modified_am5_medium_2

CultureMech:002477 bacterial COMPLEX LIQUID
Original name: MODIFIED AM5 MEDIUM 2

Overview

External ontology
mediadive.medium:J1313 (source link unavailable) — MODIFIED AM5 MEDIUM 2
Applications
  • Microbial cultivation
pH
7.3
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1313

Composition

flowchart LR
    CultureMech_002477["modified_am5_medium_2"]
    ing0_NaCl["NaCl"]
    CultureMech_002477 --> ing0_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing0_NaCl -.-> CHEBI_26710
    ing1_KCl["KCl"]
    CultureMech_002477 --> ing1_KCl
    CHEBI_32588["CHEBI:32588"]
    ing1_KCl -.-> CHEBI_32588
    ing2_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002477 --> 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_002477 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_NH4Cl["NH4Cl"]
    CultureMech_002477 --> ing4_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing4_NH4Cl -.-> CHEBI_31206
    ing5_KH2PO4["KH2PO4"]
    CultureMech_002477 --> ing5_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing5_KH2PO4 -.-> CHEBI_63036
    ing6_L_Cysteine_HCl_x_H2O["L-Cysteine HCl x H2O"]
    CultureMech_002477 --> ing6_L_Cysteine_HCl_x_H2O
    CHEBI_91248["CHEBI:91248"]
    ing6_L_Cysteine_HCl_x_H2O -.-> CHEBI_91248
    ing7_Resazurin["Resazurin"]
    CultureMech_002477 --> ing7_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing7_Resazurin -.-> CHEBI_8806
    ing8_NaHCO3["NaHCO3"]
    CultureMech_002477 --> ing8_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing8_NaHCO3 -.-> CHEBI_32139
    ing9_Trace_vitamins__see_Medium_No__197_["Trace vitamins (see Medium No. 197)"]
    CultureMech_002477 --> ing9_Trace_vitamins__see_Medium_No__197_
    ing10_Fatty_acid_mixture__see_Medium_No__266_["Fatty acid mixture (see Medium No. 266)"]
    CultureMech_002477 --> ing10_Fatty_acid_mixture__see_Medium_No__266_
    CHEBI_35366["CHEBI:35366"]
    ing10_Fatty_acid_mixture__see_Medium_No__266_ -.-> CHEBI_35366
    ing11_Yeast_extract["Yeast extract"]
    CultureMech_002477 --> ing11_Yeast_extract
    ing12_Casamino_acids["Casamino acids"]
    CultureMech_002477 --> ing12_Casamino_acids
    ing13_Glucose["Glucose"]
    CultureMech_002477 --> ing13_Glucose
    CHEBI_17234["CHEBI:17234"]
    ing13_Glucose -.-> CHEBI_17234
    ing14_Dithiothreitol["Dithiothreitol"]
    CultureMech_002477 --> ing14_Dithiothreitol
    CHEBI_18320["CHEBI:18320"]
    ing14_Dithiothreitol -.-> CHEBI_18320
    ing15_ZnCl2["ZnCl2"]
    CultureMech_002477 --> ing15_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing15_ZnCl2 -.-> CHEBI_49976
    ing16_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_002477 --> ing16_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing16_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing17_H3BO3["H3BO3"]
    CultureMech_002477 --> ing17_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing17_H3BO3 -.-> CHEBI_33118
    ing18_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_002477 --> ing18_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing18_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing19_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_002477 --> ing19_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing19_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing20_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_002477 --> ing20_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing20_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing21_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_002477 --> ing21_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing21_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing22_HCl["HCl"]
    CultureMech_002477 --> ing22_HCl
    CHEBI_17883["CHEBI:17883"]
    ing22_HCl -.-> CHEBI_17883
    ing23_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
    CultureMech_002477 --> ing23_FeCl2_x_4_H2O
    CHEBI_86249["CHEBI:86249"]
    ing23_FeCl2_x_4_H2O -.-> CHEBI_86249
    ing24_NaOH["NaOH"]
    CultureMech_002477 --> ing24_NaOH
    CHEBI_32145["CHEBI:32145"]
    ing24_NaOH -.-> CHEBI_32145
    ing25_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
    CultureMech_002477 --> ing25_Na2SeO3_x_5_H2O
    CHEBI_131361["CHEBI:131361"]
    ing25_Na2SeO3_x_5_H2O -.-> CHEBI_131361
    ing26_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
    CultureMech_002477 --> ing26_Na2WO4_x_2_H2O
    CHEBI_63939["CHEBI:63939"]
    ing26_Na2WO4_x_2_H2O -.-> CHEBI_63939
    ing27_Phenyl_acetic_acid["Phenyl acetic acid"]
    CultureMech_002477 --> ing27_Phenyl_acetic_acid
    CHEBI_30745["CHEBI:30745"]
    ing27_Phenyl_acetic_acid -.-> CHEBI_30745
    ing28_Phenyl_propionic_acid["Phenyl propionic acid"]
    CultureMech_002477 --> ing28_Phenyl_propionic_acid
    CHEBI_28631["CHEBI:28631"]
    ing28_Phenyl_propionic_acid -.-> CHEBI_28631
    ing29_4_Hydroxyphenyl_acetic_acid["4-Hydroxyphenyl acetic acid"]
    CultureMech_002477 --> ing29_4_Hydroxyphenyl_acetic_acid
    CHEBI_18101["CHEBI:18101"]
    ing29_4_Hydroxyphenyl_acetic_acid -.-> CHEBI_18101
    CultureMech_002477 --> more["...1 more"]

Ingredients (31)

# Ingredient Concentration Ontology Notes
1 NaCl
Cl.Na 58.443 g/mol
0.998004 G_PER_L CHEBI:26710
sodium chloride
2 KCl
Cl.K 74.551 g/mol
0.499002 G_PER_L CHEBI:32588
potassium chloride
3 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
0.399202 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
4 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.0998004 G_PER_L CHEBI:86158
calcium chloride dihydrate
5 NH4Cl
Cl.H4N 53.492 g/mol
0.299401 G_PER_L CHEBI:31206
ammonium chloride
6 KH2PO4
H2O4P.K 136.084 g/mol
0.199601 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
7 L-Cysteine HCl x H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
0.199601 G_PER_L CHEBI:91248
L-cysteine hydrochloride hydrate
8 Resazurin
C12H7NO4 229.191 g/mol
0.000399202 G_PER_L CHEBI:8806
Resazurin
9 NaHCO3
CHO3.Na 84.006 g/mol
40 G_PER_L CHEBI:32139
sodium hydrogencarbonate
10 Trace vitamins (see Medium No. 197) 10 G_PER_L
11 Fatty acid mixture (see Medium No. 266)
CHO2R 45.017 g/mol
1 G_PER_L CHEBI:35366
fatty acid
12 Yeast extract 10 G_PER_L
13 Casamino acids 10 G_PER_L
14 Glucose
C6H12O6 180.156 g/mol
5 G_PER_L CHEBI:17234
glucose
15 Dithiothreitol
C4H10O2S2 154.256 g/mol
10 G_PER_L CHEBI:18320
1,4-dithiothreitol
16 ZnCl2
2Cl.Zn 136.296 g/mol
0.07 G_PER_L CHEBI:49976
zinc dichloride
17 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
0.1 G_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
18 H3BO3
H3BO3 61.833 g/mol
0.006 G_PER_L CHEBI:33118
boric acid
19 CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
0.19 G_PER_L CHEBI:53503
cobalt chloride hexahydrate
20 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.002 G_PER_L CHEBI:86318
copper(II) chloride dihydrate
21 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.024 G_PER_L CHEBI:34887
nickel dichloride
22 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.036 G_PER_L CHEBI:75213
sodium molybdate dihydrate
23 HCl
HCl 36.461 g/mol
2.5 G_PER_L CHEBI:17883
hydrogen chloride
24 FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
1.5 G_PER_L CHEBI:86249
iron dichloride tetrahydrate
25 NaOH
HO.Na 39.997 g/mol
100.4 G_PER_L CHEBI:32145
sodium hydroxide
 [Merged 2 duplicates: 0.4, 100.0]
26 Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
0.006 G_PER_L CHEBI:131361
disodium selenite pentahydrate
27 Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
0.008 G_PER_L CHEBI:63939
sodium tungstate dihydrate
28 Phenyl acetic acid
C8H8O2 136.15 g/mol
0.68 G_PER_L CHEBI:30745
phenylacetic acid
29 Phenyl propionic acid
C9H10O2 150.177 g/mol
0.75 G_PER_L CHEBI:28631
3-phenylpropionic acid
30 4-Hydroxyphenyl acetic acid
C8H8O3 152.149 g/mol
0.76 G_PER_L CHEBI:18101
4-hydroxyphenylacetic acid
31 3-Indolyl acetic acid
C10H9NO2 175.187 g/mol
0.88 G_PER_L CHEBI:16411
indole-3-acetic acid

Preparation

  1. Mix components thoroughly and autoclave under a N2-CO2 (9:1, v/v) gas mixture. After cooling, aseptically and anaerobically add the following solutions (autoclaved or *filter-sterilized):
  2. Readjust pH to 7.3, if necessary.
  3. Menadione solution:
  4. Autoclave 100 mg menadione (vitamin K3) with 100 ml 5% NaHCO3 solution. Remove insoluble residue by filtration. Store the solution under a N2-CO2 (8:2, v/v) gas mixture.
  5. Autoclave and store under a N2 atmosphere.

Solutions

Vitamin B12 solution (see Medium No. 403)

Dose: 1 G_PER_L

Menadione solution

Dose: 1 G_PER_L

See mediadive_5549_Menadione_solution.yaml for composition

Target organisms

No target organisms are recorded.

Provenance

Merged from 1 source record.

TimestampCuratorActionNotes
2026-06-14T05:58:58.561437+00:00 idnf-grounding-fix-v1.0 Fixed ID_NOT_FOUND term groundings Absent/obsolete CHEBI term ids fixed - 1 re-grounded to the correct CHEBI, 0 de-grounded (mixture or unverifiable).
2026-01-26T17:53:19.407864Z mediadive-import Imported from MediaDive Source: JCM, ID: J1313
2026-01-28T19:48:38.670783Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-09T08:05:04.746691+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 2 solution(s) from ingredients
2026-03-13T03:09:36.711530Z data-quality-cleanup-v1.0 Data quality fixes Merged 1 duplicate ingredient(s)
2026-03-13T06:19:13.658410Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002477
2026-03-14T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default solution name; Added default solution name
2026-03-17T06:30:48.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:26.802862+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "MODIFIED AM5 MEDIUM 2" to "modified_am5_medium_2" for consistent matching
2026-05-16T09:04:25.026177+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=1
2026-06-05T07:41:36.151718+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 25 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:48.696706+00:00 chebi-regrounding-v1.0 Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24) Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md.
2026-06-10T07:47:08.506353+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.
2026-08-06T03:05:47.942671+00:00 merge_recipes.py MERGED_RECIPES merged 1 source recipe(s) on fingerprint b39ba35da1d303743a7f0522a8b8f89ba0d0bc9921dcd88dc3f35c6df6e16420