methanocaldococcus_leighii_medium

CultureMech:002380 archaea DEFINED LIQUID
Original name: METHANOCALDOCOCCUS LEIGHII MEDIUM

Overview

External ontology
mediadive.medium:J1211 (source link unavailable) — METHANOCALDOCOCCUS LEIGHII MEDIUM
Applications
  • Microbial cultivation
pH
6.5
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1211

Composition

flowchart LR
    CultureMech_002380["methanocaldococcus_leighii_medium"]
    ing0_NaCl["NaCl"]
    CultureMech_002380 --> ing0_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing0_NaCl -.-> CHEBI_26710
    ing1_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002380 --> ing1_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing1_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing2_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_002380 --> ing2_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing2_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing3_NH4Cl["NH4Cl"]
    CultureMech_002380 --> ing3_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing3_NH4Cl -.-> CHEBI_31206
    ing4_KCl["KCl"]
    CultureMech_002380 --> ing4_KCl
    CHEBI_32588["CHEBI:32588"]
    ing4_KCl -.-> CHEBI_32588
    ing5_K2HPO4["K2HPO4"]
    CultureMech_002380 --> ing5_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing5_K2HPO4 -.-> CHEBI_131527
    ing6_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_002380 --> ing6_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing6_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing7_FeSO4_x_7_H2O["FeSO4 x 7 H2O"]
    CultureMech_002380 --> ing7_FeSO4_x_7_H2O
    CHEBI_75836["CHEBI:75836"]
    ing7_FeSO4_x_7_H2O -.-> CHEBI_75836
    ing8_Sodium_acetate_x_3_H2O["Sodium acetate x 3 H2O"]
    CultureMech_002380 --> ing8_Sodium_acetate_x_3_H2O
    CHEBI_32954["CHEBI:32954"]
    ing8_Sodium_acetate_x_3_H2O -.-> CHEBI_32954
    ing9_PIPES["PIPES"]
    CultureMech_002380 --> ing9_PIPES
    CHEBI_39033["CHEBI:39033"]
    ing9_PIPES -.-> CHEBI_39033
    ing10_NaHCO3["NaHCO3"]
    CultureMech_002380 --> ing10_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing10_NaHCO3 -.-> CHEBI_32139
    ing11_Resazurin["Resazurin"]
    CultureMech_002380 --> ing11_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing11_Resazurin -.-> CHEBI_8806
    ing12_Na2S_x_9_H2O["Na2S x 9 H2O"]
    CultureMech_002380 --> ing12_Na2S_x_9_H2O
    CHEBI_76209["CHEBI:76209"]
    ing12_Na2S_x_9_H2O -.-> CHEBI_76209
    ing13_Trisodium_citrate_x_2_H2O["Trisodium citrate x 2 H2O"]
    CultureMech_002380 --> ing13_Trisodium_citrate_x_2_H2O
    CHEBI_53258["CHEBI:53258"]
    ing13_Trisodium_citrate_x_2_H2O -.-> CHEBI_53258
    ing14_MnSO4_x_n_H2O["MnSO4 x n H2O"]
    CultureMech_002380 --> ing14_MnSO4_x_n_H2O
    CHEBI_86360["CHEBI:86360"]
    ing14_MnSO4_x_n_H2O -.-> CHEBI_86360
    ing15_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
    CultureMech_002380 --> ing15_CoSO4_x_7_H2O
    CHEBI_91244["CHEBI:91244"]
    ing15_CoSO4_x_7_H2O -.-> CHEBI_91244
    ing16_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
    CultureMech_002380 --> ing16_ZnSO4_x_7_H2O
    CHEBI_32312["CHEBI:32312"]
    ing16_ZnSO4_x_7_H2O -.-> CHEBI_32312
    ing17_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_002380 --> ing17_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing17_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing18_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_002380 --> ing18_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing18_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing19_Na2SeO3["Na2SeO3"]
    CultureMech_002380 --> ing19_Na2SeO3
    CHEBI_48843["CHEBI:48843"]
    ing19_Na2SeO3 -.-> CHEBI_48843
    ing20_CuSO4_x_5_H2O["CuSO4 x 5 H2O"]
    CultureMech_002380 --> ing20_CuSO4_x_5_H2O
    CHEBI_31440["CHEBI:31440"]
    ing20_CuSO4_x_5_H2O -.-> CHEBI_31440
    ing21_AlK_SO4_2["AlK(SO4)2"]
    CultureMech_002380 --> ing21_AlK_SO4_2
    CHEBI_86463["CHEBI:86463"]
    ing21_AlK_SO4_2 -.-> CHEBI_86463
    ing22_H3BO3["H3BO3"]
    CultureMech_002380 --> ing22_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing22_H3BO3 -.-> CHEBI_33118
    ing23_VOSO4_x_n_H2O["VOSO4 x n H2O"]
    CultureMech_002380 --> ing23_VOSO4_x_n_H2O
    CHEBI_87020["CHEBI:87020"]
    ing23_VOSO4_x_n_H2O -.-> CHEBI_87020
    ing24_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
    CultureMech_002380 --> ing24_Na2WO4_x_2_H2O
    CHEBI_63939["CHEBI:63939"]
    ing24_Na2WO4_x_2_H2O -.-> CHEBI_63939
    ing25_Biotin["Biotin"]
    CultureMech_002380 --> ing25_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing25_Biotin -.-> CHEBI_15956
    ing26_Folic_acid["Folic acid"]
    CultureMech_002380 --> ing26_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing26_Folic_acid -.-> CHEBI_27470
    ing27_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_002380 --> ing27_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing27_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing28_Thiamine_HCl["Thiamine HCl"]
    CultureMech_002380 --> ing28_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing28_Thiamine_HCl -.-> CHEBI_49105
    ing29_Riboflavin["Riboflavin"]
    CultureMech_002380 --> ing29_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing29_Riboflavin -.-> CHEBI_17015
    CultureMech_002380 --> more["...5 more"]

Ingredients (35)

# Ingredient Concentration Ontology Notes
1 NaCl
Cl.Na 58.443 g/mol
10.8374 G_PER_L CHEBI:26710
sodium chloride
2 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
1.33005 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
3 MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
3.15271 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 [Merged 2 duplicates: 1.67488, 1.47783]
4 NH4Cl
Cl.H4N 53.492 g/mol
0.246305 G_PER_L CHEBI:31206
ammonium chloride
5 KCl
Cl.K 74.551 g/mol
0.162562 G_PER_L CHEBI:32588
potassium chloride
6 K2HPO4
HO4P.2K 174.174 g/mol
0.0689655 G_PER_L CHEBI:131527
dipotassium hydrogen phosphate
7 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.0689655 G_PER_L CHEBI:86158
calcium chloride dihydrate
8 FeSO4 x 7 H2O
Fe.7H2O.O4S 278.013 g/mol
0.0046798 G_PER_L CHEBI:75836
iron(2+) sulfate heptahydrate
9 Sodium acetate x 3 H2O
C2H3O2.Na 82.034 g/mol
0.689655 G_PER_L CHEBI:32954
sodium acetate
10 PIPES 7.44828 G_PER_L CHEBI:39033
PIPES
11 NaHCO3
CHO3.Na 84.006 g/mol
0.492611 G_PER_L CHEBI:32139
sodium hydrogencarbonate
12 Resazurin
C12H7NO4 229.191 g/mol
0.000492611 G_PER_L CHEBI:8806
Resazurin
13 Na2S x 9 H2O
9H2O.2Na.S 240.182 g/mol
10 G_PER_L CHEBI:76209
sodium sulfide nonahydrate
14 Trisodium citrate x 2 H2O
C6H5O7.3Na 258.069 g/mol
1.03448 G_PER_L CHEBI:53258
sodium citrate
15 MnSO4 x n H2O
Mn.O4S 151.001 g/mol
0.246305 G_PER_L CHEBI:86360
manganese(II) sulfate
16 CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
0.0492611 G_PER_L CHEBI:91244
cobalt(2+) sulfate heptahydrate
17 ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
0.0492611 G_PER_L CHEBI:32312
zinc sulfate heptahydrate
18 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.0492611 G_PER_L CHEBI:75213
sodium molybdate dihydrate
19 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.0123153 G_PER_L CHEBI:34887
nickel dichloride
20 Na2SeO3
2Na.O3Se 172.937 g/mol
0.00985222 G_PER_L CHEBI:48843
disodium selenite
21 CuSO4 x 5 H2O
Cu.5H2O.O4S 249.684 g/mol
0.00492611 G_PER_L CHEBI:31440
copper(II) sulfate pentahydrate
22 AlK(SO4)2
Al.K.2O4S 258.206 g/mol
0.00492611 G_PER_L CHEBI:86463
potassium aluminium sulfate
23 H3BO3
H3BO3 61.833 g/mol
0.00492611 G_PER_L CHEBI:33118
boric acid
24 VOSO4 x n H2O
(H2O)n.O5SV 181.021 g/mol
0.00492611 G_PER_L CHEBI:87020
vanadyl sulfate hydrate
25 Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
0.00162562 G_PER_L CHEBI:63939
sodium tungstate dihydrate
26 Biotin
C10H16N2O3S 244.316 g/mol
0.002 G_PER_L CHEBI:15956
biotin
27 Folic acid
C19H19N7O6 441.404 g/mol
0.002 G_PER_L CHEBI:27470
folic acid
28 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.01 G_PER_L CHEBI:30961
pyridoxine hydrochloride
29 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.005 G_PER_L CHEBI:49105
thiamine hydrochloride
30 Riboflavin
C17H20N4O6 376.369 g/mol
0.005 G_PER_L CHEBI:17015
riboflavin
31 Nicotinic acid
C6H5NO2 123.111 g/mol
0.005 G_PER_L CHEBI:15940
nicotinic acid
32 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.005 G_PER_L CHEBI:31345
Calcium pantothenate
33 Vitamin B12 0.0001 G_PER_L CHEBI:176843
vitamin B12
34 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.005 G_PER_L CHEBI:30753
4-aminobenzoic acid
35 Lipoic acid
C8H14O2S2 206.332 g/mol
0.005 G_PER_L CHEBI:16494
lipoic acid

Preparation

  1. Mix components, except NaHCO3, and adjust pH to 6.0. Bring to a boil for 5-10 sec, cool down under a stream of H2-CO2 (80:20, v/v) and add NaHCO3 to the medium. Dispense the medium into suitable culture vessels (e.g., 5 ml in Balch type tubes) under the same gas mixture, seal with butyl rubber stoppers and autoclave. After cooling, add per liter the following solution (autoclaved and stored under N2):
  2. Pressurize the inoculated vessels to 200 kPa H2-CO2 (80:20, v/v).
  3. Comment: For growth by nitrogen-fixation, remove NH4Cl from the medium and cultivate under a H2-N2-CO2 (60:20:20, v/v/v, 200 kPa) gas mixture.
  4. Trace mineral solution:
  5. Dissolve trisodium citrate and adjust pH to 6.5. Then proceed to add minerals.

Solutions

Trace mineral solution

Dose: 10 G_PER_L

See mediadive_5445_Trace_mineral_solution.yaml for composition

Target organisms

No target organisms are recorded.

Provenance

Merged from 1 source record.

TimestampCuratorActionNotes
2026-01-26T17:53:19.034089Z mediadive-import Imported from MediaDive Source: JCM, ID: J1211
2026-01-28T19:48:20.703148Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-09T08:04:34.333448+00:00 solution-migrator-v1.0 Migrated solutions from ingredients to solutions array Moved 1 solution(s) from ingredients
2026-03-13T03:09:03.890101Z data-quality-cleanup-v1.0 Data quality fixes Merged 1 duplicate ingredient(s)
2026-03-13T06:19:12.864022Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002380
2026-03-14T00:00:00+00:00 schema-defaulter-v1.0 Applied schema defaults and normalizations Added default solution name
2026-03-17T06:30:09.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:25.908177+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "METHANOCALDOCOCCUS LEIGHII MEDIUM" to "methanocaldococcus_leighii_medium" for consistent matching
2026-05-16T09:04:21.598822+00:00 migrate_legacy_fields.py MIGRATED_LEGACY_FIELDS curation_history.date->timestamp=1
2026-06-05T07:41:31.065211+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 33 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:47:06.797450+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.
2026-08-06T03:04:29.937129+00:00 merge_recipes.py MERGED_RECIPES merged 1 source recipe(s) on fingerprint 0076a77f80a27631ca57cde780d5600e54a1a56a1b19c0a6c670130864caafe9