pe_medium (CultureMech:009509)

Overview

External ontology

TOGO:M298 — PE Medium

Applications

Microbial cultivation

pH

7.5

High-metal flag

True

Notes

TOGO M298 mirrors JCM Medium 303: PE Medium combines 5 mL Basal salts solution, 5 mL Phosphate solution, 1 mL Vitamin solution, seven direct 0.5 g/L ingredients, and distilled water; the complete medium is adjusted to pH 7.5.

Composition

flowchart LR
    CultureMech_009509["pe_medium"]
    ing0__NH4_2SO4["(NH4)2SO4"]
    CultureMech_009509 --> ing0__NH4_2SO4
    CHEBI_62946["CHEBI:62946"]
    ing0__NH4_2SO4 -.-> CHEBI_62946
    ing1_Sodium_glutamate["Sodium glutamate"]
    CultureMech_009509 --> ing1_Sodium_glutamate
    CHEBI_64220["CHEBI:64220"]
    ing1_Sodium_glutamate -.-> CHEBI_64220
    ing2_Sodium_succinate["Sodium succinate"]
    CultureMech_009509 --> ing2_Sodium_succinate
    CHEBI_63675["CHEBI:63675"]
    ing2_Sodium_succinate -.-> CHEBI_63675
    ing3_Sodium_acetate["Sodium acetate"]
    CultureMech_009509 --> ing3_Sodium_acetate
    CHEBI_32954["CHEBI:32954"]
    ing3_Sodium_acetate -.-> CHEBI_32954
    ing4_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
    CultureMech_009509 --> ing4_Yeast_extract__BD_Difco_
    ing5_Casamino_acids__BD_Difco_["Casamino acids (BD-Difco)"]
    CultureMech_009509 --> ing5_Casamino_acids__BD_Difco_
    ing6_Na2S2O3["Na2S2O3"]
    CultureMech_009509 --> ing6_Na2S2O3
    CHEBI_132112["CHEBI:132112"]
    ing6_Na2S2O3 -.-> CHEBI_132112
    ing7_Distilled_water["Distilled water"]
    CultureMech_009509 --> ing7_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing7_Distilled_water -.-> CHEBI_15377

Ingredients (8)

#	Ingredient	Concentration	Ontology	Notes
1	(NH4)2SO4 2H4N.O4S 132.141 g/mol	0.5 G_PER_L	CHEBI:62946 ammonium sulfate	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
2	Sodium glutamate C5H8NO4.Na 169.112 g/mol	0.5 G_PER_L	CHEBI:64220 monosodium glutamate	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
3	Sodium succinate C4H4O4.2Na 162.052 g/mol	0.5 G_PER_L	CHEBI:63675 sodium succinate (anhydrous)	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
4	Sodium acetate C2H3O2.Na 82.034 g/mol	0.5 G_PER_L	CHEBI:32954 sodium acetate	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
5	Yeast extract (BD-Difco)	0.5 G_PER_L		TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
6	Casamino acids (BD-Difco)	0.5 G_PER_L		TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
7	Na2S2O3 2Na.O3S2 158.111 g/mol	0.5 G_PER_L	CHEBI:132112 sodium thiosulfate	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.
8	Distilled water H2O 18.015 g/mol	1000 ML_PER_L	CHEBI:15377 water	TOGO M298 and JCM Medium 303 list this component for PE Medium; TOGO M331/JCM Medium 336 and TOGO M332/JCM Medium 337 use the same formulation adjusted to different final pH values.

Preparation

Prepare the Basal salts, Phosphate, Vitamin, and Trace elements stock solutions.
Combine 5 mL Basal salts solution, 5 mL Phosphate solution, 1 mL Vitamin solution, the direct PE Medium ingredients, and distilled water; bring the final volume to 1 L.
Adjust the complete medium to pH 7.5.
Autoclave at 121 C for 15 min.

Solutions

Basal salts solution

Dose: 5 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
EDTA.3Na	4.12 G_PER_L	JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.
FeSO4.H2O	1.11 G_PER_L	JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.
MgSO4 x 7 H2O	24.65 G_PER_L	JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.
CaCl2 x 2 H2O	2.94 G_PER_L	JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.
NaCl	23.4 G_PER_L	JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.
Distilled water	1000 ML_PER_L	JCM Medium 303 lists 1 L distilled water for Basal salts solution; concentrations are normalized per liter of stock.

JCM Medium 303 adds 5 mL Basal salts solution per final liter of PE Medium.

Phosphate solution

Dose: 5 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
KH2PO4	75 G_PER_L	JCM Medium 303 adds 5 mL Phosphate solution per final liter of PE Medium.
K2HPO4	78 G_PER_L	JCM Medium 303 adds 5 mL Phosphate solution per final liter of PE Medium.
Distilled water	1000 ML_PER_L	JCM Medium 303 lists 1 L distilled water for Phosphate solution; concentrations are normalized per liter of stock.

JCM Medium 303 adds 5 mL Phosphate solution per final liter of PE Medium.

Vitamin solution

Dose: 1 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
Nicotinic acid	1 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Thiamine.HCl	1 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Biotin	0.05 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
p-Aminobenzoic acid	0.5 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Vitamin B12	0.01 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Calcium pantothenate	0.5 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Pyridoxine.HCl	0.5 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Folic acid	0.5 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
EDTA.3Na	2 G_PER_L	JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.
Distilled water	1000 ML_PER_L	JCM Medium 303 lists 100 mL distilled water for Vitamin solution; concentrations are normalized per liter of stock.

JCM Medium 303 adds 1 mL Vitamin solution per final liter of PE Medium.

Trace elements solution

Dose: 10 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
MnSO4.xH2O	11.16 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
ZnSO4 x 7 H2O	2.88 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
Co(NO3)2 x 6 H2O	2.92 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
CuSO4 x 5 H2O	2.52 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
Na2MoO4 x 2 H2O	2.42 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
H3BO3	3.1 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
EDTA.3Na	41.2 G_PER_L	JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.
Distilled water	1000 ML_PER_L	JCM Medium 303 lists 500 mL distilled water for Trace elements solution; concentrations are normalized per liter of stock.

JCM Medium 303 adds 10 mL Trace elements solution per liter of Basal salts solution.

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:54.791665Z	togo-import	Imported from TOGO Medium	Source: JCM, ID: M298
2026-01-28T19:48:27.682231Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-09T08:04:45.802682+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 4 solution(s) from ingredients
2026-03-13T03:09:16.305027Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 6 duplicate ingredient(s)
2026-03-13T06:20:06.463111Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:009509
2026-03-14T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name; Added default solution name; Added default solution name; Added default solution name
2026-03-17T06:30:24.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:25.466977+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "PE Medium" to "pe_medium" for consistent matching
2026-05-16T09:03:16.329697+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=1
2026-06-05T07:40:39.590772+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 16 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:33.812729+00:00	chebi-regrounding-v1.0	Corrected CHEBI ingredient grounding (audit G21/G22)	Re-grounded 1 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).
2026-06-10T06:57:28.996695+00:00	mgso4-heptahydrate-term-fix-v1.0	Corrected MgSO4·7H2O primary term grounding to heptahydrate	Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched.
2026-06-10T07:46:50.028106+00:00	primary-term-label-canonicalization-v1.0	Canonicalized primary term label to OBO canonical (OAK)	4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-09-06T00:00:00-07:00	repair_jcm_ph_score40.py	RESOLVED_JCM_PH_SCORE40_GRAPH	TOGO M298 mirrors JCM Medium 303: PE Medium combines 5 mL Basal salts solution, 5 mL Phosphate solution, 1 mL Vitamin solution, seven direct 0.5 g/L ingredients, and distilled water; the complete medium is adjusted to pH 7.5.
2026-09-06T00:00:00-07:00	repair_jcm_ph_score40.py	LINKED_JCM_PH_SCORE40_CHILDREN	Added or refreshed reciprocal parent-child link for bacterial/TOGO_M331_PE_Medium_pH_6.8.yaml.
2026-09-06T00:00:00-07:00	repair_jcm_ph_score40.py	LINKED_JCM_PH_SCORE40_CHILDREN	Added or refreshed reciprocal parent-child link for bacterial/TOGO_M332_PE_Medium_pH_7.2.yaml.