Overview
- External ontology
- TOGO:M1727 — Hydrogen-oxidizing bacteria medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1727 Original source: NBRC - NBRC_M936 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=936
Composition
flowchart LR
CultureMech_008290["hydrogen_oxidizing_bacteria_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008290 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008290 --> ing1_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing1_CaCl2_2H2O -.-> CHEBI_86158
ing2_NH4Cl["NH4Cl"]
CultureMech_008290 --> ing2_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing2_NH4Cl -.-> CHEBI_31206
ing3_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_008290 --> ing3_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing3_MgCl2_6H2O -.-> CHEBI_86345
ing4_Na2CO3["Na2CO3"]
CultureMech_008290 --> ing4_Na2CO3
CHEBI_29377["CHEBI:29377"]
ing4_Na2CO3 -.-> CHEBI_29377
ing5_Na2S2O3["Na2S2O3"]
CultureMech_008290 --> ing5_Na2S2O3
CHEBI_32150["CHEBI:32150"]
ing5_Na2S2O3 -.-> CHEBI_32150
ing6_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008290 --> ing6_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing6_Carbon_dioxide_gas -.-> CHEBI_16526
ing7_N2["N2"]
CultureMech_008290 --> ing7_N2
CHEBI_17997["CHEBI:17997"]
ing7_N2 -.-> CHEBI_17997
ing8_Oxygen_gas["Oxygen gas"]
CultureMech_008290 --> ing8_Oxygen_gas
ing9_Hydrogen_gas["Hydrogen gas"]
CultureMech_008290 --> ing9_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing9_Hydrogen_gas -.-> CHEBI_18276
ing10_KH2PO4["KH2PO4"]
CultureMech_008290 --> ing10_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing10_KH2PO4 -.-> CHEBI_63036
ing11_K2HPO4["K2HPO4"]
CultureMech_008290 --> ing11_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing11_K2HPO4 -.-> CHEBI_131527
ing12_NaCl["NaCl"]
CultureMech_008290 --> ing12_NaCl
CHEBI_26710["CHEBI:26710"]
ing12_NaCl -.-> CHEBI_26710
ing13_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008290 --> ing13_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing13_Na2MoO4_2H2O -.-> CHEBI_75213
ing14_H3BO3["H3BO3"]
CultureMech_008290 --> ing14_H3BO3
CHEBI_33118["CHEBI:33118"]
ing14_H3BO3 -.-> CHEBI_33118
ing15_MnCl2_4H2O["MnCl2·4H2O"]
CultureMech_008290 --> ing15_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing15_MnCl2_4H2O -.-> CHEBI_86368
ing16_CoCl2_6H2O["CoCl2·6H2O"]
CultureMech_008290 --> ing16_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing16_CoCl2_6H2O -.-> CHEBI_35696
ing17_NiCl2_6H2O["NiCl2·6H2O"]
CultureMech_008290 --> ing17_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing17_NiCl2_6H2O -.-> CHEBI_34887
ing18_CuCl2_2H2O["CuCl2·2H2O"]
CultureMech_008290 --> ing18_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing18_CuCl2_2H2O -.-> CHEBI_86318
ing19_ZnCl2["ZnCl2"]
CultureMech_008290 --> ing19_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing19_ZnCl2 -.-> CHEBI_49976
ing20_FeCl3_6H2O["FeCl3·6H2O"]
CultureMech_008290 --> ing20_FeCl3_6H2O
CHEBI_86254["CHEBI:86254"]
ing20_FeCl3_6H2O -.-> CHEBI_86254
ing21_KAl_SO4_2_12H2O["KAl(SO4)2·12H2O"]
CultureMech_008290 --> ing21_KAl_SO4_2_12H2O
CHEBI_86465["CHEBI:86465"]
ing21_KAl_SO4_2_12H2O -.-> CHEBI_86465
ing22_Nitrilotriacetic_acid__NTA_["Nitrilotriacetic acid (NTA)"]
CultureMech_008290 --> ing22_Nitrilotriacetic_acid__NTA_
CHEBI_44557["CHEBI:44557"]
ing22_Nitrilotriacetic_acid__NTA_ -.-> CHEBI_44557
ing23_Na2WO4["Na2WO4"]
CultureMech_008290 --> ing23_Na2WO4
CHEBI_63940["CHEBI:63940"]
ing23_Na2WO4 -.-> CHEBI_63940
ing24_Na2SeO4["Na2SeO4"]
CultureMech_008290 --> ing24_Na2SeO4
CHEBI_77775["CHEBI:77775"]
ing24_Na2SeO4 -.-> CHEBI_77775
ing25_NaOH["NaOH"]
CultureMech_008290 --> ing25_NaOH
CHEBI_32145["CHEBI:32145"]
ing25_NaOH -.-> CHEBI_32145
ing26_Biotin["Biotin"]
CultureMech_008290 --> ing26_Biotin
CHEBI_15956["CHEBI:15956"]
ing26_Biotin -.-> CHEBI_15956
ing27_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_008290 --> ing27_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing27_p_Aminobenzoic_acid -.-> CHEBI_30753
ing28_Thiamine_HCl["Thiamine-HCl"]
CultureMech_008290 --> ing28_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing28_Thiamine_HCl -.-> CHEBI_49105
ing29_Ca_pantothenate["Ca-pantothenate"]
CultureMech_008290 --> ing29_Ca_pantothenate
CHEBI_29032["CHEBI:29032"]
ing29_Ca_pantothenate -.-> CHEBI_29032
CultureMech_008290 --> more["...5 more"]
Ingredients (35)
| # | 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 4 identical duplicates: 1.0, 1.0, 1.0, 1.0] |
| 2 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.25 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.15, 0.1] |
| 3 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.54 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.75 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
Na2CO3
CO3.2Na 105.988 g/mol
|
0.5 G_PER_L |
CHEBI:29377
sodium carbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
Na2S2O3
5H2O.2Na.O3S2 248.186 g/mol
|
1.6 G_PER_L |
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Defined component, Inorganic compound, Simple component |
| 7 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 8 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 9 | Oxygen gas | variable VARIABLE | Properties: Gas | |
| 10 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: Gas |
| 11 |
KH2PO4
H2O4P.K 136.084 g/mol
|
119 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
K2HPO4
HO4P.2K 174.174 g/mol
|
21 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
NaCl
Cl.Na 58.443 g/mol
|
1 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
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 |
| 15 |
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 |
| 16 |
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 |
| 17 |
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 |
| 18 |
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 |
| 19 |
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 |
| 20 |
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 |
| 21 |
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 |
| 22 |
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 |
| 23 |
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 |
| 24 |
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 |
| 25 |
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 |
| 26 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution |
| 27 |
Biotin
C10H16N2O3S 244.316 g/mol
|
2 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
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 |
| 29 |
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 |
| 30 |
Ca-pantothenate
C9H16NO5 218.229 g/mol
|
5 G_PER_L |
CHEBI:29032
(R)-pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 |
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 |
| 32 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 33 | Vitamin B12 | 0.01 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 34 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 35 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
KP buffer*
Dose: 10 G_PER_L
Trace elements solution**
Dose: 2 G_PER_L
See mediadive_6129_Trace_elements_solution.yaml for composition
Vitamin solution***
Dose: 2 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:58.236451Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1727 |
| 2026-01-28T19:48:29.568426Z | 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: N2; Added default concentration for ingredient: Oxygen gas; Added default concentration for ingredient: Hydrogen gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: NaOH |
| 2026-03-09T08:04:49.122329+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:09:20.252197Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 5 duplicate ingredient(s) |
| 2026-03-13T06:19:55.329527Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008290 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:28.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:13.958005+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Hydrogen-oxidizing bacteria medium" to "hydrogen_oxidizing_bacteria_medium" for consistent matching |
| 2026-05-16T09:03:37.415225+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:08.866251+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. |
| 2026-06-08T23:19:39.917925+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. |
| 2026-06-10T07:46:59.855480+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 7 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-09-02T07:38:10.849959+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. |