si_medium

CultureMech:002642 bacterial COMPLEX LIQUID
Original name: SI MEDIUM

Overview

External ontology
mediadive.medium:J284 (source link unavailable) — SI MEDIUM
Applications
  • Microbial cultivation
pH
6.5
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=284

Composition

flowchart LR
    CultureMech_002642["si_medium"]
    ing0_Yeast_extract["Yeast extract"]
    CultureMech_002642 --> ing0_Yeast_extract
    ing1_KH2PO4["KH2PO4"]
    CultureMech_002642 --> ing1_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing1_KH2PO4 -.-> CHEBI_63036
    ing2_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002642 --> ing2_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing2_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing3_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_002642 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_NH4Cl["NH4Cl"]
    CultureMech_002642 --> ing4_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing4_NH4Cl -.-> CHEBI_31206
    ing5_NaHCO3["NaHCO3"]
    CultureMech_002642 --> ing5_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing5_NaHCO3 -.-> CHEBI_32139
    ing6_Resazurin["Resazurin"]
    CultureMech_002642 --> ing6_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing6_Resazurin -.-> CHEBI_8806
    ing7_Sodium_pyruvate["Sodium pyruvate"]
    CultureMech_002642 --> ing7_Sodium_pyruvate
    CHEBI_50144["CHEBI:50144"]
    ing7_Sodium_pyruvate -.-> CHEBI_50144
    ing8_Biotin["Biotin"]
    CultureMech_002642 --> ing8_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing8_Biotin -.-> CHEBI_15956
    ing9_Folic_acid["Folic acid"]
    CultureMech_002642 --> ing9_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing9_Folic_acid -.-> CHEBI_27470
    ing10_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_002642 --> ing10_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing10_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing11_Thiamine_HCl["Thiamine HCl"]
    CultureMech_002642 --> ing11_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing11_Thiamine_HCl -.-> CHEBI_49105
    ing12_Riboflavin["Riboflavin"]
    CultureMech_002642 --> ing12_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing12_Riboflavin -.-> CHEBI_17015
    ing13_Nicotinic_acid["Nicotinic acid"]
    CultureMech_002642 --> ing13_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing13_Nicotinic_acid -.-> CHEBI_15940
    ing14_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
    CultureMech_002642 --> ing14_DL_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing14_DL_Calcium_pantothenate -.-> CHEBI_31345
    ing15_Vitamin_B12["Vitamin B12"]
    CultureMech_002642 --> ing15_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing15_Vitamin_B12 -.-> CHEBI_176843
    ing16_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_002642 --> ing16_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing16_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing17_Lipoic_acid["Lipoic acid"]
    CultureMech_002642 --> ing17_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing17_Lipoic_acid -.-> CHEBI_16494
    ing18_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_002642 --> ing18_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing18_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing19_FeCl3_x_6_H2O["FeCl3 x 6 H2O"]
    CultureMech_002642 --> ing19_FeCl3_x_6_H2O
    CHEBI_86254["CHEBI:86254"]
    ing19_FeCl3_x_6_H2O -.-> CHEBI_86254
    ing20_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_002642 --> ing20_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing20_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing21_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_002642 --> ing21_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing21_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing22_ZnCl2["ZnCl2"]
    CultureMech_002642 --> ing22_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing22_ZnCl2 -.-> CHEBI_49976
    ing23_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_002642 --> ing23_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing23_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing24_H3BO3["H3BO3"]
    CultureMech_002642 --> ing24_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing24_H3BO3 -.-> CHEBI_33118
    ing25_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_002642 --> ing25_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing25_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing26_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_002642 --> ing26_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing26_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing27_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
    CultureMech_002642 --> ing27_Na2SeO3_x_5_H2O
    CHEBI_131361["CHEBI:131361"]
    ing27_Na2SeO3_x_5_H2O -.-> CHEBI_131361
    ing28_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
    CultureMech_002642 --> ing28_Na2WO4_x_2_H2O
    CHEBI_63939["CHEBI:63939"]
    ing28_Na2WO4_x_2_H2O -.-> CHEBI_63939

Ingredients (29)

# Ingredient Concentration Ontology Notes
1 Yeast extract 0.110619 G_PER_L
2 KH2PO4
H2O4P.K 136.084 g/mol
0.154867 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
3 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
0.221239 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
4 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.26592899999999997 G_PER_L CHEBI:86158
calcium chloride dihydrate
 [Merged 2 duplicates: 0.165929, 0.1]
5 NH4Cl
Cl.H4N 53.492 g/mol
0.597345 G_PER_L CHEBI:31206
ammonium chloride
6 NaHCO3
CHO3.Na 84.006 g/mol
2.76549 G_PER_L CHEBI:32139
sodium hydrogencarbonate
7 Resazurin
C12H7NO4 229.191 g/mol
0.00110619 G_PER_L CHEBI:8806
Resazurin
8 Sodium pyruvate
C3H3O3.Na 110.044 g/mol
22 G_PER_L CHEBI:50144
sodium pyruvate
9 Biotin
C10H16N2O3S 244.316 g/mol
0.0049 G_PER_L CHEBI:15956
biotin
10 Folic acid
C19H19N7O6 441.404 g/mol
0.0088 G_PER_L CHEBI:27470
folic acid
11 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.0041 G_PER_L CHEBI:30961
pyridoxine hydrochloride
12 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.0067 G_PER_L CHEBI:49105
thiamine hydrochloride
13 Riboflavin
C17H20N4O6 376.369 g/mol
0.0075 G_PER_L CHEBI:17015
riboflavin
14 Nicotinic acid
C6H5NO2 123.111 g/mol
0.0025 G_PER_L CHEBI:15940
nicotinic acid
15 DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.0095 G_PER_L CHEBI:31345
Calcium pantothenate
16 Vitamin B12 0.0271 G_PER_L CHEBI:176843
vitamin B12
17 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.0027 G_PER_L CHEBI:30753
4-aminobenzoic acid
18 Lipoic acid
C8H14O2S2 206.332 g/mol
0.0041 G_PER_L CHEBI:16494
lipoic acid
19 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
12.8 G_PER_L CHEBI:44557
nitrilotriacetic acid
20 FeCl3 x 6 H2O
Cl3Fe.6H2O 270.294 g/mol
1.35 G_PER_L CHEBI:86254
iron trichloride hexahydrate
21 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
0.1 G_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
22 CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
0.024 G_PER_L CHEBI:53503
cobalt chloride hexahydrate
23 ZnCl2
2Cl.Zn 136.296 g/mol
0.1 G_PER_L CHEBI:49976
zinc dichloride
24 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.025 G_PER_L CHEBI:86318
copper(II) chloride dihydrate
25 H3BO3
H3BO3 61.833 g/mol
0.01 G_PER_L CHEBI:33118
boric acid
26 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.024 G_PER_L CHEBI:75213
sodium molybdate dihydrate
27 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.12 G_PER_L CHEBI:34887
nickel dichloride
28 Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
0.004 G_PER_L CHEBI:131361
disodium selenite pentahydrate
29 Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
0.004 G_PER_L CHEBI:63939
sodium tungstate dihydrate

Preparation

  1. Mix components except NaHCO3 and adjust pH to 6.5. Bring to a boil for 5-10 sec, then, cool down under a stream of N2-CO2 (80:20, v/v) and add NaHCO3 to the solution. Dispense 0.9 volume of the medium into culture vessels (e.g., 18 ml of the medium in 50 ml serum bottle) under a stream of N2-CO2 (80:20, v/v) and seal with butyl rubber stoppers. After autoclaving, stand the medium overnight.
  2. Adjust pH to 7.0 and filter-sterilize. Keep the solution under a N2 atmosphere.
  3. To complete the medium, add 0.1 volume of Solution B to the culture vessels containing Solution A. Prior to inoculation, aseptically and anaerobically add 0.01 volume of L-cysteine x HCl x H2O and Na2S x 9H2O solutions to the medium (3% solutions, autoclaved and stored under a N2 atmosphere).
  4. Comment: For strain JCM 10971, incubate with a 10% inoculum.
  5. Dissolve nitrilotriacetic acid first in 200 ml of distilled water and adjust pH to 6.5 with KOH. Then add the remaining salts and bring volume to 1.0 L. Readjust pH to 7.0 with KOH.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:16.176395Z mediadive-import Imported from MediaDive Source: JCM, ID: J284
2026-03-13T03:09:26.490420Z data-quality-cleanup-v1.0 Data quality fixes Merged 1 duplicate ingredient(s)
2026-03-13T06:19:14.731851Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002642
2026-03-17T06:30:35.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:28.029713+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "SI MEDIUM" to "si_medium" for consistent matching
2026-06-05T07:41:45.845816+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.
2026-06-10T07:47:11.487784+00:00 primary-term-label-canonicalization-v1.0 Canonicalized primary term label to OBO canonical (OAK) 3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.