pyvg_medium

CultureMech:007572 bacterial COMPLEX LIQUID
Original name: Pyvg Medium

Overview

External ontology
TOGO:M1056 — Pyvg Medium
Applications
  • Microbial cultivation
Notes
Source: https://togomedium.org/medium/M1056 Original source: JCM - JCM_M1000 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1000

Composition

flowchart LR
    CultureMech_007572["pyvg_medium"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_007572 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_Glucose["Glucose"]
    CultureMech_007572 --> ing1_Glucose
    CHEBI_17234["CHEBI:17234"]
    ing1_Glucose -.-> CHEBI_17234
    ing2_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
    CultureMech_007572 --> ing2_Yeast_extract__BD_Difco_
    ing3_Bacto_peptone__BD_Difco_["Bacto peptone (BD-Difco)"]
    CultureMech_007572 --> ing3_Bacto_peptone__BD_Difco_
    ing4_Trypticase_peptone__BD_BBL_["Trypticase peptone (BD-BBL)"]
    CultureMech_007572 --> ing4_Trypticase_peptone__BD_BBL_
    ing5_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
    CultureMech_007572 --> ing5_L__Cysteine_HCl_H2O
    CHEBI_91248["CHEBI:91248"]
    ing5_L__Cysteine_HCl_H2O -.-> CHEBI_91248
    ing6_N2["N2"]
    CultureMech_007572 --> ing6_N2
    CHEBI_17997["CHEBI:17997"]
    ing6_N2 -.-> CHEBI_17997
    ing7_MgSO4_7H2O["MgSO4・7H2O"]
    CultureMech_007572 --> ing7_MgSO4_7H2O
    CHEBI_31795["CHEBI:31795"]
    ing7_MgSO4_7H2O -.-> CHEBI_31795
    ing8_NaCl["NaCl"]
    CultureMech_007572 --> ing8_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing8_NaCl -.-> CHEBI_26710
    ing9_CaCl2_2H2O["CaCl2・2H2O"]
    CultureMech_007572 --> ing9_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing9_CaCl2_2H2O -.-> CHEBI_86158
    ing10_KH2PO4["KH2PO4"]
    CultureMech_007572 --> ing10_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing10_KH2PO4 -.-> CHEBI_63036
    ing11_K2HPO4["K2HPO4"]
    CultureMech_007572 --> ing11_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing11_K2HPO4 -.-> CHEBI_131527
    ing12_NaHCO3["NaHCO3"]
    CultureMech_007572 --> ing12_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing12_NaHCO3 -.-> CHEBI_32139

Ingredients (13)

# Ingredient Concentration Ontology Notes
1 Distilled water
H2O 18.015 g/mol
1.0 G_PER_L CHEBI:15377
water
 Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component [Collapsed 2 identical duplicates: 1.0, 1.0]
2 Glucose
C6H12O6 180.156 g/mol
10 G_PER_L CHEBI:17234
glucose
 Role: Carbon source; Properties: Defined component, Simple component, Organic compound
3 Yeast extract (BD-Difco) 10 G_PER_L Properties: Undefined component
4 Bacto peptone (BD-Difco) 5 G_PER_L Properties: Undefined component
5 Trypticase peptone (BD-BBL) 5 G_PER_L Properties: Undefined component
6 L--Cysteine・HCl・H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
0.5 G_PER_L CHEBI:91248
L-cysteine hydrochloride hydrate
 Properties: Organic compound, Simple component, Defined component
7 N2
N2 28.014 g/mol
variable VARIABLE CHEBI:17997
dinitrogen
 Properties: Gas
8 MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
0.48 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
9 NaCl
Cl.Na 58.443 g/mol
2 G_PER_L CHEBI:26710
sodium chloride
 Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound
10 CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
0.2 G_PER_L CHEBI:86158
calcium chloride dihydrate
 Role: Mineral source; Properties: Simple component, Defined component, Inorganic compound
11 KH2PO4
H2O4P.K 136.084 g/mol
1 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 Role: Buffer; Properties: Simple component, Inorganic compound, Defined component
12 K2HPO4
HO4P.2K 174.174 g/mol
1 G_PER_L CHEBI:131527
dipotassium hydrogen phosphate
 Role: Buffer; Properties: Defined component, Simple component, Inorganic compound
13 NaHCO3
CHO3.Na 84.006 g/mol
10 G_PER_L CHEBI:32139
sodium hydrogencarbonate
 Role: Buffer; Properties: Defined component, Simple component, Inorganic compound

Solutions

0.05% Resazurin solution

Dose: 1 G_PER_L

Role: pH dependent redox indicator; Properties: Defined component, Solution

Hemin solution (see Medium [M470])

Dose: 10 G_PER_L

Cross-reference to Medium M470

Menadione solution (see Medium [M470])

Dose: 10 G_PER_L

Cross-reference to Medium M470

VFA solution (see Medium [M124])

Dose: 3.1 G_PER_L

Cross-reference to Medium M124

Salt solution (see below)

Dose: 40 G_PER_L

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-27T06:35:53.837844Z togo-import Imported from TOGO Medium Source: JCM, ID: M1056
2026-01-28T19:48:37.208165Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-03T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default concentration for ingredient: N2
2026-03-09T08:05:02.081328+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 5 solution(s) from ingredients
2026-03-13T03:09:33.949928Z data-quality-cleanup-v1.0 Data quality fixes Merged 1 duplicate ingredient(s)
2026-03-13T06:19:49.767080Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007572
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; Added default solution name
2026-03-17T06:30:44.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:08.117889+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Pyvg Medium" to "pyvg_medium" for consistent matching
2026-05-16T09:03:07.239078+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=2
2026-06-05T07:40:30.071435+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 6 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T06:57:20.948590+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.
2026-06-10T07:46:46.806189+00:00 primary-term-label-canonicalization-v1.0 Canonicalized primary term label to OBO canonical (OAK) 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-09-02T07:37:42.512902+00:00 repair_merged_duplicates.py REPAIRED_SUMMED_DUPLICATE_MERGE Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched.