spizizens_medium_trace_elements_amino_acids_sln_1_glucose_nakano_et_al_n

CultureMech:007108 bacterial DEFINED LIQUID
Original name: Spizizen's medium + trace elements + amino acids sln + 1% glucose; Nakano et al

Overview

External ontology
MEDIADB:214 (source link unavailable) — Spizizen's medium + trace elements + amino acids sln + 1% glucose; Nakano et al
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_007108["spizizens_medium_trace_elements_amino_acids_sln_1_glucose_nakano_et..."]
    ing0_L_Glutamate["L-Glutamate"]
    CultureMech_007108 --> ing0_L_Glutamate
    CHEBI_16015["CHEBI:16015"]
    ing0_L_Glutamate -.-> CHEBI_16015
    ing1_D_Glucose["D-Glucose"]
    CultureMech_007108 --> ing1_D_Glucose
    CHEBI_17634["CHEBI:17634"]
    ing1_D_Glucose -.-> CHEBI_17634
    ing2_Glycine["Glycine"]
    CultureMech_007108 --> ing2_Glycine
    CHEBI_15428["CHEBI:15428"]
    ing2_Glycine -.-> CHEBI_15428
    ing3_L_Methionine["L-Methionine"]
    CultureMech_007108 --> ing3_L_Methionine
    CHEBI_16643["CHEBI:16643"]
    ing3_L_Methionine -.-> CHEBI_16643
    ing4_Glutamine["Glutamine"]
    CultureMech_007108 --> ing4_Glutamine
    ing5_DL_Serine["DL-Serine"]
    CultureMech_007108 --> ing5_DL_Serine
    ing6_Cysteine["Cysteine"]
    CultureMech_007108 --> ing6_Cysteine
    CHEBI_15356["CHEBI:15356"]
    ing6_Cysteine -.-> CHEBI_15356
    ing7_Histidine["Histidine"]
    CultureMech_007108 --> ing7_Histidine
    CHEBI_27570["CHEBI:27570"]
    ing7_Histidine -.-> CHEBI_27570
    ing8_Tryptophan["Tryptophan"]
    CultureMech_007108 --> ing8_Tryptophan
    CHEBI_27897["CHEBI:27897"]
    ing8_Tryptophan -.-> CHEBI_27897
    ing9_Alanine["Alanine"]
    CultureMech_007108 --> ing9_Alanine
    CHEBI_16977["CHEBI:16977"]
    ing9_Alanine -.-> CHEBI_16977
    ing10_DL_Tyrosine["DL-Tyrosine"]
    CultureMech_007108 --> ing10_DL_Tyrosine
    CHEBI_18186["CHEBI:18186"]
    ing10_DL_Tyrosine -.-> CHEBI_18186
    ing11_Phenylalanine["Phenylalanine"]
    CultureMech_007108 --> ing11_Phenylalanine
    CHEBI_17295["CHEBI:17295"]
    ing11_Phenylalanine -.-> CHEBI_17295
    ing12_Arginine["Arginine"]
    CultureMech_007108 --> ing12_Arginine
    CHEBI_29016["CHEBI:29016"]
    ing12_Arginine -.-> CHEBI_29016
    ing13_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007108 --> ing13_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing13_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing14_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
    CultureMech_007108 --> ing14_Potassium_dibasic_phosphate
    CHEBI_131527["CHEBI:131527"]
    ing14_Potassium_dibasic_phosphate -.-> CHEBI_131527
    ing15_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007108 --> ing15_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing15_Sodium_molybdate -.-> CHEBI_75215
    ing16_Aspartate["Aspartate"]
    CultureMech_007108 --> ing16_Aspartate
    CHEBI_29995["CHEBI:29995"]
    ing16_Aspartate -.-> CHEBI_29995
    ing17_Isoleucine["Isoleucine"]
    CultureMech_007108 --> ing17_Isoleucine
    CHEBI_17191["CHEBI:17191"]
    ing17_Isoleucine -.-> CHEBI_17191
    ing18_Proline["Proline"]
    CultureMech_007108 --> ing18_Proline
    CHEBI_26271["CHEBI:26271"]
    ing18_Proline -.-> CHEBI_26271
    ing19_Valine["Valine"]
    CultureMech_007108 --> ing19_Valine
    CHEBI_16414["CHEBI:16414"]
    ing19_Valine -.-> CHEBI_16414
    ing20_Asparagine["Asparagine"]
    CultureMech_007108 --> ing20_Asparagine
    CHEBI_22653["CHEBI:22653"]
    ing20_Asparagine -.-> CHEBI_22653
    ing21_Leucine["Leucine"]
    CultureMech_007108 --> ing21_Leucine
    CHEBI_15603["CHEBI:15603"]
    ing21_Leucine -.-> CHEBI_15603
    ing22_Lysine["Lysine"]
    CultureMech_007108 --> ing22_Lysine
    CHEBI_25094["CHEBI:25094"]
    ing22_Lysine -.-> CHEBI_25094
    ing23_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
    CultureMech_007108 --> ing23_Potassium_dihydrogen_phosphate
    CHEBI_63036["CHEBI:63036"]
    ing23_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
    ing24_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007108 --> ing24_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing24_Magnesium_sulfate -.-> CHEBI_32599
    ing25_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007108 --> ing25_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing25_Manganese_sulfate -.-> CHEBI_86364
    ing26_Cobalt_chloride["Cobalt chloride"]
    CultureMech_007108 --> ing26_Cobalt_chloride
    CHEBI_35696["CHEBI:35696"]
    ing26_Cobalt_chloride -.-> CHEBI_35696
    ing27_Ammonium_sulfate["Ammonium sulfate"]
    CultureMech_007108 --> ing27_Ammonium_sulfate
    CHEBI_62946["CHEBI:62946"]
    ing27_Ammonium_sulfate -.-> CHEBI_62946
    ing28_Cupric_chloride["Cupric chloride"]
    CultureMech_007108 --> ing28_Cupric_chloride
    CHEBI_49553["CHEBI:49553"]
    ing28_Cupric_chloride -.-> CHEBI_49553
    ing29_Sodium_selenate["Sodium selenate"]
    CultureMech_007108 --> ing29_Sodium_selenate
    CHEBI_77775["CHEBI:77775"]
    ing29_Sodium_selenate -.-> CHEBI_77775
    CultureMech_007108 --> more["...4 more"]

Ingredients (34)

# Ingredient Concentration Ontology Notes
1 L-Glutamate
C5H9NO4 147.13 g/mol
0.339836 MILLIMOLAR CHEBI:16015
L-glutamic acid
 Cross-references: KEGG:glu-L
2 D-Glucose
C6H12O6 180.156 g/mol
83.2593 MILLIMOLAR CHEBI:17634
D-glucose
 Cross-references: KEGG:glc_D
3 Glycine
C2H5NO2 75.067 g/mol
0.666045 MILLIMOLAR CHEBI:15428
glycine
 Cross-references: KEGG:gly
4 L-Methionine
C5H11NO2S 149.215 g/mol
0.335098 MILLIMOLAR CHEBI:16643
L-methionine
 Cross-references: KEGG:met-L
5 Glutamine 0.342138 MILLIMOLAR
6 DL-Serine 0.475783 MILLIMOLAR
7 Cysteine
C3H7NO2S 121.161 g/mol
0.412677 MILLIMOLAR CHEBI:15356
cysteine
8 Histidine
C6H9N3O2 155.157 g/mol
0.322269 MILLIMOLAR CHEBI:27570
histidine
9 Tryptophan
C11H12N2O2 204.229 g/mol
0.244822 MILLIMOLAR CHEBI:27897
tryptophan
10 Alanine
C3H7NO2 89.094 g/mol
0.56123 MILLIMOLAR CHEBI:16977
L-alanine
11 DL-Tyrosine
C9H11NO3 181.191 g/mol
0.275953 MILLIMOLAR CHEBI:18186
tyrosine
12 Phenylalanine
C9H11NO2 165.192 g/mol
0.302682 MILLIMOLAR CHEBI:17295
L-phenylalanine
13 Arginine
C6H14N4O2 174.204 g/mol
0.287026 MILLIMOLAR CHEBI:29016
arginine
14 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.049556 MILLIMOLAR CHEBI:3312
calcium dichloride
15 Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
80.3673 MILLIMOLAR CHEBI:131527
dipotassium hydrogen phosphate
16 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.00247985 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
17 Aspartate
C4H5NO4 131.087 g/mol
0.375657 MILLIMOLAR CHEBI:29995
aspartate(2-)
18 Isoleucine
C6H13NO2 131.175 g/mol
0.381185 MILLIMOLAR CHEBI:17191
L-isoleucine
19 Proline
C5H9NO2 115.132 g/mol
0.434292 MILLIMOLAR CHEBI:26271
proline
20 Valine
C5H11NO2 117.148 g/mol
0.426803 MILLIMOLAR CHEBI:16414
L-valine
21 Asparagine
C4H8N2O3 132.119 g/mol
0.378444 MILLIMOLAR CHEBI:22653
asparagine
22 Leucine
C6H13NO2 131.175 g/mol
0.381185 MILLIMOLAR CHEBI:15603
L-leucine
23 Lysine
C6H14N2O2 146.19 g/mol
0.342021 MILLIMOLAR CHEBI:25094
lysine
24 Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
44.0898 MILLIMOLAR CHEBI:63036
potassium dihydrogen phosphate
25 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.811458 MILLIMOLAR CHEBI:32599
magnesium sulfate
26 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.0044828 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
27 Cobalt chloride
2Cl.Co 129.839 g/mol
0.0046211 MILLIMOLAR CHEBI:35696
cobalt dichloride
28 Ammonium sulfate
2H4N.O4S 132.141 g/mol
15.1355 MILLIMOLAR CHEBI:62946
ammonium sulfate
29 Cupric chloride
Cl2Cu 134.452 g/mol
0.0025222 MILLIMOLAR CHEBI:49553
copper(II) chloride
30 Sodium selenate
2Na.O4Se 188.936 g/mol
0.00248756 MILLIMOLAR CHEBI:77775
sodium selenate
31 Sodium citrate
C6H5O7.3Na 258.069 g/mol
3.4002 MILLIMOLAR CHEBI:53258
sodium citrate
32 Iron(III) chloride 0.04994 MILLIMOLAR
33 Zinc Chloride
2Cl.Zn 136.296 g/mol
0.012471 MILLIMOLAR CHEBI:49976
zinc dichloride
34 Threonine
C4H9NO3 119.119 g/mol
0.419745 MILLIMOLAR CHEBI:26986
threonine

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
2026-01-27T07:21:44.542361Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 214, Reference: Mazumdar et al. (2014) PLOS One
2026-03-13T06:19:46.197843Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007108
2026-03-17T06:30:46.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:04.336884+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Spizizen's medium + trace elements + amino acids sln + 1% glucose; Nakano et al','N" to "spizizens_medium_trace_elements_amino_acids_sln_1_glucose_nakano_et_al_n" for consistent matching
2026-06-05T07:41:46.544217+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 14 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-08-20T19:03:07.165380+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).
2026-08-31T04:07:11.276428+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:214's own compound list in media_database.07Oct2015.sql, requiring a unique prefix match and, where more than one matched, an equal Amount_mM.
2026-08-31T06:27:07.259050+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.