db_characterization_medium_no_2 (CultureMech:009974)

Overview

External ontology

TOGO:M578 — DB Characterization Medium NO. 2

Applications

Microbial cultivation

High-metal flag

True

Notes

Source: https://togomedium.org/medium/M578 Original source: JCM - JCM_M574 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=574

Composition

flowchart LR
    CultureMech_009974["db_characterization_medium_no_2"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_009974 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
    CultureMech_009974 --> ing1_Yeast_extract__BD_Difco_
    ing2_Peptone__Oxoid_["Peptone (Oxoid)"]
    CultureMech_009974 --> ing2_Peptone__Oxoid_
    ing3_MDS_salt_water__see_below_["MDS salt water (see below)"]
    CultureMech_009974 --> ing3_MDS_salt_water__see_below_
    ing4_1_M_NH4Cl["1 M NH4Cl"]
    CultureMech_009974 --> ing4_1_M_NH4Cl
    ing5_Potassium_phosphate_buffer___see_below_["Potassium phosphate buffer* (see below)"]
    CultureMech_009974 --> ing5_Potassium_phosphate_buffer___see_below_
    ing6_MgSO4_7H2O["MgSO4・7H2O"]
    CultureMech_009974 --> ing6_MgSO4_7H2O
    CHEBI_31795["CHEBI:31795"]
    ing6_MgSO4_7H2O -.-> CHEBI_31795
    ing7_NaCl["NaCl"]
    CultureMech_009974 --> ing7_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing7_NaCl -.-> CHEBI_26710
    ing8_MgCl2_6H2O["MgCl2・6H2O"]
    CultureMech_009974 --> ing8_MgCl2_6H2O
    CHEBI_86345["CHEBI:86345"]
    ing8_MgCl2_6H2O -.-> CHEBI_86345
    ing9_KCl["KCl"]
    CultureMech_009974 --> ing9_KCl
    CHEBI_32588["CHEBI:32588"]
    ing9_KCl -.-> CHEBI_32588
    ing10_Tris_base["Tris base"]
    CultureMech_009974 --> ing10_Tris_base
    CHEBI_9754["CHEBI:9754"]
    ing10_Tris_base -.-> CHEBI_9754
    ing11_1_M_K2HPO4["1 M K2HPO4"]
    CultureMech_009974 --> ing11_1_M_K2HPO4
    ing12_1_M_KH2PO4["1 M KH2PO4"]
    CultureMech_009974 --> ing12_1_M_KH2PO4
    ing13_Biotin["Biotin"]
    CultureMech_009974 --> ing13_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing13_Biotin -.-> CHEBI_15956
    ing14_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
    CultureMech_009974 --> ing14_p__Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing14_p__Aminobenzoic_acid -.-> CHEBI_30753
    ing15_Thiamine_HCl["Thiamine・HCl"]
    CultureMech_009974 --> ing15_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing15_Thiamine_HCl -.-> CHEBI_49105
    ing16_Pyridoxine_HCl["Pyridoxine・HCl"]
    CultureMech_009974 --> ing16_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing16_Pyridoxine_HCl -.-> CHEBI_30961
    ing17_Folic_acid["Folic acid"]
    CultureMech_009974 --> ing17_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing17_Folic_acid -.-> CHEBI_27470
    ing18_Vitamin_B12["Vitamin B12"]
    CultureMech_009974 --> ing18_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing18_Vitamin_B12 -.-> CHEBI_176843
    ing19_Riboflavin["Riboflavin"]
    CultureMech_009974 --> ing19_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing19_Riboflavin -.-> CHEBI_17015
    ing20_Nicotinic_acid["Nicotinic acid"]
    CultureMech_009974 --> ing20_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing20_Nicotinic_acid -.-> CHEBI_15940
    ing21_Lipoic_acid["Lipoic acid"]
    CultureMech_009974 --> ing21_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing21_Lipoic_acid -.-> CHEBI_16494
    ing22_DL__Calcium_pantothenate["DL--Calcium pantothenate"]
    CultureMech_009974 --> ing22_DL__Calcium_pantothenate

Ingredients (23)

#	Ingredient	Concentration	Ontology	Notes
1	Distilled water H2O 18.015 g/mol	247.0 G_PER_L	CHEBI:15377 water	Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 4 duplicates: 145.0, 1.0, 100.0, 1.0]
2	Yeast extract (BD-Difco)	0.05 G_PER_L		Properties: Undefined component
3	Peptone (Oxoid)	0.25 G_PER_L		Properties: Undefined component
4	MDS salt water (see below)	833 G_PER_L
5	1 M NH4Cl	5 G_PER_L		Role: Nitrogen source; Properties: Defined component, Inorganic compound, Solution
6	*Potassium phosphate buffer (see below)**	2 G_PER_L
7	MgSO4・7H2O 7H2O.Mg.O4S 246.473 g/mol	35 G_PER_L	CHEBI:31795 magnesium sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
8	NaCl Cl.Na 58.443 g/mol	240 G_PER_L	CHEBI:26710 sodium chloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
9	MgCl2・6H2O 2Cl.6H2O.Mg 203.301 g/mol	30 G_PER_L	CHEBI:86345 magnesium dichloride hexahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
10	KCl Cl.K 74.551 g/mol	7 G_PER_L	CHEBI:32588 potassium chloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
11	Tris base C4H11NO3 121.136 g/mol	variable VARIABLE	CHEBI:9754 tris	Role: Buffer; Properties: Defined component, Organic compound, Simple component
12	1 M K2HPO4	83.4 G_PER_L		Role: Buffer; Properties: Defined component, Inorganic compound, Solution
13	1 M KH2PO4	16.6 G_PER_L		Role: Buffer; Properties: Defined component, Solution, Inorganic compound
14	Biotin C10H16N2O3S 244.316 g/mol	3 G_PER_L	CHEBI:15956 biotin	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
15	p--Aminobenzoic acid C7H7NO2 137.138 g/mol	13 G_PER_L	CHEBI:30753 4-aminobenzoic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
16	Thiamine・HCl C12H17N4OS.Cl.HCl 337.276 g/mol	33 G_PER_L	CHEBI:49105 thiamine hydrochloride	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
17	Pyridoxine・HCl C8H11NO3.HCl 205.641 g/mol	50 G_PER_L	CHEBI:30961 pyridoxine hydrochloride	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
18	Folic acid C19H19N7O6 441.404 g/mol	4 G_PER_L	CHEBI:27470 folic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
19	Vitamin B12	17 G_PER_L	CHEBI:176843 vitamin B12	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
20	Riboflavin C17H20N4O6 376.369 g/mol	10 G_PER_L	CHEBI:17015 riboflavin	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
21	Nicotinic acid C6H5NO2 123.111 g/mol	33 G_PER_L	CHEBI:15940 nicotinic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
22	Lipoic acid C8H14O2S2 206.332 g/mol	10 G_PER_L	CHEBI:16494 lipoic acid	Role: Growth factor; Properties: Organic compound, Defined component, Simple component
23	DL--Calcium pantothenate	17 G_PER_L		Role: Vitamin; Properties: Organic compound, Defined component, Simple component

Solutions

FeCl2 solution (see Medium [M180])

Dose: 1 G_PER_L

Cross-reference to Medium M180

Trace element solution (see Medium [M180])

Dose: 1 G_PER_L

Cross-reference to Medium M180

1 M Sodium pyruvate solution

Dose: 10 G_PER_L

Role: Carbon source; Properties: Solution, Organic compound, Defined component

Vitamin solution (see below)

Dose: 3 G_PER_L

Na2CO3 solution

Dose: variable VARIABLE

Role: Buffer; Properties: Defined component, Inorganic compound, Solution

1 M CaCl2 solution

Dose: 5 G_PER_L

Role: Mineral source; Properties: Defined component, Inorganic compound, Solution

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:55.337582Z	togo-import	Imported from TOGO Medium	Source: JCM, ID: M578
2026-01-28T19:48:40.664910Z	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: Na2CO3 solution; Added default concentration for ingredient: Tris base
2026-03-09T08:05:08.523588+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 6 solution(s) from ingredients
2026-03-13T03:09:40.262155Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 3 duplicate ingredient(s)
2026-03-13T06:20:10.424176Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:009974
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; Added default solution name
2026-03-17T06:30:52.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:29.354586+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "DB Characterization Medium NO. 2" to "db_characterization_medium_no_2" for consistent matching
2026-05-16T09:03:19.252975+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=2
2026-06-05T07:40:42.696952+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 11 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:34.686865+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).
2026-06-10T06:57:31.599626+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.
2026-09-05T00:00:00-07:00	repair_togo_jcm_cross_references.py	LINKED_JCM_CROSS_REFERENCE_CHILDREN	Added or refreshed reciprocal parent-child link for bacterial/TOGO_M1125_DB_Characterization_Medium_NO.2_With_1_Sea_Salts.yaml.