Overview
- External ontology
- TOGO:M1908 — Methanococcoides medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1908 Original source: NBRC - NBRC_M1168 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=1168
Composition
flowchart LR
CultureMech_008485["methanococcoides_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008485 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_008485 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_NaCl["NaCl"]
CultureMech_008485 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008485 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_NH4Cl["NH4Cl"]
CultureMech_008485 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_K2HPO4["K2HPO4"]
CultureMech_008485 --> ing5_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing5_K2HPO4 -.-> CHEBI_131527
ing6_Resazurin["Resazurin"]
CultureMech_008485 --> ing6_Resazurin
CHEBI_8806["CHEBI:8806"]
ing6_Resazurin -.-> CHEBI_8806
ing7_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_008485 --> ing7_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing7_MgCl2_6H2O -.-> CHEBI_86345
ing8_Na2S_9H2O["Na2S·9H2O"]
CultureMech_008485 --> ing8_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing8_Na2S_9H2O -.-> CHEBI_76209
ing9_KCl["KCl"]
CultureMech_008485 --> ing9_KCl
CHEBI_32588["CHEBI:32588"]
ing9_KCl -.-> CHEBI_32588
ing10_NaHCO3["NaHCO3"]
CultureMech_008485 --> ing10_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing10_NaHCO3 -.-> CHEBI_32139
ing11_Sodium_acetate["Sodium acetate"]
CultureMech_008485 --> ing11_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing11_Sodium_acetate -.-> CHEBI_32954
ing12_Trimethylamine_HCl["Trimethylamine-HCl"]
CultureMech_008485 --> ing12_Trimethylamine_HCl
CHEBI_64700["CHEBI:64700"]
ing12_Trimethylamine_HCl -.-> CHEBI_64700
ing13_Fe_NH4_2_SO4_2_7H2O["Fe(NH4)2(SO4)2·7H2O"]
CultureMech_008485 --> ing13_Fe_NH4_2_SO4_2_7H2O
CHEBI_131378["CHEBI:131378"]
ing13_Fe_NH4_2_SO4_2_7H2O -.-> CHEBI_131378
ing14_Bacto_Yeast_Extract__Difco_["Bacto Yeast Extract (Difco)"]
CultureMech_008485 --> ing14_Bacto_Yeast_Extract__Difco_
ing15_Cysteine_HCl["Cysteine-HCl"]
CultureMech_008485 --> ing15_Cysteine_HCl
CHEBI_91247["CHEBI:91247"]
ing15_Cysteine_HCl -.-> CHEBI_91247
ing16_Polypeptone["Polypeptone"]
CultureMech_008485 --> ing16_Polypeptone
ing17_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008485 --> ing17_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing17_Carbon_dioxide_gas -.-> CHEBI_16526
ing18_Nitrogen_gas["Nitrogen gas"]
CultureMech_008485 --> ing18_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing18_Nitrogen_gas -.-> CHEBI_17997
ing19_Biotin["Biotin"]
CultureMech_008485 --> ing19_Biotin
CHEBI_15956["CHEBI:15956"]
ing19_Biotin -.-> CHEBI_15956
ing20_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_008485 --> ing20_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing20_p_Aminobenzoic_acid -.-> CHEBI_30753
ing21_Thiamine_HCl["Thiamine-HCl"]
CultureMech_008485 --> ing21_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing21_Thiamine_HCl -.-> CHEBI_49105
ing22_Ca_pantothenate["Ca-pantothenate"]
CultureMech_008485 --> ing22_Ca_pantothenate
CHEBI_29032["CHEBI:29032"]
ing22_Ca_pantothenate -.-> CHEBI_29032
ing23_Pyridoxine_HCl["Pyridoxine-HCl"]
CultureMech_008485 --> ing23_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing23_Pyridoxine_HCl -.-> CHEBI_30961
ing24_Folic_acid["Folic acid"]
CultureMech_008485 --> ing24_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing24_Folic_acid -.-> CHEBI_27470
ing25_Vitamin_B12["Vitamin B12"]
CultureMech_008485 --> ing25_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing25_Vitamin_B12 -.-> CHEBI_176843
ing26_Riboflavin["Riboflavin"]
CultureMech_008485 --> ing26_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing26_Riboflavin -.-> CHEBI_17015
ing27_Nicotinic_acid["Nicotinic acid"]
CultureMech_008485 --> ing27_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing27_Nicotinic_acid -.-> CHEBI_15940
ing28_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008485 --> ing28_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing28_Na2MoO4_2H2O -.-> CHEBI_75213
ing29_H3BO3["H3BO3"]
CultureMech_008485 --> ing29_H3BO3
CHEBI_33118["CHEBI:33118"]
ing29_H3BO3 -.-> CHEBI_33118
CultureMech_008485 --> more["...11 more"]
Ingredients (41)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 3 identical duplicates: 1.0, 1.0, 1.0] |
| 2 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
3.45 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
NaCl
Cl.Na 58.443 g/mol
|
19.0 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 18.0, 1.0] |
| 4 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.24000000000000002 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.14, 0.1] |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.24 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.14 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
Resazurin
C12H7NO4 229.191 g/mol
|
1 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 8 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
4 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Na2S·9H2O
9H2O.2Na.S 240.182 g/mol
|
0.5 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
KCl
Cl.K 74.551 g/mol
|
0.335 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
NaHCO3
CHO3.Na 84.006 g/mol
|
5 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
1 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 13 |
Trimethylamine-HCl
C3H9N.HCl 95.573 g/mol
|
3 G_PER_L |
CHEBI:64700
trimethylamine hydrochloride
|
Role: Nutrient source; Properties: Organic compound, Defined component, Simple component |
| 14 |
Fe(NH4)2(SO4)2·7H2O
Fe.7H2O.2H4N.2O4S 410.154 g/mol
|
2 G_PER_L |
CHEBI:131378
ferrous ammonium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 | Bacto Yeast Extract (Difco) | 2 G_PER_L | Properties: Undefined component | |
| 16 |
Cysteine-HCl
C3H7NO2S.HCl 157.622 g/mol
|
0.5 G_PER_L |
CHEBI:91247
L-cysteine hydrochloride
|
Properties: Organic compound, Simple component, Defined component |
| 17 | Polypeptone | 2 G_PER_L | Properties: Undefined component | |
| 18 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 19 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 20 |
Biotin
C10H16N2O3S 244.316 g/mol
|
2 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 21 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
1 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 22 |
Thiamine-HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
5 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 23 |
Ca-pantothenate
C9H16NO5 218.229 g/mol
|
5 G_PER_L |
CHEBI:29032
(R)-pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 24 |
Pyridoxine-HCl
C8H11NO3.HCl 205.641 g/mol
|
10 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 25 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 26 | Vitamin B12 | 0.01 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 27 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 29 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.024 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 30 |
H3BO3
H3BO3 61.833 g/mol
|
0.01 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 31 |
MnCl2·4H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.1 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 32 |
CoCl2·6H2O
2Cl.Co 129.839 g/mol
|
0.024 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 33 |
NiCl2·6H2O
Cl2Ni 129.599 g/mol
|
0.12 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 34 |
CuCl2·2H2O
Cl2Cu.2H2O 170.482 g/mol
|
0.025 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 35 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
0.1 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 36 |
FeCl3·6H2O
Cl3Fe.6H2O 270.294 g/mol
|
1.35 G_PER_L |
CHEBI:86254
iron trichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 37 |
KAl(SO4)2·12H2O
Al.12H2O.K.2O4S 474.386 g/mol
|
0.02 G_PER_L |
CHEBI:86465
potassium aluminium sulfate dodecahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 38 |
Nitrilotriacetic acid (NTA)
C6H9NO6 191.139 g/mol
|
12.8 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 39 |
Na2WO4
2Na.O4W 293.816 g/mol
|
0.004 G_PER_L |
CHEBI:63940
sodium tungstate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 40 |
Na2SeO4
2Na.O4Se 188.936 g/mol
|
0.004 G_PER_L |
CHEBI:77775
sodium selenate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 41 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution |
Solutions
Vitamin solution*
Dose: 10 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Trace elements solution**
Dose: 10 G_PER_L
See mediadive_6129_Trace_elements_solution.yaml for composition
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:58.629731Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1908 |
| 2026-01-28T19:48:33.599322Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: NaOH |
| 2026-03-09T08:04:55.707832+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:27.239976Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:57.334923Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008485 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:36.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:15.945527+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methanococcoides medium" to "methanococcoides_medium" for consistent matching |
| 2026-05-16T09:03:11.733207+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:34.862860+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. |
| 2026-06-08T23:19:31.358780+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. |
| 2026-06-10T06:57:24.935388+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:46:48.380114+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. |
| 2026-09-02T07:37:26.601171+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |