db_characterization_medium_no_2

CultureMech:002922 bacterial COMPLEX LIQUID
Original name: DB CHARACTERIZATION MEDIUM NO. 2

Overview

External ontology
mediadive.medium:J574 (source link unavailable) — DB CHARACTERIZATION MEDIUM NO. 2
Applications
  • Microbial cultivation
pH
7.5
High-metal flag
True
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=574

Composition

flowchart LR
    CultureMech_002922["db_characterization_medium_no_2"]
    ing0_Peptone["Peptone"]
    CultureMech_002922 --> ing0_Peptone
    ing1_Yeast_extract["Yeast extract"]
    CultureMech_002922 --> ing1_Yeast_extract
    ing2_NH4Cl["NH4Cl"]
    CultureMech_002922 --> ing2_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing2_NH4Cl -.-> CHEBI_31206
    ing3_Sodium_pyruvate["Sodium pyruvate"]
    CultureMech_002922 --> ing3_Sodium_pyruvate
    CHEBI_50144["CHEBI:50144"]
    ing3_Sodium_pyruvate -.-> CHEBI_50144
    ing4_NaCl["NaCl"]
    CultureMech_002922 --> ing4_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing4_NaCl -.-> CHEBI_26710
    ing5_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002922 --> ing5_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing5_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing6_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_002922 --> ing6_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing6_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing7_KCl["KCl"]
    CultureMech_002922 --> ing7_KCl
    CHEBI_32588["CHEBI:32588"]
    ing7_KCl -.-> CHEBI_32588
    ing8_CaCl2["CaCl2"]
    CultureMech_002922 --> ing8_CaCl2
    CHEBI_3312["CHEBI:3312"]
    ing8_CaCl2 -.-> CHEBI_3312
    ing9_K2HPO4["K2HPO4"]
    CultureMech_002922 --> ing9_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing9_K2HPO4 -.-> CHEBI_131527
    ing10_KH2PO4["KH2PO4"]
    CultureMech_002922 --> ing10_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing10_KH2PO4 -.-> CHEBI_63036
    ing11_Biotin["Biotin"]
    CultureMech_002922 --> ing11_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing11_Biotin -.-> CHEBI_15956
    ing12_Folic_acid["Folic acid"]
    CultureMech_002922 --> ing12_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing12_Folic_acid -.-> CHEBI_27470
    ing13_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_002922 --> ing13_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing13_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing14_Thiamine_HCl["Thiamine HCl"]
    CultureMech_002922 --> ing14_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing14_Thiamine_HCl -.-> CHEBI_49105
    ing15_Riboflavin["Riboflavin"]
    CultureMech_002922 --> ing15_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing15_Riboflavin -.-> CHEBI_17015
    ing16_Nicotinic_acid["Nicotinic acid"]
    CultureMech_002922 --> ing16_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing16_Nicotinic_acid -.-> CHEBI_15940
    ing17_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
    CultureMech_002922 --> ing17_DL_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing17_DL_Calcium_pantothenate -.-> CHEBI_31345
    ing18_Vitamin_B12["Vitamin B12"]
    CultureMech_002922 --> ing18_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing18_Vitamin_B12 -.-> CHEBI_176843
    ing19_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_002922 --> ing19_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing19_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing20_Lipoic_acid["Lipoic acid"]
    CultureMech_002922 --> ing20_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing20_Lipoic_acid -.-> CHEBI_16494
    ing21_HCl["HCl"]
    CultureMech_002922 --> ing21_HCl
    CHEBI_17883["CHEBI:17883"]
    ing21_HCl -.-> CHEBI_17883
    ing22_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
    CultureMech_002922 --> ing22_FeCl2_x_4_H2O
    CHEBI_86249["CHEBI:86249"]
    ing22_FeCl2_x_4_H2O -.-> CHEBI_86249
    ing23_ZnCl2["ZnCl2"]
    CultureMech_002922 --> ing23_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing23_ZnCl2 -.-> CHEBI_49976
    ing24_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_002922 --> ing24_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing24_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing25_H3BO3["H3BO3"]
    CultureMech_002922 --> ing25_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing25_H3BO3 -.-> CHEBI_33118
    ing26_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_002922 --> ing26_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing26_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing27_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_002922 --> ing27_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing27_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing28_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_002922 --> ing28_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing28_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing29_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_002922 --> ing29_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing29_Na2MoO4_x_2_H2O -.-> CHEBI_75213

Ingredients (30)

# Ingredient Concentration Ontology Notes
1 Peptone 0.25 G_PER_L
2 Yeast extract 0.05 G_PER_L
3 NH4Cl
Cl.H4N 53.492 g/mol
0.26745 G_PER_L CHEBI:31206
ammonium chloride
4 Sodium pyruvate
C3H3O3.Na 110.044 g/mol
1.1004 G_PER_L CHEBI:50144
sodium pyruvate
5 NaCl
Cl.Na 58.443 g/mol
240 G_PER_L CHEBI:26710
sodium chloride
6 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
30 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
7 MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
35 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
8 KCl
Cl.K 74.551 g/mol
7 G_PER_L CHEBI:32588
potassium chloride
9 CaCl2
Ca.2Cl 110.984 g/mol
0.5549 G_PER_L CHEBI:3312
calcium dichloride
10 K2HPO4
HO4P.2K 174.174 g/mol
14.5263 G_PER_L CHEBI:131527
dipotassium hydrogen phosphate
11 KH2PO4
H2O4P.K 136.084 g/mol
2.25901 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
12 Biotin
C10H16N2O3S 244.316 g/mol
0.003 G_PER_L CHEBI:15956
biotin
13 Folic acid
C19H19N7O6 441.404 g/mol
0.004 G_PER_L CHEBI:27470
folic acid
14 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.05 G_PER_L CHEBI:30961
pyridoxine hydrochloride
15 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.033 G_PER_L CHEBI:49105
thiamine hydrochloride
16 Riboflavin
C17H20N4O6 376.369 g/mol
0.01 G_PER_L CHEBI:17015
riboflavin
17 Nicotinic acid
C6H5NO2 123.111 g/mol
0.033 G_PER_L CHEBI:15940
nicotinic acid
18 DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.017 G_PER_L CHEBI:31345
Calcium pantothenate
19 Vitamin B12 0.017 G_PER_L CHEBI:176843
vitamin B12
20 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.013 G_PER_L CHEBI:30753
4-aminobenzoic acid
21 Lipoic acid
C8H14O2S2 206.332 g/mol
0.01 G_PER_L CHEBI:16494
lipoic acid
22 HCl
HCl 36.461 g/mol
2.5 G_PER_L CHEBI:17883
hydrogen chloride
23 FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
1.5 G_PER_L CHEBI:86249
iron dichloride tetrahydrate
24 ZnCl2
2Cl.Zn 136.296 g/mol
0.07 G_PER_L CHEBI:49976
zinc dichloride
25 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
0.1 G_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
26 H3BO3
H3BO3 61.833 g/mol
0.006 G_PER_L CHEBI:33118
boric acid
27 CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
0.19 G_PER_L CHEBI:53503
cobalt chloride hexahydrate
28 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.002 G_PER_L CHEBI:86318
copper(II) chloride dihydrate
29 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.024 G_PER_L CHEBI:34887
nickel dichloride
30 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.036 G_PER_L CHEBI:75213
sodium molybdate dihydrate

Preparation

  1. Add components and bring volume to 980 ml with distilled water. For preparation of solid medium, add 20 g/L agar (if necessary, use washed agar as described below). Autoclave, and after cooling, add the following solutions (filter-sterilized or *autoclaved) to the medium:
  2. Readjust pH to 7.0 - 7.5 with a sterilized 10% Na2CO3 solution, if necessary.
  3. Stir agar in distilled water and stand still for 30 min. Then, remove supernatant by decantation. Repeat the washing at least twice.
  4. Add components to distilled water and bring volume to 1.0 L. Adjust pH to 7.5 with 1 M Tris base.
  5. Combine the two solutions and check that pH is close to 7.5. Add an equal volume of distilled water.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:16.974993Z mediadive-import Imported from MediaDive Source: JCM, ID: J574
2026-03-13T06:19:16.591535Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002922
2026-03-17T06:30:29.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:30.161868+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
2026-06-05T07:40:55.309862+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 28 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:55.115882+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.