modified_vogel_medium_xylose

CultureMech:007210 bacterial DEFINED LIQUID
Original name: Modified Vogel Medium (xylose)

Overview

External ontology
MEDIADB:311 (source link unavailable) — Modified Vogel Medium (xylose)
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_007210["modified_vogel_medium_xylose"]
    ing0_Xylose["Xylose"]
    CultureMech_007210 --> ing0_Xylose
    CHEBI_18222["CHEBI:18222"]
    ing0_Xylose -.-> CHEBI_18222
    ing1_Sodium_molybdate["Sodium molybdate"]
    CultureMech_007210 --> ing1_Sodium_molybdate
    CHEBI_75215["CHEBI:75215"]
    ing1_Sodium_molybdate -.-> CHEBI_75215
    ing2_Uridine["Uridine"]
    CultureMech_007210 --> ing2_Uridine
    CHEBI_16704["CHEBI:16704"]
    ing2_Uridine -.-> CHEBI_16704
    ing3_Cupric_sulfate["Cupric sulfate"]
    CultureMech_007210 --> ing3_Cupric_sulfate
    CHEBI_23414["CHEBI:23414"]
    ing3_Cupric_sulfate -.-> CHEBI_23414
    ing4_Ferrous_ammonium_sulfate["Ferrous ammonium sulfate"]
    CultureMech_007210 --> ing4_Ferrous_ammonium_sulfate
    ing5_Boric_acid["Boric acid"]
    CultureMech_007210 --> ing5_Boric_acid
    CHEBI_33118["CHEBI:33118"]
    ing5_Boric_acid -.-> CHEBI_33118
    ing6_Manganese_sulfate["Manganese sulfate"]
    CultureMech_007210 --> ing6_Manganese_sulfate
    CHEBI_86364["CHEBI:86364"]
    ing6_Manganese_sulfate -.-> CHEBI_86364
    ing7_Zinc_sulfate["Zinc sulfate"]
    CultureMech_007210 --> ing7_Zinc_sulfate
    CHEBI_35176["CHEBI:35176"]
    ing7_Zinc_sulfate -.-> CHEBI_35176
    ing8_Citrate["Citrate"]
    CultureMech_007210 --> ing8_Citrate
    CHEBI_16947["CHEBI:16947"]
    ing8_Citrate -.-> CHEBI_16947
    ing9_Sodium_citrate["Sodium citrate"]
    CultureMech_007210 --> ing9_Sodium_citrate
    CHEBI_53258["CHEBI:53258"]
    ing9_Sodium_citrate -.-> CHEBI_53258
    ing10_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007210 --> ing10_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing10_Magnesium_sulfate -.-> CHEBI_32599
    ing11_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007210 --> ing11_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing11_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing12_Ammonium_nitrate["Ammonium nitrate"]
    CultureMech_007210 --> ing12_Ammonium_nitrate
    CHEBI_63038["CHEBI:63038"]
    ing12_Ammonium_nitrate -.-> CHEBI_63038
    ing13_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
    CultureMech_007210 --> ing13_Potassium_dihydrogen_phosphate
    CHEBI_63036["CHEBI:63036"]
    ing13_Potassium_dihydrogen_phosphate -.-> CHEBI_63036

Ingredients (14)

# Ingredient Concentration Ontology Notes
1 Xylose
C5H10O5 150.13 g/mol
133.2 MILLIMOLAR CHEBI:18222
xylose
2 Sodium molybdate
MoO4.2Na 205.916 g/mol
0.0002066 MILLIMOLAR CHEBI:75215
sodium molybdate (anhydrous)
3 Uridine
C9H12N2O6 244.203 g/mol
9.992 MILLIMOLAR CHEBI:16704
uridine
 Cross-references: KEGG:uri
4 Cupric sulfate
Cu.O4S 159.609 g/mol
0.001002 MILLIMOLAR CHEBI:23414
copper(II) sulfate
5 Ferrous ammonium sulfate 0.00255 MILLIMOLAR
6 Boric acid
H3BO3 61.833 g/mol
0.0008087 MILLIMOLAR CHEBI:33118
boric acid
7 Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
0.0002189 MILLIMOLAR CHEBI:86364
manganese(II) sulfate monohydrate
8 Zinc sulfate
O4S.Zn 161.453 g/mol
0.01739 MILLIMOLAR CHEBI:35176
zinc sulfate
9 Citrate
C6H5O7 189.099 g/mol
0.02379 MILLIMOLAR CHEBI:16947
citrate(3-)
 Cross-references: KEGG:cit
10 Sodium citrate
C6H5O7.3Na 258.069 g/mol
9.691 MILLIMOLAR CHEBI:53258
sodium citrate
11 Magnesium sulfate
Mg.O4S 120.368 g/mol
0.8115 MILLIMOLAR CHEBI:32599
magnesium sulfate
12 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.68 MILLIMOLAR CHEBI:3312
calcium dichloride
13 Ammonium nitrate
H4N.NO3 80.043 g/mol
24.99 MILLIMOLAR CHEBI:63038
ammonium nitrate
14 Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
36.74 MILLIMOLAR CHEBI:63036
potassium dihydrogen phosphate

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
2026-01-27T07:21:45.428518Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 311, Reference: Mazumdar et al. (2014) PLOS One
2026-03-13T06:19:46.891100Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007210
2026-03-17T06:30:42.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:05.074518+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "'Modified Vogel Medium (xylose" to "modified_vogel_medium_xylose" for consistent matching
2026-06-05T07:41:37.978028+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 7 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-08-31T06:18:17.812635+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.