Overview
- External ontology
- TOGO:M500 — Sulfate-Free Syntrophomonus Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M500 Original source: JCM - JCM_M499 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=499
Composition
flowchart LR
CultureMech_009890["sulfate_free_syntrophomonus_medium"]
ing0_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009890 --> ing0_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing0_Carbon_dioxide_gas -.-> CHEBI_16526
ing1_Nitrogen_gas["Nitrogen gas"]
CultureMech_009890 --> ing1_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing1_Nitrogen_gas -.-> CHEBI_17997
ing2_Distilled_water["Distilled water"]
CultureMech_009890 --> ing2_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing2_Distilled_water -.-> CHEBI_15377
ing3_Resazurin["Resazurin"]
CultureMech_009890 --> ing3_Resazurin
CHEBI_8806["CHEBI:8806"]
ing3_Resazurin -.-> CHEBI_8806
ing4_Crotonic_acid["Crotonic acid"]
CultureMech_009890 --> ing4_Crotonic_acid
CHEBI_41131["CHEBI:41131"]
ing4_Crotonic_acid -.-> CHEBI_41131
ing5_Trypticase_peptone__BD_BBL_["Trypticase peptone (BD-BBL)"]
CultureMech_009890 --> ing5_Trypticase_peptone__BD_BBL_
ing6_NaHCO3["NaHCO3"]
CultureMech_009890 --> ing6_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing6_NaHCO3 -.-> CHEBI_32139
ing7_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
CultureMech_009890 --> ing7_L__Cysteine_HCl_H2O
CHEBI_91248["CHEBI:91248"]
ing7_L__Cysteine_HCl_H2O -.-> CHEBI_91248
ing8_N2["N2"]
CultureMech_009890 --> ing8_N2
ing8_N2 -.-> CHEBI_17997
ing9_Na2S_9H2O["Na2S・9H2O"]
CultureMech_009890 --> ing9_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing9_Na2S_9H2O -.-> CHEBI_76209
ing10_NaCl["NaCl"]
CultureMech_009890 --> ing10_NaCl
CHEBI_26710["CHEBI:26710"]
ing10_NaCl -.-> CHEBI_26710
ing11_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009890 --> ing11_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing11_CaCl2_2H2O -.-> CHEBI_86158
ing12_KH2PO4["KH2PO4"]
CultureMech_009890 --> ing12_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing12_KH2PO4 -.-> CHEBI_63036
ing13_NH4Cl["NH4Cl"]
CultureMech_009890 --> ing13_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing13_NH4Cl -.-> CHEBI_31206
ing14_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009890 --> ing14_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing14_MgCl2_6H2O -.-> CHEBI_86345
ing15_Biotin["Biotin"]
CultureMech_009890 --> ing15_Biotin
CHEBI_15956["CHEBI:15956"]
ing15_Biotin -.-> CHEBI_15956
ing16_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_009890 --> ing16_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing16_p__Aminobenzoic_acid -.-> CHEBI_30753
ing17_Thiamine_HCl["Thiamine・HCl"]
CultureMech_009890 --> ing17_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing17_Thiamine_HCl -.-> CHEBI_49105
ing18_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_009890 --> ing18_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing18_Pyridoxine_HCl -.-> CHEBI_30961
ing19_Nicotinic_acid["Nicotinic acid"]
CultureMech_009890 --> ing19_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing19_Nicotinic_acid -.-> CHEBI_15940
ing20_Pantothenic_acid["Pantothenic acid"]
CultureMech_009890 --> ing20_Pantothenic_acid
CHEBI_7916["CHEBI:7916"]
ing20_Pantothenic_acid -.-> CHEBI_7916
Ingredients (21)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 2 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 3 |
Distilled water
H2O 18.015 g/mol
|
902.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 6 duplicates: 810.0, 70.0, 10.0, 10.0, 1.0, 1.0] |
| 4 |
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 |
| 5 |
Crotonic acid
C4H6O2 86.09 g/mol
|
1.7 G_PER_L |
CHEBI:41131
crotonic acid
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 6 | Trypticase peptone (BD-BBL) | 1 G_PER_L | Properties: Undefined component | |
| 7 |
NaHCO3
CHO3.Na 84.006 g/mol
|
3.5 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
L--Cysteine・HCl・H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
|
0.3 G_PER_L |
CHEBI:91248
L-cysteine hydrochloride hydrate
|
Properties: Defined component, Simple component, Organic compound |
| 9 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 10 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
0.3 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
NaCl
Cl.Na 58.443 g/mol
|
8 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
KH2PO4
H2O4P.K 136.084 g/mol
|
10 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
NH4Cl
Cl.H4N 53.492 g/mol
|
8 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
6.6 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.25 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
1.25 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
1.25 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
6.2 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 20 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
2.5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 21 |
Pantothenic acid
C9H17NO5 219.237 g/mol
|
0.62 G_PER_L |
CHEBI:7916
pantothenic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
Solution A
Dose: 916 G_PER_L
See mediadive_5342_Solution_A.yaml for composition
Solution B
Dose: 70 G_PER_L
See mediadive_5343_Solution_B.yaml for composition
Solution C
Dose: 10 G_PER_L
See mediadive_5312_Solution_C.yaml for composition
Solution D
Dose: 10 G_PER_L
See mediadive_5313_Solution_D.yaml for composition
Mineral solution (see below)
Dose: 50 G_PER_L
Trace element solution SL--10 (see Medium [M433])
Dose: 1 G_PER_L
Cross-reference to Medium M433
Rumen fluid, clarified (see Medium [M258])
Dose: 50 G_PER_L
Cross-reference to Medium M258
Vitamin solution (see below)
Dose: 5 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M500_Sulfate-Free_Syntrophomonus_Medium (CultureMech:009890)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.172744Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M500 |
| 2026-01-28T19:48:14.291553Z | 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: Nitrogen gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: N2 |
| 2026-03-09T08:04:23.763049+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 8 solution(s) from ingredients |
| 2026-03-13T03:08:52.068571Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 6 duplicate ingredient(s) |
| 2026-03-13T06:20:09.685038Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009890 |
| 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 |
| 2026-03-17T06:29:56.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:28.645047+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Sulfate-Free Syntrophomonus Medium" to "sulfate_free_syntrophomonus_medium" for consistent matching |
| 2026-05-16T09:03:18.521820+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:41.950931+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 11 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:34.415068+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). |
| 2026-06-10T07:46:50.788696+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. |
| 2026-08-06T03:05:16.702788+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 918eed8275e59de39624b076da5e949a5cc06340c0e9d1d5fa4536e09d431d23 |