spizizens_medium_trace_elements_amino_acids_sln_1_glycerol_0_2_fumarate_nakano_et_al_n

CultureMech:007113 bacterial DEFINED LIQUID
Original name: Spizizen's medium + trace elements + amino acids sln + 1% glycerol + 0.2% fumarate; Nakano et al

Overview

External ontology
MEDIADB:219 (source link unavailable) — Spizizen's medium + trace elements + amino acids sln + 1% glycerol + 0.2% fumarate; 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_007113["spizizens_medium_trace_elements_amino_acids_sln_1_glycerol_0_2_fuma..."]
    ing0_L_Glutamate["L-Glutamate"]
    CultureMech_007113 --> ing0_L_Glutamate
    CHEBI_16015["CHEBI:16015"]
    ing0_L_Glutamate -.-> CHEBI_16015
    ing1_Glycine["Glycine"]
    CultureMech_007113 --> ing1_Glycine
    CHEBI_15428["CHEBI:15428"]
    ing1_Glycine -.-> CHEBI_15428
    ing2_L_Methionine["L-Methionine"]
    CultureMech_007113 --> ing2_L_Methionine
    CHEBI_16643["CHEBI:16643"]
    ing2_L_Methionine -.-> CHEBI_16643
    ing3_Glycerol["Glycerol"]
    CultureMech_007113 --> ing3_Glycerol
    CHEBI_17754["CHEBI:17754"]
    ing3_Glycerol -.-> CHEBI_17754
    ing4_Glutamine["Glutamine"]
    CultureMech_007113 --> ing4_Glutamine
    ing5_DL_Serine["DL-Serine"]
    CultureMech_007113 --> ing5_DL_Serine
    ing6_Cysteine["Cysteine"]
    CultureMech_007113 --> ing6_Cysteine
    CHEBI_15356["CHEBI:15356"]
    ing6_Cysteine -.-> CHEBI_15356
    ing7_Histidine["Histidine"]
    CultureMech_007113 --> ing7_Histidine
    CHEBI_27570["CHEBI:27570"]
    ing7_Histidine -.-> CHEBI_27570
    ing8_Tryptophan["Tryptophan"]
    CultureMech_007113 --> ing8_Tryptophan
    CHEBI_27897["CHEBI:27897"]
    ing8_Tryptophan -.-> CHEBI_27897
    ing9_Alanine["Alanine"]
    CultureMech_007113 --> ing9_Alanine
    CHEBI_16977["CHEBI:16977"]
    ing9_Alanine -.-> CHEBI_16977
    ing10_DL_Tyrosine["DL-Tyrosine"]
    CultureMech_007113 --> ing10_DL_Tyrosine
    CHEBI_18186["CHEBI:18186"]
    ing10_DL_Tyrosine -.-> CHEBI_18186
    ing11_Phenylalanine["Phenylalanine"]
    CultureMech_007113 --> ing11_Phenylalanine
    CHEBI_17295["CHEBI:17295"]
    ing11_Phenylalanine -.-> CHEBI_17295
    ing12_Arginine["Arginine"]
    CultureMech_007113 --> ing12_Arginine
    CHEBI_29016["CHEBI:29016"]
    ing12_Arginine -.-> CHEBI_29016
    ing13_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007113 --> ing13_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing13_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing14_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
    CultureMech_007113 --> ing14_Potassium_dibasic_phosphate
    CHEBI_131527["CHEBI:131527"]
    ing14_Potassium_dibasic_phosphate -.-> CHEBI_131527
    ing15_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007113 --> ing15_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing15_Sodium_molybdate -.-> CHEBI_75215
    ing16_Aspartate["Aspartate"]
    CultureMech_007113 --> ing16_Aspartate
    CHEBI_29995["CHEBI:29995"]
    ing16_Aspartate -.-> CHEBI_29995
    ing17_Isoleucine["Isoleucine"]
    CultureMech_007113 --> ing17_Isoleucine
    CHEBI_17191["CHEBI:17191"]
    ing17_Isoleucine -.-> CHEBI_17191
    ing18_Proline["Proline"]
    CultureMech_007113 --> ing18_Proline
    CHEBI_26271["CHEBI:26271"]
    ing18_Proline -.-> CHEBI_26271
    ing19_Valine["Valine"]
    CultureMech_007113 --> ing19_Valine
    CHEBI_16414["CHEBI:16414"]
    ing19_Valine -.-> CHEBI_16414
    ing20_Asparagine["Asparagine"]
    CultureMech_007113 --> ing20_Asparagine
    CHEBI_22653["CHEBI:22653"]
    ing20_Asparagine -.-> CHEBI_22653
    ing21_Leucine["Leucine"]
    CultureMech_007113 --> ing21_Leucine
    CHEBI_15603["CHEBI:15603"]
    ing21_Leucine -.-> CHEBI_15603
    ing22_Lysine["Lysine"]
    CultureMech_007113 --> ing22_Lysine
    CHEBI_25094["CHEBI:25094"]
    ing22_Lysine -.-> CHEBI_25094
    ing23_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
    CultureMech_007113 --> ing23_Potassium_dihydrogen_phosphate
    CHEBI_63036["CHEBI:63036"]
    ing23_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
    ing24_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007113 --> ing24_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing24_Magnesium_sulfate -.-> CHEBI_32599
    ing25_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007113 --> ing25_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing25_Manganese_sulfate -.-> CHEBI_86364
    ing26_Cobalt_chloride["Cobalt chloride"]
    CultureMech_007113 --> ing26_Cobalt_chloride
    CHEBI_35696["CHEBI:35696"]
    ing26_Cobalt_chloride -.-> CHEBI_35696
    ing27_Ammonium_sulfate["Ammonium sulfate"]
    CultureMech_007113 --> ing27_Ammonium_sulfate
    CHEBI_62946["CHEBI:62946"]
    ing27_Ammonium_sulfate -.-> CHEBI_62946
    ing28_Cupric_chloride["Cupric chloride"]
    CultureMech_007113 --> ing28_Cupric_chloride
    CHEBI_49553["CHEBI:49553"]
    ing28_Cupric_chloride -.-> CHEBI_49553
    ing29_Sodium_selenate["Sodium selenate"]
    CultureMech_007113 --> ing29_Sodium_selenate
    CHEBI_77775["CHEBI:77775"]
    ing29_Sodium_selenate -.-> CHEBI_77775
    CultureMech_007113 --> more["...5 more"]

Ingredients (35)

# 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 Glycine
C2H5NO2 75.067 g/mol
0.666045 MILLIMOLAR CHEBI:15428
glycine
 Cross-references: KEGG:gly
3 L-Methionine
C5H11NO2S 149.215 g/mol
0.335098 MILLIMOLAR CHEBI:16643
L-methionine
 Cross-references: KEGG:met-L
4 Glycerol
C3H8O3 92.094 g/mol
108.589 MILLIMOLAR CHEBI:17754
glycerol
 Cross-references: KEGG:glyc
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
35 sodium fumarate
C4H2O4.2Na 160.036 g/mol
12.4969 MILLIMOLAR CHEBI:115156
disodium fumarate

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
2026-01-27T07:21:44.612816Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 219, Reference: Mazumdar et al. (2014) PLOS One
2026-03-13T06:19:46.259998Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007113
2026-03-17T06:29:50.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:04.405257+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Spizizen's medium + trace elements + amino acids sln + 1% glycerol + 0.2% fumarate; Nakano et al','N" to "spizizens_medium_trace_elements_amino_acids_sln_1_glycerol_0_2_fumarate_nakano_et_al_n" for consistent matching
2026-06-05T07:41:46.559587+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 15 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-08-20T19:03:07.182002+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).
2026-08-31T04:07:11.294872+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:219's own compound list in media_database.07Oct2015.sql, requiring a unique prefix match and, where more than one matched, an equal Amount_mM.
2026-08-31T06:27:07.275572+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.