Overview
- External ontology
- mediadive.medium:J513 (source link unavailable) — CALDOCOCCUS MEDIUM
- Applications
-
- Microbial cultivation
- pH
- 2.7
- Notes
- Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=513
Composition
flowchart LR
CultureMech_002864["caldococcus_medium"]
ing0_NaCl["NaCl"]
CultureMech_002864 --> ing0_NaCl
CHEBI_26710["CHEBI:26710"]
ing0_NaCl -.-> CHEBI_26710
ing1_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_002864 --> ing1_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing1_CaCl2_x_2_H2O -.-> CHEBI_86158
ing2_FeSO4_x_7_H2O["FeSO4 x 7 H2O"]
CultureMech_002864 --> ing2_FeSO4_x_7_H2O
CHEBI_75836["CHEBI:75836"]
ing2_FeSO4_x_7_H2O -.-> CHEBI_75836
ing3_Yeast_extract["Yeast extract"]
CultureMech_002864 --> ing3_Yeast_extract
ing4_Casamino_acids["Casamino acids"]
CultureMech_002864 --> ing4_Casamino_acids
ing5_Peptone["Peptone"]
CultureMech_002864 --> ing5_Peptone
ing6_Sulfur["Sulfur"]
CultureMech_002864 --> ing6_Sulfur
CHEBI_26833["CHEBI:26833"]
ing6_Sulfur -.-> CHEBI_26833
ing7_Resazurin["Resazurin"]
CultureMech_002864 --> ing7_Resazurin
CHEBI_8806["CHEBI:8806"]
ing7_Resazurin -.-> CHEBI_8806
ing8_Na2S_x_9_H2O["Na2S x 9 H2O"]
CultureMech_002864 --> ing8_Na2S_x_9_H2O
CHEBI_76209["CHEBI:76209"]
ing8_Na2S_x_9_H2O -.-> CHEBI_76209
ing9_MnSO4_x_n_H2O["MnSO4 x n H2O"]
CultureMech_002864 --> ing9_MnSO4_x_n_H2O
CHEBI_86360["CHEBI:86360"]
ing9_MnSO4_x_n_H2O -.-> CHEBI_86360
ing10_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
CultureMech_002864 --> ing10_CoSO4_x_7_H2O
CHEBI_91244["CHEBI:91244"]
ing10_CoSO4_x_7_H2O -.-> CHEBI_91244
ing11_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
CultureMech_002864 --> ing11_ZnSO4_x_7_H2O
CHEBI_32312["CHEBI:32312"]
ing11_ZnSO4_x_7_H2O -.-> CHEBI_32312
ing12_CuSO4_x_5_H2O["CuSO4 x 5 H2O"]
CultureMech_002864 --> ing12_CuSO4_x_5_H2O
CHEBI_31440["CHEBI:31440"]
ing12_CuSO4_x_5_H2O -.-> CHEBI_31440
ing13_H3BO3["H3BO3"]
CultureMech_002864 --> ing13_H3BO3
CHEBI_33118["CHEBI:33118"]
ing13_H3BO3 -.-> CHEBI_33118
ing14_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
CultureMech_002864 --> ing14_Na2MoO4_x_2_H2O
CHEBI_75213["CHEBI:75213"]
ing14_Na2MoO4_x_2_H2O -.-> CHEBI_75213
ing15_Biotin["Biotin"]
CultureMech_002864 --> ing15_Biotin
CHEBI_15956["CHEBI:15956"]
ing15_Biotin -.-> CHEBI_15956
ing16_Folic_acid["Folic acid"]
CultureMech_002864 --> ing16_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing16_Folic_acid -.-> CHEBI_27470
ing17_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
CultureMech_002864 --> ing17_Pyridoxine_hydrochloride
CHEBI_30961["CHEBI:30961"]
ing17_Pyridoxine_hydrochloride -.-> CHEBI_30961
ing18_Thiamine_HCl["Thiamine HCl"]
CultureMech_002864 --> ing18_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing18_Thiamine_HCl -.-> CHEBI_49105
ing19_Riboflavin["Riboflavin"]
CultureMech_002864 --> ing19_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing19_Riboflavin -.-> CHEBI_17015
ing20_Nicotinic_acid["Nicotinic acid"]
CultureMech_002864 --> ing20_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing20_Nicotinic_acid -.-> CHEBI_15940
ing21_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_002864 --> ing21_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing21_Calcium_pantothenate -.-> CHEBI_31345
ing22_Vitamin_B12["Vitamin B12"]
CultureMech_002864 --> ing22_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing22_Vitamin_B12 -.-> CHEBI_176843
ing23_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_002864 --> ing23_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing23_p_Aminobenzoic_acid -.-> CHEBI_30753
ing24_Lipoic_acid["Lipoic acid"]
CultureMech_002864 --> ing24_Lipoic_acid
CHEBI_16494["CHEBI:16494"]
ing24_Lipoic_acid -.-> CHEBI_16494
Ingredients (25)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
NaCl
Cl.Na 58.443 g/mol
|
0.098912 G_PER_L |
CHEBI:26710
sodium chloride
|
|
| 2 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.098912 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
|
| 3 |
FeSO4 x 7 H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.049456 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
|
| 4 | Yeast extract | 0.098912 G_PER_L | ||
| 5 | Casamino acids | 0.098912 G_PER_L | ||
| 6 | Peptone | 0.791296 G_PER_L | ||
| 7 |
Sulfur
S 32.067 g/mol
|
1.97824 G_PER_L |
CHEBI:26833
sulfur atom
|
|
| 8 |
Resazurin
C12H7NO4 229.191 g/mol
|
0.00098912 G_PER_L |
CHEBI:8806
Resazurin
|
|
| 9 |
Na2S x 9 H2O
9H2O.2Na.S 240.182 g/mol
|
0.49456 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
|
| 10 |
MnSO4 x n H2O
Mn.O4S 151.001 g/mol
|
5 G_PER_L |
CHEBI:86360
manganese(II) sulfate
|
|
| 11 |
CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
|
1 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
|
| 12 |
ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
|
1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
|
| 13 |
CuSO4 x 5 H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.1 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
|
| 14 |
H3BO3
H3BO3 61.833 g/mol
|
0.1 G_PER_L |
CHEBI:33118
boric acid
|
|
| 15 |
Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.1 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
|
| 16 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.002 G_PER_L |
CHEBI:15956
biotin
|
|
| 17 |
Folic acid
C19H19N7O6 441.404 g/mol
|
0.002 G_PER_L |
CHEBI:27470
folic acid
|
|
| 18 |
Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
|
0.01 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 19 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.005 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
|
| 20 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.005 G_PER_L |
CHEBI:17015
riboflavin
|
|
| 21 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
0.005 G_PER_L |
CHEBI:15940
nicotinic acid
|
|
| 22 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.005 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
|
| 23 | Vitamin B12 | 0.0001 G_PER_L |
CHEBI:176843
vitamin B12
|
|
| 24 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
0.005 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
|
| 25 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
0.005 G_PER_L |
CHEBI:16494
lipoic acid
|
Preparation
- Mix ingredients except vitamins, sulfur and Na2S x 9H2O, adjust pH to 2.7 with H2SO4 and autoclave. Separately autoclave 5% (w/v) Na2S x 9H2O solution under a N2 atmosphere. Steam sulfur for 3 hr on each of 3 successive days. Filter-sterilize Trace vitamins solution. Distribute the medium into culture vessels (e.g., 20 ml per 100 ml serum bottles) containing Trace vitamins and sulfur, replace the gas phase with a H2-CO2 (80:20) gas atmosphere and seal with butyl rubber stoppers. Prior to inoculation, add sterile Na2S x 9H2O solution and adjust pH to 3.0 with sterile 1 N H2SO4. Pressurize the inoculated bottle to 200 kPa H2-CO2 (80:20).
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- caldococcus_medium (CultureMech:002864)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-26T17:53:16.805699Z | mediadive-import | Imported from MediaDive | Source: JCM, ID: J513 |
| 2026-01-28T19:48:13.245709Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-03-13T06:19:16.177462Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:002864 |
| 2026-03-17T06:29:53.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:45:29.688775+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "CALDOCOCCUS MEDIUM" to "caldococcus_medium" for consistent matching |
| 2026-06-05T07:40:52.308063+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 22 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:36.120373+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 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). |
| 2026-06-10T07:46:54.228530+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-06T03:04:28.426345+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint ec9b2b10a5a58bb37738b997b1c9dc715d24bc047d628e4078ec708faf4c5b91 |