Overview
- External ontology
- komodo.medium:508 (source link unavailable) — PYRODICTIUM ABYSSI medium
- Applications
-
- Microbial cultivation
- pH range
- {'min': 5.5, 'max': 6.0}
- Notes
- Source: KOMODO ModelSEED | ID: 508 | DSMZ Medium: 508 (mediadive.medium:508) | Aerobic: No
Composition
flowchart LR
CultureMech_005709["pyrodictium_abyssi_medium"]
ing0_KCl["KCl"]
CultureMech_005709 --> ing0_KCl
CHEBI_32588["CHEBI:32588"]
ing0_KCl -.-> CHEBI_32588
ing1_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
CultureMech_005709 --> ing1_MgCl2_x_6_H2O
CHEBI_86345["CHEBI:86345"]
ing1_MgCl2_x_6_H2O -.-> CHEBI_86345
ing2_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
CultureMech_005709 --> ing2_CaCl2_x_2_H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_x_2_H2O -.-> CHEBI_86158
ing3_NH4Cl["NH4Cl"]
CultureMech_005709 --> ing3_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing3_NH4Cl -.-> CHEBI_31206
ing4_KH2PO4["KH2PO4"]
CultureMech_005709 --> ing4_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing4_KH2PO4 -.-> CHEBI_63036
ing5_Sodium_resazurin["Sodium resazurin"]
CultureMech_005709 --> ing5_Sodium_resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Sodium_resazurin -.-> CHEBI_8806
ing6_Na2CO3["Na2CO3"]
CultureMech_005709 --> ing6_Na2CO3
CHEBI_29377["CHEBI:29377"]
ing6_Na2CO3 -.-> CHEBI_29377
ing7_Na_pyruvate["Na-pyruvate"]
CultureMech_005709 --> ing7_Na_pyruvate
CHEBI_50144["CHEBI:50144"]
ing7_Na_pyruvate -.-> CHEBI_50144
ing8_Yeast_extract["Yeast extract"]
CultureMech_005709 --> ing8_Yeast_extract
ing9_Na2S_x_9_H2O["Na2S x 9 H2O"]
CultureMech_005709 --> ing9_Na2S_x_9_H2O
CHEBI_76209["CHEBI:76209"]
ing9_Na2S_x_9_H2O -.-> CHEBI_76209
ing10_Na2_EDTA["Na2-EDTA"]
CultureMech_005709 --> ing10_Na2_EDTA
CHEBI_64734["CHEBI:64734"]
ing10_Na2_EDTA -.-> CHEBI_64734
ing11_FeSO4_x_7_H2O["FeSO4 x 7 H2O"]
CultureMech_005709 --> ing11_FeSO4_x_7_H2O
CHEBI_75836["CHEBI:75836"]
ing11_FeSO4_x_7_H2O -.-> CHEBI_75836
ing12_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
CultureMech_005709 --> ing12_ZnSO4_x_7_H2O
CHEBI_32312["CHEBI:32312"]
ing12_ZnSO4_x_7_H2O -.-> CHEBI_32312
ing13_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
CultureMech_005709 --> ing13_MnCl2_x_4_H2O
CHEBI_86368["CHEBI:86368"]
ing13_MnCl2_x_4_H2O -.-> CHEBI_86368
ing14_H3BO3["H3BO3"]
CultureMech_005709 --> ing14_H3BO3
CHEBI_33118["CHEBI:33118"]
ing14_H3BO3 -.-> CHEBI_33118
ing15_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
CultureMech_005709 --> ing15_CoCl2_x_6_H2O
CHEBI_53503["CHEBI:53503"]
ing15_CoCl2_x_6_H2O -.-> CHEBI_53503
ing16_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
CultureMech_005709 --> ing16_CuCl2_x_2_H2O
CHEBI_86318["CHEBI:86318"]
ing16_CuCl2_x_2_H2O -.-> CHEBI_86318
ing17_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
CultureMech_005709 --> ing17_NiCl2_x_6_H2O
CHEBI_34887["CHEBI:34887"]
ing17_NiCl2_x_6_H2O -.-> CHEBI_34887
ing18_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
CultureMech_005709 --> ing18_Na2MoO4_x_2_H2O
CHEBI_75213["CHEBI:75213"]
ing18_Na2MoO4_x_2_H2O -.-> CHEBI_75213
ing19_D_____biotin["D-(+)-biotin"]
CultureMech_005709 --> ing19_D_____biotin
CHEBI_15956["CHEBI:15956"]
ing19_D_____biotin -.-> CHEBI_15956
ing20_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_005709 --> ing20_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing20_Calcium_pantothenate -.-> CHEBI_31345
ing21_Biotin["Biotin"]
CultureMech_005709 --> ing21_Biotin
ing21_Biotin -.-> CHEBI_15956
ing22_Folic_acid["Folic acid"]
CultureMech_005709 --> ing22_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing22_Folic_acid -.-> CHEBI_27470
ing23_Thiamine_HCl["Thiamine HCl"]
CultureMech_005709 --> ing23_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing23_Thiamine_HCl -.-> CHEBI_49105
ing24_Riboflavin["Riboflavin"]
CultureMech_005709 --> ing24_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing24_Riboflavin -.-> CHEBI_17015
ing25_Calcium_D_____pantothenate["Calcium D-(+)-pantothenate"]
CultureMech_005709 --> ing25_Calcium_D_____pantothenate
ing25_Calcium_D_____pantothenate -.-> CHEBI_31345
ing26__DL__alpha_Lipoic_acid["(DL)-alpha-Lipoic acid"]
CultureMech_005709 --> ing26__DL__alpha_Lipoic_acid
CHEBI_16494["CHEBI:16494"]
ing26__DL__alpha_Lipoic_acid -.-> CHEBI_16494
Ingredients (27)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
KCl
Cl.K 74.551 g/mol
|
0.326087 G_PER_L |
CHEBI:32588
potassium chloride
|
|
| 2 |
MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.513834 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 3 |
CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.286561 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
|
| 4 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.326087 G_PER_L |
CHEBI:31206
ammonium chloride
|
|
| 5 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.326087 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 6 |
Sodium resazurin
C12H7NO4 229.191 g/mol
|
0.000494071 G_PER_L |
CHEBI:8806
Resazurin
|
|
| 7 |
Na2CO3
CO3.2Na 105.988 g/mol
|
0.988142 G_PER_L |
CHEBI:29377
sodium carbonate
|
|
| 8 |
Na-pyruvate
C3H3O3.Na 110.044 g/mol
|
2.47036 G_PER_L |
CHEBI:50144
sodium pyruvate
|
|
| 9 | Yeast extract | 0.0494071 G_PER_L | ||
| 10 |
Na2S x 9 H2O
9H2O.2Na.S 240.182 g/mol
|
0.296443 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
|
| 11 |
Na2-EDTA
C10H14N2O8.2Na 336.208 g/mol
|
0.5 G_PER_L |
CHEBI:64734
EDTA disodium salt (anhydrous)
|
|
| 12 |
FeSO4 x 7 H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.2 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
|
| 13 |
ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
|
0.1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
|
| 14 |
MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.03 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
|
| 15 |
H3BO3
H3BO3 61.833 g/mol
|
0.3 G_PER_L |
CHEBI:33118
boric acid
|
|
| 16 |
CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
|
0.2 G_PER_L |
CHEBI:53503
cobalt chloride hexahydrate
|
|
| 17 |
CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
|
0.01 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
|
| 18 |
NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
|
0.02 G_PER_L |
CHEBI:34887
nickel dichloride
|
|
| 19 |
Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.03 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
|
| 20 |
D-(+)-biotin
C10H16N2O3S 244.316 g/mol
|
0.02 G_PER_L |
CHEBI:15956
biotin
|
|
| 21 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.1 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
|
| 22 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.02 G_PER_L |
CHEBI:15956
biotin
|
|
| 23 |
Folic acid
C19H19N7O6 441.404 g/mol
|
0.02 G_PER_L |
CHEBI:27470
folic acid
|
|
| 24 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.05 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
|
| 25 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.05 G_PER_L |
CHEBI:17015
riboflavin
|
|
| 26 |
Calcium D-(+)-pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.05 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
|
| 27 |
(DL)-alpha-Lipoic acid
C8H14O2S2 206.332 g/mol
|
0.05 G_PER_L |
CHEBI:16494
lipoic acid
|
Solutions
Seven vitamins solution
Dose: 1 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Thiamine-HCl x 2 H2O | 0.2 G_PER_L | |
| Nicotinic acid | 0.2 G_PER_L | [Merged 2 duplicates: 0.2, 0.05] |
| p-Aminobenzoic acid | 0.08 G_PER_L | [Merged 2 duplicates: 0.08, 0.05] |
| Pyridoxine hydrochloride | 0.3 G_PER_L | [Merged 2 duplicates: 0.3, 0.1] |
| Vitamin B12 | 0.1 G_PER_L | [Merged 2 duplicates: 0.1, 0.001] |
Wolin's vitamin solution (10x)
Dose: 1 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Nicotinic acid | 0.05 G_PER_L | [Merged 2 duplicates: 0.2, 0.05] |
| p-Aminobenzoic acid | 0.05 G_PER_L | [Merged 2 duplicates: 0.08, 0.05] |
| Pyridoxine hydrochloride | 0.1 G_PER_L | [Merged 2 duplicates: 0.3, 0.1] |
| Vitamin B12 | 0.001 G_PER_L | [Merged 2 duplicates: 0.1, 0.001] |
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T01:15:02.fZ | komodo-web-import | Imported from KOMODO web table | Source: KOMODO, ID: 508 |
| 2026-02-03T11:18:54.985208 | dsmz-resolver-v1.0 | Enriched with DSMZ composition | Copied ingredients from DSMZ Medium 508 |
| 2026-02-06T05:10:13.193075Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T03:08:39.506040Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:35.628676Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:005709 |
| 2026-03-17T06:29:41.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:45:52.063906+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "PYRODICTIUM ABYSSI medium" to "pyrodictium_abyssi_medium" for consistent matching |
| 2026-05-20T06:02:03.506642+00:00 | migrate_ph_range.py | MIGRATED_PH_RANGE | ph_range '5.5-6.0' -> {'min': 5.5, 'max': 6.0} |
| 2026-06-05T07:41:43.361830+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 29 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:47:10.688908+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 5 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-15T00:17:28.251306+00:00 | apply_cocktail_nesting.py | NESTED_FLATTENED_COCKTAIL | Moved 5 stock-strength component(s) out of ingredients into 2 solution(s): 1 -> 'Seven vitamins solution' @ 1 ml/l; 0 -> "Wolin's vitamin solution (10x)" @ 1 ml/l. 4 component(s) were SUMMED across stocks by the flattening and are restored to each stock's own value, verified by exact sum: nicotinic acid, p-aminobenzoic acid, pyridoxine hydrochloride, vitamin b12. Each moved component matched the MediaDive stock by name AND value; bulk ingredients sharing a name were left in place (#150). |
| 2026-08-15T05:34:42.277319+00:00 | promote_komodo_volume_candidates.py | ASSERTED_VOLUME_FROM_COMPOSITION_MATCH | This record reproduces MediaDive medium 508 ('CARBOXYDOTHERMUS MEDIUM (HETEROTROPH)') across 32 shared compounds at 100% identical values. That identifies the medium despite the name difference, so its stated addition volume is now asserted rather than proposed (#262). |