C3H7NO2 89.094 g/mol
|
2.694 MILLIMOLAR |
CHEBI:16977
L-alanine
|
|
| 11 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
12.19 MILLIMOLAR |
CHEBI:32954
sodium acetate
|
|
| 12 | Ammonium citrate | 2.467 MILLIMOLAR | ||
| 13 |
Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
|
66.13 MILLIMOLAR |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 14 |
Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
|
42.92 MILLIMOLAR |
CHEBI:131527
dipotassium hydrogen phosphate
|
|
| 15 |
Adenine
C5H5N5 135.13 g/mol
|
0.037 MILLIMOLAR |
CHEBI:16708
adenine
|
Cross-references: KEGG:ade |
| 16 |
Guanine
C5H5N5O 151.129 g/mol
|
0.006617 MILLIMOLAR |
CHEBI:16235
guanine
|
Cross-references: KEGG:gua |
| 17 |
Uracil
C4H4N2O2 112.088 g/mol
|
0.04461 MILLIMOLAR |
CHEBI:17568
uracil
|
Cross-references: KEGG:ura |
| 18 | Vitamin B12 | 0.0007378 MILLIMOLAR |
CHEBI:176843
vitamin B12
|
|
| 19 |
Xanthine
C5H4N4O2 152.111 g/mol
|
0.03287 MILLIMOLAR |
CHEBI:15318
xanthine
|
Cross-references: KEGG:xan |
| 20 |
4-Aminobenzoate
C7H6NO2 136.13 g/mol
|
0.07292 MILLIMOLAR |
CHEBI:17836
4-aminobenzoate
|
Cross-references: KEGG:4abz |
| 21 |
Pyridoxamine
C8H12N2O2 168.196 g/mol
|
0.02973 MILLIMOLAR |
CHEBI:16410
pyridoxamine
|
Cross-references: KEGG:pydam |
| 22 |
Folate
C19H19N7O6 441.404 g/mol
|
0.002266 MILLIMOLAR |
CHEBI:27470
folic acid
|
Cross-references: KEGG:fol |
| 23 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.04093 MILLIMOLAR |
CHEBI:15956
biotin
|
Cross-references: KEGG:btn |
| 24 |
Thymidine
C10H14N2O5 242.231 g/mol
|
0.0221 MILLIMOLAR |
CHEBI:17748
thymidine
|
Cross-references: KEGG:thymd |
| 25 | Orotate | 0.03203 MILLIMOLAR | Cross-references: KEGG:orot | |
| 26 |
Lipoate
C8H14O2S2 206.332 g/mol
|
0.01212 MILLIMOLAR |
CHEBI:16494
lipoic acid
|
Cross-references: KEGG:lipoate |
| 27 |
Inosine
C10H12N4O5 268.229 g/mol
|
0.01864 MILLIMOLAR |
CHEBI:17596
inosine
|
Cross-references: KEGG:ins |
| 28 |
Valine
C5H11NO2 117.148 g/mol
|
2.817 MILLIMOLAR |
CHEBI:16414
L-valine
|
|
| 29 |
DL-Tyrosine
C9H11NO3 181.191 g/mol
|
1.601 MILLIMOLAR |
CHEBI:18186
tyrosine
|
|
| 30 |
Glucose
C6H12O6 180.156 g/mol
|
55.51 MILLIMOLAR |
CHEBI:17234
glucose
|
|
| 31 | DL-Serine | 3.235 MILLIMOLAR | ||
| 32 |
Proline
C5H9NO2 115.132 g/mol
|
5.906 MILLIMOLAR |
CHEBI:26271
proline
|
|
| 33 |
Tryptophan
C11H12N2O2 204.229 g/mol
|
0.2448 MILLIMOLAR |
CHEBI:27897
tryptophan
|
|
| 34 |
Threonine
C4H9NO3 119.119 g/mol
|
1.931 MILLIMOLAR |
CHEBI:26986
threonine
|
|
| 35 |
Phenylalanine
C9H11NO2 165.192 g/mol
|
1.695 MILLIMOLAR |
CHEBI:17295
L-phenylalanine
|
|
| 36 |
DL-methionine
C5H11NO2S 149.215 g/mol
|
0.8042 MILLIMOLAR |
CHEBI:16811
methionine
|
|
| 37 |
Nicotinate
C6H5NO2 123.111 g/mol
|
0.008123 MILLIMOLAR |
CHEBI:15940
nicotinic acid
|
Cross-references: KEGG:nac |
| 38 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.002099 MILLIMOLAR |
CHEBI:31345
Calcium pantothenate
|
|
| 39 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.01739 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 40 |
Cobalt chloride
2Cl.Co 129.839 g/mol
|
0.01051 MILLIMOLAR |
CHEBI:35696
cobalt dichloride
|
|
| 41 |
Ferrous sulfate
Fe.O4S 151.908 g/mol
|
0.04911 MILLIMOLAR |
CHEBI:75832
iron(2+) sulfate (anhydrous)
|
|
| 42 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.3401 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 43 |
Pyridoxine
C8H11NO3 169.18 g/mol
|
0.01182 MILLIMOLAR |
CHEBI:16709
pyridoxine
|
Cross-references: KEGG:pydxn |
| 44 |
Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
|
0.9838 MILLIMOLAR |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 45 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.002657 MILLIMOLAR |
CHEBI:17015
riboflavin
|
Cross-references: KEGG:ribflv |
| 46 |
Thiamine
C12H17N4OS 265.362 g/mol
|
0.003769 MILLIMOLAR |
CHEBI:18385
thiamine(1+)
|
Cross-references: KEGG:thm |
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
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:46.321011Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 407, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:26.118163Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:35.099949Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:19:47.636700Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007307 |
| 2026-03-17T06:30:20.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:05.921915+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "MCD Medium" to "mcd_medium" for consistent matching |
| 2026-06-05T07:41:13.421176+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 22 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-08-20T19:01:57.293541+00:00 | apply_mim_groundings.py | Adopted MIM published grounding | Grounded 2 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308). |