fermentation_medium_glucose_urea

CultureMech:007265 bacterial DEFINED LIQUID
Original name: Fermentation Medium (Glucose+Urea)

Overview

External ontology
MEDIADB:363 (source link unavailable) — Fermentation Medium (Glucose+Urea)
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_007265["fermentation_medium_glucose_urea"]
    ing0_Glucose["Glucose"]
    CultureMech_007265 --> ing0_Glucose
    CHEBI_17234["CHEBI:17234"]
    ing0_Glucose -.-> CHEBI_17234
    ing1_Biotin["Biotin"]
    CultureMech_007265 --> ing1_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing1_Biotin -.-> CHEBI_15956
    ing2_Riboflavin["Riboflavin"]
    CultureMech_007265 --> ing2_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing2_Riboflavin -.-> CHEBI_17015
    ing3_Magnesium_sulfate["Magnesium sulfate"]
    CultureMech_007265 --> ing3_Magnesium_sulfate
    CHEBI_32599["CHEBI:32599"]
    ing3_Magnesium_sulfate -.-> CHEBI_32599
    ing4_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_007265 --> ing4_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing4_Pyridoxine_HCl -.-> CHEBI_30961
    ing5_Nicotinate["Nicotinate"]
    CultureMech_007265 --> ing5_Nicotinate
    CHEBI_15940["CHEBI:15940"]
    ing5_Nicotinate -.-> CHEBI_15940
    ing6_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
    CultureMech_007265 --> ing6_Potassium_dihydrogen_phosphate
    CHEBI_63036["CHEBI:63036"]
    ing6_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
    ing7_Thiamine_HCl["Thiamine HCl"]
    CultureMech_007265 --> ing7_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing7_Thiamine_HCl -.-> CHEBI_49105
    ing8_Urea["Urea"]
    CultureMech_007265 --> ing8_Urea
    CHEBI_16199["CHEBI:16199"]
    ing8_Urea -.-> CHEBI_16199

Ingredients (9)

# Ingredient Concentration Ontology Notes
1 Glucose
C6H12O6 180.156 g/mol
111.0 MILLIMOLAR CHEBI:17234
glucose
2 Biotin
C10H16N2O3S 244.316 g/mol
0.0001228 MILLIMOLAR CHEBI:15956
biotin
 Cross-references: KEGG:btn
3 Riboflavin
C17H20N4O6 376.369 g/mol
0.0003986 MILLIMOLAR CHEBI:17015
riboflavin
 Cross-references: KEGG:ribflv
4 Magnesium sulfate
Mg.O4S 120.368 g/mol
3.246 MILLIMOLAR CHEBI:32599
magnesium sulfate
5 Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
0.001459 MILLIMOLAR CHEBI:30961
pyridoxine hydrochloride
6 Nicotinate
C6H5NO2 123.111 g/mol
0.09747 MILLIMOLAR CHEBI:15940
nicotinic acid
 Cross-references: KEGG:nac
7 Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
36.74 MILLIMOLAR CHEBI:63036
potassium dihydrogen phosphate
8 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0001334 MILLIMOLAR CHEBI:49105
thiamine hydrochloride
9 Urea
CH4N2O 60.056 g/mol
130.9 MILLIMOLAR CHEBI:16199
urea
 Cross-references: KEGG:urea

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
2026-01-27T07:21:45.908409Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 363, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:23.994980Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-06T05:10:32.529879Z invalid-chebi-removal Removed 1 invalid CHEBI ID(s) Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data
2026-03-13T06:19:47.279330Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007265
2026-03-17T06:30:16.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:05.489831+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "'Fermentation Medium (Glucose+Urea" to "fermentation_medium_glucose_urea" for consistent matching
2026-06-05T07:41:00.049430+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.
2026-06-08T23:19:38.296472+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).
2026-08-31T06:17:28.477768+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.