Overview
- External ontology
- TOGO:M1608 — Methanospirillum Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1608 Original source: NBRC - NBRC_M808 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=808
Composition
flowchart LR
CultureMech_008161["methanospirillum_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008161 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO2_7H2O["MgSO2·7H2O"]
CultureMech_008161 --> ing1_MgSO2_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO2_7H2O -.-> CHEBI_31795
ing2_NaCl["NaCl"]
CultureMech_008161 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008161 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_KH2PO4["KH2PO4"]
CultureMech_008161 --> ing4_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing4_KH2PO4 -.-> CHEBI_63036
ing5_K2HPO4["K2HPO4"]
CultureMech_008161 --> ing5_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing5_K2HPO4 -.-> CHEBI_131527
ing6_Resazurin["Resazurin"]
CultureMech_008161 --> ing6_Resazurin
CHEBI_8806["CHEBI:8806"]
ing6_Resazurin -.-> CHEBI_8806
ing7_Na2S_9H2O["Na2S·9H2O"]
CultureMech_008161 --> ing7_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing7_Na2S_9H2O -.-> CHEBI_76209
ing8_FeSO2_7H2O["FeSO2·7H2O"]
CultureMech_008161 --> ing8_FeSO2_7H2O
ing9_NaHCO3["NaHCO3"]
CultureMech_008161 --> ing9_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing9_NaHCO3 -.-> CHEBI_32139
ing10__NH4_2SO4["(NH4)2SO4"]
CultureMech_008161 --> ing10__NH4_2SO4
CHEBI_62946["CHEBI:62946"]
ing10__NH4_2SO4 -.-> CHEBI_62946
ing11_Sodium_acetate["Sodium acetate"]
CultureMech_008161 --> ing11_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing11_Sodium_acetate -.-> CHEBI_32954
ing12_Bacto_Yeast_Extract__Difco_["Bacto Yeast Extract (Difco)"]
CultureMech_008161 --> ing12_Bacto_Yeast_Extract__Difco_
ing13_Cysteine_HCl["Cysteine-HCl"]
CultureMech_008161 --> ing13_Cysteine_HCl
CHEBI_91247["CHEBI:91247"]
ing13_Cysteine_HCl -.-> CHEBI_91247
ing14_Trypticase_peptone__BBL_["Trypticase peptone (BBL)"]
CultureMech_008161 --> ing14_Trypticase_peptone__BBL_
ing15_Sodium_formate["Sodium formate"]
CultureMech_008161 --> ing15_Sodium_formate
CHEBI_62965["CHEBI:62965"]
ing15_Sodium_formate -.-> CHEBI_62965
ing16_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_008161 --> ing16_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing16_Carbon_dioxide_gas -.-> CHEBI_16526
ing17_N2["N2"]
CultureMech_008161 --> ing17_N2
CHEBI_17997["CHEBI:17997"]
ing17_N2 -.-> CHEBI_17997
ing18_Hydrogen_gas["Hydrogen gas"]
CultureMech_008161 --> ing18_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing18_Hydrogen_gas -.-> CHEBI_18276
ing19_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_008161 --> ing19_MgSO4_7H2O
ing19_MgSO4_7H2O -.-> CHEBI_31795
ing20_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008161 --> ing20_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing20_Na2MoO4_2H2O -.-> CHEBI_75213
ing21_H3BO3["H3BO3"]
CultureMech_008161 --> ing21_H3BO3
CHEBI_33118["CHEBI:33118"]
ing21_H3BO3 -.-> CHEBI_33118
ing22_FeSO4_7H2O["FeSO4·7H2O"]
CultureMech_008161 --> ing22_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing22_FeSO4_7H2O -.-> CHEBI_75836
ing23_ZnSO4_7H2O["ZnSO4·7H2O"]
CultureMech_008161 --> ing23_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing23_ZnSO4_7H2O -.-> CHEBI_32312
ing24_CuSO4_5H2O["CuSO4·5H2O"]
CultureMech_008161 --> ing24_CuSO4_5H2O
CHEBI_31440["CHEBI:31440"]
ing24_CuSO4_5H2O -.-> CHEBI_31440
ing25_CoSO4_7H2O["CoSO4·7H2O"]
CultureMech_008161 --> ing25_CoSO4_7H2O
CHEBI_91244["CHEBI:91244"]
ing25_CoSO4_7H2O -.-> CHEBI_91244
ing26_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_008161 --> ing26_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing26_Nitrilotriacetic_acid -.-> CHEBI_44557
ing27_MnSO4_xH2O["MnSO4·xH2O"]
CultureMech_008161 --> ing27_MnSO4_xH2O
ing28_AlK_SO4_2["AlK(SO4)2"]
CultureMech_008161 --> ing28_AlK_SO4_2
CHEBI_86463["CHEBI:86463"]
ing28_AlK_SO4_2 -.-> CHEBI_86463
ing29_Biotin["Biotin"]
CultureMech_008161 --> ing29_Biotin
CHEBI_15956["CHEBI:15956"]
ing29_Biotin -.-> CHEBI_15956
CultureMech_008161 --> more["...9 more"]
Ingredients (39)
| # | 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 |
MgSO2·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.13 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
|
1.6 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.6, 1.0] |
| 4 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
8.1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 8.0, 0.1] |
| 5 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.3 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.3 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 |
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 |
| 9 | FeSO2·7H2O | 2 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component | |
| 10 |
NaHCO3
CHO3.Na 84.006 g/mol
|
5 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
(NH4)2SO4
2H4N.O4S 132.141 g/mol
|
0.3 G_PER_L |
CHEBI:62946
ammonium sulfate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
2.5 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 13 | Bacto Yeast Extract (Difco) | 2 G_PER_L | Properties: Undefined component | |
| 14 |
Cysteine-HCl
C3H7NO2S.HCl 157.622 g/mol
|
0.5 G_PER_L |
CHEBI:91247
L-cysteine hydrochloride
|
Properties: Defined component, Simple component, Organic compound |
| 15 | Trypticase peptone (BBL) | 2 G_PER_L | Properties: Undefined component | |
| 16 |
Sodium formate
CHO2.Na 68.007 g/mol
|
2.5 G_PER_L |
CHEBI:62965
sodium formate
|
Properties: Defined component, Simple component, Inorganic compound |
| 17 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 18 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 19 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: ガス |
| 20 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
3 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.01 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
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 |
| 23 |
FeSO4·7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.1 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
ZnSO4·7H2O
7H2O.O4S.Zn 287.558 g/mol
|
0.1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
CuSO4·5H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.01 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 26 |
CoSO4·7H2O
Co.7H2O.O4S 281.101 g/mol
|
0.1 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 27 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
1.5 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 28 | MnSO4·xH2O | 0.5 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component | |
| 29 |
AlK(SO4)2
Al.K.2O4S 258.206 g/mol
|
0.01 G_PER_L |
CHEBI:86463
potassium aluminium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 30 |
Biotin
C10H16N2O3S 244.316 g/mol
|
2 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
5 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 32 |
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 |
| 33 |
Ca-pantothenate
C9H16NO5 218.229 g/mol
|
5 G_PER_L |
CHEBI:29032
(R)-pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 34 |
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 |
| 35 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 36 | Vitamin B12 | 0.1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 37 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 38 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 39 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
5 G_PER_L |
CHEBI:16494
lipoic acid
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
Solutions
Trace minerals*
Dose: 10 G_PER_L
See mediadive_5363_Trace_minerals.yaml for composition
Trace vitamins**
Dose: 10 G_PER_L
See mediadive_5469_Trace_vitamins.yaml for composition
KOH solution
Dose: variable VARIABLE
Role: Mineral source; Properties: Defined component, Solution
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:57.938392Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1608 |
| 2026-01-28T19:48:24.344914Z | 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: Hydrogen gas; Added default concentration for ingredient: KOH solution |
| 2026-03-09T08:04:40.227029+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:09:10.167409Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:19:54.028203Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008161 |
| 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 |
| 2026-03-17T06:30:16.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:12.593443+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methanospirillum Medium" to "methanospirillum_medium" for consistent matching |
| 2026-05-16T09:04:22.786686+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:32.775821+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 28 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:47.989245+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). |
| 2026-06-10T06:58:23.540186+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. |
| 2026-06-10T07:47:07.429402+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. |
| 2026-09-02T07:37:31.075487+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. |