Overview
- External ontology
- TOGO:M862 — Dehalococcoides Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M862 Original source: JCM - JCM_M827 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=827
Composition
flowchart LR
CultureMech_010279["dehalococcoides_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010279 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_010279 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010279 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_KH2PO4["KH2PO4"]
CultureMech_010279 --> ing3_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing3_KH2PO4 -.-> CHEBI_63036
ing4_NH4Cl["NH4Cl"]
CultureMech_010279 --> ing4_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing4_NH4Cl -.-> CHEBI_31206
ing5_Resazurin["Resazurin"]
CultureMech_010279 --> ing5_Resazurin
CHEBI_8806["CHEBI:8806"]
ing5_Resazurin -.-> CHEBI_8806
ing6_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_010279 --> ing6_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing6_MgCl2_6H2O -.-> CHEBI_86345
ing7_KCl["KCl"]
CultureMech_010279 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_Sodium_acetate["Sodium acetate"]
CultureMech_010279 --> ing8_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing8_Sodium_acetate -.-> CHEBI_32954
ing9_N2["N2"]
CultureMech_010279 --> ing9_N2
CHEBI_17997["CHEBI:17997"]
ing9_N2 -.-> CHEBI_17997
ing10_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010279 --> ing10_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing10_Carbon_dioxide_gas -.-> CHEBI_16526
ing11_Nitrogen_gas["Nitrogen gas"]
CultureMech_010279 --> ing11_Nitrogen_gas
ing11_Nitrogen_gas -.-> CHEBI_17997
ing12_Hydrogen_gas["Hydrogen gas"]
CultureMech_010279 --> ing12_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing12_Hydrogen_gas -.-> CHEBI_18276
ing13_Trichloroethylene__10_mg_ml_in_methanol_["Trichloroethylene (10 mg/ml in methanol)"]
CultureMech_010279 --> ing13_Trichloroethylene__10_mg_ml_in_methanol_
ing14_Biotin["Biotin"]
CultureMech_010279 --> ing14_Biotin
CHEBI_15956["CHEBI:15956"]
ing14_Biotin -.-> CHEBI_15956
ing15_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010279 --> ing15_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing15_p__Aminobenzoic_acid -.-> CHEBI_30753
ing16_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010279 --> ing16_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing16_Thiamine_HCl -.-> CHEBI_49105
ing17_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010279 --> ing17_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing17_Pyridoxine_HCl -.-> CHEBI_30961
ing18_Folic_acid["Folic acid"]
CultureMech_010279 --> ing18_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing18_Folic_acid -.-> CHEBI_27470
ing19_Vitamin_B12["Vitamin B12"]
CultureMech_010279 --> ing19_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing19_Vitamin_B12 -.-> CHEBI_176843
ing20_Riboflavin["Riboflavin"]
CultureMech_010279 --> ing20_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing20_Riboflavin -.-> CHEBI_17015
ing21_Nicotinic_acid["Nicotinic acid"]
CultureMech_010279 --> ing21_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing21_Nicotinic_acid -.-> CHEBI_15940
ing22_Lipoic_acid["Lipoic acid"]
CultureMech_010279 --> ing22_Lipoic_acid
CHEBI_16494["CHEBI:16494"]
ing22_Lipoic_acid -.-> CHEBI_16494
ing23_DL__Calcium_pantothenate["DL--Calcium pantothenate"]
CultureMech_010279 --> ing23_DL__Calcium_pantothenate
ing24_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_010279 --> ing24_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing24_Nitrilotriacetic_acid -.-> CHEBI_44557
ing25_Anaerobic_water["Anaerobic water"]
CultureMech_010279 --> ing25_Anaerobic_water
ing26_TiCl3["TiCl3"]
CultureMech_010279 --> ing26_TiCl3
ing27_NaOH["NaOH"]
CultureMech_010279 --> ing27_NaOH
CHEBI_32145["CHEBI:32145"]
ing27_NaOH -.-> CHEBI_32145
Ingredients (28)
| # | 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 |
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 |
| 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 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.2 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.27 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
Resazurin
C12H7NO4 229.191 g/mol
|
0.25 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 7 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
0.41 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
KCl
Cl.K 74.551 g/mol
|
0.52 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
0.41 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 10 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 11 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 12 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 13 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: Gas |
| 14 | Trichloroethylene (10 mg/ml in methanol) | 0.7 G_PER_L | Role: Nutrient source; Properties: Inorganic compound, Defined component, Simple component | |
| 15 |
Biotin
C10H16N2O3S 244.316 g/mol
|
10 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 |
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 |
| 17 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
20 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 |
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 |
| 19 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 20 | Vitamin B12 | 25 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 21 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 22 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
100 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 23 |
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 |
| 24 | DL--Calcium pantothenate | 10 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 25 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
9.6 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 26 | Anaerobic water | 300 G_PER_L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component | |
| 27 | TiCl3 | variable VARIABLE | Properties: Defined component, Inorganic compound, Solution | |
| 28 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution |
Solutions
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
Selenite--tungstate solution (see Medium [M431])
Dose: 1 G_PER_L
Cross-reference to Medium M431
5% Na2S・9H2O solution
Dose: 1 G_PER_L
Role: Reducing agent; Properties: Solution, Inorganic compound, Defined component
5% L--Cysteine・HCl・H2O solution
Dose: 1 G_PER_L
Properties: Defined component, Organic compound, Solution
8% NaHCO3 solution
Dose: 10 G_PER_L
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
1.0 M MOPS solution (pH 7.4)
Dose: 20 G_PER_L
Role: Buffer; Properties: Defined component, Organic compound, Solution
25 mM Ti(III) NTA solution (see below)
Dose: 20 G_PER_L
Vitamin solution (see below)
Dose: 1 G_PER_L
Na2CO3 solution
Dose: variable VARIABLE
Role: Buffer; Properties: Defined component, Inorganic compound, Solution
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M862_Dehalococcoides_Medium (CultureMech:010279)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.854404Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M862 |
| 2026-01-28T19:48:22.131537Z | 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: N2; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: Hydrogen gas; Added default concentration for ingredient: TiCl3; Added default concentration for ingredient: Na2CO3 solution; Added default concentration for ingredient: NaOH; Added default concentration for ingredient: N2 |
| 2026-02-06T05:10:30.640486Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-09T08:04:36.971210+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 10 solution(s) from ingredients |
| 2026-03-13T03:09:06.481346Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:20:12.649880Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010279 |
| 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; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:12.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:31.596418+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Dehalococcoides Medium" to "dehalococcoides_medium" for consistent matching |
| 2026-05-16T09:03:21.511586+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:45.146065+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 16 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:35.081789+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). |
| 2026-06-10T07:46:51.863707+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. |
| 2026-08-06T03:05:19.972488+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 7a6b28a7354031772872fdc424f70697c1109b2012835117a81c2a1554e6c294 |