Overview
- External ontology
- TOGO:M1253 — M39 Methylomonas Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1253 Original source: JCM - JCM_M1171 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1171
Composition
flowchart LR
CultureMech_007784["m39_methylomonas_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_007784 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4・7H2O"]
CultureMech_007784 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_007784 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_NaNO3["NaNO3"]
CultureMech_007784 --> ing3_NaNO3
CHEBI_63005["CHEBI:63005"]
ing3_NaNO3 -.-> CHEBI_63005
ing4_K2SO4["K2SO4"]
CultureMech_007784 --> ing4_K2SO4
CHEBI_32036["CHEBI:32036"]
ing4_K2SO4 -.-> CHEBI_32036
ing5_H2SO4["H2SO4"]
CultureMech_007784 --> ing5_H2SO4
CHEBI_26836["CHEBI:26836"]
ing5_H2SO4 -.-> CHEBI_26836
ing6_methane["methane"]
CultureMech_007784 --> ing6_methane
ing7_FeCl2_4H2O["FeCl2・4H2O"]
CultureMech_007784 --> ing7_FeCl2_4H2O
CHEBI_86249["CHEBI:86249"]
ing7_FeCl2_4H2O -.-> CHEBI_86249
ing8_EDTA_Na2["EDTA・Na2"]
CultureMech_007784 --> ing8_EDTA_Na2
ing9_Biotin["Biotin"]
CultureMech_007784 --> ing9_Biotin
CHEBI_15956["CHEBI:15956"]
ing9_Biotin -.-> CHEBI_15956
ing10_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_007784 --> ing10_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing10_p_Aminobenzoic_acid -.-> CHEBI_30753
ing11_Thiamine_HCl["Thiamine・HCl"]
CultureMech_007784 --> ing11_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing11_Thiamine_HCl -.-> CHEBI_49105
ing12_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_007784 --> ing12_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing12_Calcium_pantothenate -.-> CHEBI_31345
ing13_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_007784 --> ing13_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing13_Pyridoxine_HCl -.-> CHEBI_30961
ing14_Folic_acid["Folic acid"]
CultureMech_007784 --> ing14_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing14_Folic_acid -.-> CHEBI_27470
ing15_Vitamin_B12["Vitamin B12"]
CultureMech_007784 --> ing15_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing15_Vitamin_B12 -.-> CHEBI_176843
ing16_Riboflavin["Riboflavin"]
CultureMech_007784 --> ing16_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing16_Riboflavin -.-> CHEBI_17015
ing17_Nicotinic_acid["Nicotinic acid"]
CultureMech_007784 --> ing17_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing17_Nicotinic_acid -.-> CHEBI_15940
ing18_Nicotinamide["Nicotinamide"]
CultureMech_007784 --> ing18_Nicotinamide
CHEBI_17154["CHEBI:17154"]
ing18_Nicotinamide -.-> CHEBI_17154
ing19_Hemin["Hemin"]
CultureMech_007784 --> ing19_Hemin
CHEBI_50385["CHEBI:50385"]
ing19_Hemin -.-> CHEBI_50385
ing20_Lipoic_acid["Lipoic acid"]
CultureMech_007784 --> ing20_Lipoic_acid
CHEBI_16494["CHEBI:16494"]
ing20_Lipoic_acid -.-> CHEBI_16494
ing21_1_4_Naphthoquinone["1,4-Naphthoquinone"]
CultureMech_007784 --> ing21_1_4_Naphthoquinone
CHEBI_27418["CHEBI:27418"]
ing21_1_4_Naphthoquinone -.-> CHEBI_27418
Ingredients (22)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
2.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 1.0, 1.0] |
| 2 |
MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.099 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.147 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
NaNO3
NO3.Na 84.994 g/mol
|
0.17 G_PER_L |
CHEBI:63005
sodium nitrate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
K2SO4
2K.O4S 174.259 g/mol
|
0.349 G_PER_L |
CHEBI:32036
potassium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
H2SO4
H2O4S 98.079 g/mol
|
variable VARIABLE |
CHEBI:26836
sulfuric acid
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution |
| 7 | methane | variable VARIABLE | Properties: Gas | |
| 8 |
FeCl2・4H2O
Cl2Fe.4H2O 198.811 g/mol
|
1.5 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 | EDTA・Na2 | 3 G_PER_L | Properties: Defined component, Organic compound, Simple component | |
| 10 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.1 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 11 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
0.25 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 12 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.25 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 13 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.25 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 14 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
0.5 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 15 |
Folic acid
C19H19N7O6 441.404 g/mol
|
0.1 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 | Vitamin B12 | 0.05 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.25 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
0.25 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Nicotinamide
C6H6N2O 122.127 g/mol
|
0.25 G_PER_L |
CHEBI:17154
nicotinamide
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 20 |
Hemin
C34H32ClFeN4O4 651.952 g/mol
|
0.05 G_PER_L |
CHEBI:50385
hemin
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 21 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
0.25 G_PER_L |
CHEBI:16494
lipoic acid
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 22 |
1,4-Naphthoquinone
C10H6O2 158.156 g/mol
|
0.2 G_PER_L |
CHEBI:27418
1,4-naphthoquinone
|
Role: Growth factor |
Solutions
1.0 M NaHCO3 solution*
Dose: 3 G_PER_L
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
1.0 M KH2PO4 solution
Dose: 1 G_PER_L
Role: Buffer; Properties: Defined component, Solution, Inorganic compound
0.2 M CeCl3 solution*
Dose: 0.1 G_PER_L
Role: Mineral source
Selenite--tungstate solution (see Medium [M431])
Dose: 1 G_PER_L
Cross-reference to Medium M431
Trace element solution* (see below)
Dose: 1 G_PER_L
Vitamins solution* (see below)
Dose: 0.1 G_PER_L
SL-6 trace element solution (see Medium [M158])
Dose: 1 G_PER_L
Cross-reference to Medium M158
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M1253_M39_Methylomonas_Medium (CultureMech:007784)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.225464Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M1253 |
| 2026-01-28T19:48:18.032024Z | 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: H2SO4; Added default concentration for ingredient: methane |
| 2026-03-09T08:04:29.860815+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 7 solution(s) from ingredients |
| 2026-03-13T03:08:58.752208Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:51.440726Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007784 |
| 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; Added default solution name; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:03.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:09.865444+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "M39 Methylomonas Medium" to "m39_methylomonas_medium" for consistent matching |
| 2026-05-16T09:03:08.869482+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:31.780969+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 15 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:30.141972+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 1 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). |
| 2026-06-10T06:57:22.260313+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. |
| 2026-06-10T07:46:47.396248+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 1 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-06T03:05:07.165579+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 42ecf60f4994f2c89d16deca2bac6375212053648152b9eb64e760f8abe31b6d |