Overview
- External ontology
- TOGO:M560 — Methylosoma Difficile Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M560 Original source: JCM - JCM_M556 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=556
Composition
flowchart LR
CultureMech_009955["methylosoma_difficile_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009955 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_009955 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009955 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009955 --> ing3_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing3_MgCl2_6H2O -.-> CHEBI_86345
ing4_KCl["KCl"]
CultureMech_009955 --> ing4_KCl
CHEBI_32588["CHEBI:32588"]
ing4_KCl -.-> CHEBI_32588
ing5_Na2SO4["Na2SO4"]
CultureMech_009955 --> ing5_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing5_Na2SO4 -.-> CHEBI_32149
ing6_2_M_HEPES_buffer__pH_7_0_["2 M HEPES buffer (pH 7.0)"]
CultureMech_009955 --> ing6_2_M_HEPES_buffer__pH_7_0_
ing7_1_M_Phosphate_buffer__pH_7_2__see_below_["1 M Phosphate buffer (pH 7.2, see below)"]
CultureMech_009955 --> ing7_1_M_Phosphate_buffer__pH_7_2__see_below_
ing8_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009955 --> ing8_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing8_Carbon_dioxide_gas -.-> CHEBI_16526
ing9_Methane_gas["Methane gas"]
CultureMech_009955 --> ing9_Methane_gas
ing10_Air["Air"]
CultureMech_009955 --> ing10_Air
ing11_KH2PO4["KH2PO4"]
CultureMech_009955 --> ing11_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing11_KH2PO4 -.-> CHEBI_63036
ing12_Na2HPO4["Na2HPO4"]
CultureMech_009955 --> ing12_Na2HPO4
CHEBI_34683["CHEBI:34683"]
ing12_Na2HPO4 -.-> CHEBI_34683
ing13_Biotin["Biotin"]
CultureMech_009955 --> ing13_Biotin
CHEBI_15956["CHEBI:15956"]
ing13_Biotin -.-> CHEBI_15956
ing14_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_009955 --> ing14_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing14_p__Aminobenzoic_acid -.-> CHEBI_30753
ing15_Thiamine_HCl["Thiamine・HCl"]
CultureMech_009955 --> ing15_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing15_Thiamine_HCl -.-> CHEBI_49105
ing16_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_009955 --> ing16_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing16_Pyridoxine_HCl -.-> CHEBI_30961
ing17_Vitamin_B12["Vitamin B12"]
CultureMech_009955 --> ing17_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing17_Vitamin_B12 -.-> CHEBI_176843
ing18_Nicotinic_acid["Nicotinic acid"]
CultureMech_009955 --> ing18_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing18_Nicotinic_acid -.-> CHEBI_15940
ing19_DL__Calcium_pantothenate["DL--Calcium pantothenate"]
CultureMech_009955 --> ing19_DL__Calcium_pantothenate
Ingredients (20)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
994.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 993.0, 1.0] |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
0.1 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.015 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.04 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
KCl
Cl.K 74.551 g/mol
|
0.05 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
Na2SO4
2Na.O4S 142.043 g/mol
|
0.016 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 | 2 M HEPES buffer (pH 7.0) | 5 G_PER_L | Role: Buffer; Properties: Solution, Defined component | |
| 8 | 1 M Phosphate buffer (pH 7.2, see below) | 0.15 G_PER_L | ||
| 9 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 10 | Methane gas | variable VARIABLE | Properties: ガス | |
| 11 | Air | variable VARIABLE | Properties: ガス | |
| 12 |
KH2PO4
H2O4P.K 136.084 g/mol
|
28 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Defined component, Inorganic compound, Solution |
| 13 |
Na2HPO4
HO4P.2Na 141.958 g/mol
|
78 G_PER_L |
CHEBI:34683
disodium hydrogenphosphate
|
Role: Buffer; Properties: Defined component, Solution, Inorganic compound |
| 14 |
Biotin
C10H16N2O3S 244.316 g/mol
|
10 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 15 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
50 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
50 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
250 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 | Vitamin B12 | 50 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
100 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 20 | DL--Calcium pantothenate | 25 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
0.09 M KNO3 solution
Dose: 0.544 G_PER_L
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution
FeCl2 solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Trace element solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Vitamin solution (filter--sterilized, see below)
Dose: 1 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.302597Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M560 |
| 2026-01-28T19:48:21.063923Z | 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: Methane gas; Added default concentration for ingredient: Air |
| 2026-03-09T08:04:34.918715+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T03:09:04.476745Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:20:10.273248Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009955 |
| 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 |
| 2026-03-17T06:30:10.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:29.203048+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Methylosoma Difficile Medium" to "methylosoma_difficile_medium" for consistent matching |
| 2026-05-16T09:03:19.096850+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:42.545944+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 10 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:34.647834+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). |
| 2026-06-10T07:46:51.005582+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |