Overview
- External ontology
- TOGO:M888 — Spirochaeta Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M888 Original source: JCM - JCM_M852 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=852
Composition
flowchart LR
CultureMech_010306["spirochaeta_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010306 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Yeast_extract["Yeast extract"]
CultureMech_010306 --> ing1_Yeast_extract
ing2_NaCl["NaCl"]
CultureMech_010306 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010306 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_KH2PO4["KH2PO4"]
CultureMech_010306 --> ing4_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing4_KH2PO4 -.-> CHEBI_63036
ing5_NH4Cl["NH4Cl"]
CultureMech_010306 --> ing5_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing5_NH4Cl -.-> CHEBI_31206
ing6_Resazurin["Resazurin"]
CultureMech_010306 --> ing6_Resazurin
CHEBI_8806["CHEBI:8806"]
ing6_Resazurin -.-> CHEBI_8806
ing7_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_010306 --> ing7_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing7_MgCl2_6H2O -.-> CHEBI_86345
ing8_Na2S_9H2O["Na2S・9H2O"]
CultureMech_010306 --> ing8_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing8_Na2S_9H2O -.-> CHEBI_76209
ing9_NaHCO3["NaHCO3"]
CultureMech_010306 --> ing9_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing9_NaHCO3 -.-> CHEBI_32139
ing10_Sucrose["Sucrose"]
CultureMech_010306 --> ing10_Sucrose
CHEBI_17992["CHEBI:17992"]
ing10_Sucrose -.-> CHEBI_17992
ing11_Maltose["Maltose"]
CultureMech_010306 --> ing11_Maltose
CHEBI_18167["CHEBI:18167"]
ing11_Maltose -.-> CHEBI_18167
ing12_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
CultureMech_010306 --> ing12_L__Cysteine_HCl_H2O
CHEBI_91248["CHEBI:91248"]
ing12_L__Cysteine_HCl_H2O -.-> CHEBI_91248
ing13_Na2MoO4_2H2O["Na2MoO4・2H2O"]
CultureMech_010306 --> ing13_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing13_Na2MoO4_2H2O -.-> CHEBI_75213
ing14_H3BO3["H3BO3"]
CultureMech_010306 --> ing14_H3BO3
CHEBI_33118["CHEBI:33118"]
ing14_H3BO3 -.-> CHEBI_33118
ing15_MnCl2_4H2O["MnCl2・4H2O"]
CultureMech_010306 --> ing15_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing15_MnCl2_4H2O -.-> CHEBI_86368
ing16_CoCl2_6H2O["CoCl2・6H2O"]
CultureMech_010306 --> ing16_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing16_CoCl2_6H2O -.-> CHEBI_35696
ing17_NiCl2_6H2O["NiCl2・6H2O"]
CultureMech_010306 --> ing17_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing17_NiCl2_6H2O -.-> CHEBI_34887
ing18_CuCl2_2H2O["CuCl2・2H2O"]
CultureMech_010306 --> ing18_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing18_CuCl2_2H2O -.-> CHEBI_86318
ing19_ZnCl2["ZnCl2"]
CultureMech_010306 --> ing19_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing19_ZnCl2 -.-> CHEBI_49976
ing20_AlCl3["AlCl3"]
CultureMech_010306 --> ing20_AlCl3
CHEBI_30114["CHEBI:30114"]
ing20_AlCl3 -.-> CHEBI_30114
ing21_FeCl2_4H2O["FeCl2・4H2O"]
CultureMech_010306 --> ing21_FeCl2_4H2O
CHEBI_86249["CHEBI:86249"]
ing21_FeCl2_4H2O -.-> CHEBI_86249
ing22_Na2SeO3_5H2O["Na2SeO3・5H2O"]
CultureMech_010306 --> ing22_Na2SeO3_5H2O
CHEBI_131361["CHEBI:131361"]
ing22_Na2SeO3_5H2O -.-> CHEBI_131361
ing23_Na2WO4_2H2O["Na2WO4・2H2O"]
CultureMech_010306 --> ing23_Na2WO4_2H2O
CHEBI_63939["CHEBI:63939"]
ing23_Na2WO4_2H2O -.-> CHEBI_63939
ing24_Biotin["Biotin"]
CultureMech_010306 --> ing24_Biotin
CHEBI_15956["CHEBI:15956"]
ing24_Biotin -.-> CHEBI_15956
ing25_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010306 --> ing25_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing25_p__Aminobenzoic_acid -.-> CHEBI_30753
ing26_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010306 --> ing26_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing26_Thiamine_HCl -.-> CHEBI_49105
ing27_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010306 --> ing27_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing27_Pyridoxine_HCl -.-> CHEBI_30961
ing28_Folic_acid["Folic acid"]
CultureMech_010306 --> ing28_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing28_Folic_acid -.-> CHEBI_27470
ing29_Vitamin_B12["Vitamin B12"]
CultureMech_010306 --> ing29_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing29_Vitamin_B12 -.-> CHEBI_176843
CultureMech_010306 --> more["...6 more"]
Ingredients (36)
| # | 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 4 identical duplicates: 1.0, 1.0, 1.0, 1.0] |
| 2 | Yeast extract | 1 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 3 |
NaCl
Cl.Na 58.443 g/mol
|
25 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
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 |
| 5 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.1 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.5 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; 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 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
4 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
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 |
| 10 |
NaHCO3
CHO3.Na 84.006 g/mol
|
2 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
Sucrose
C12H22O11 342.297 g/mol
|
1.7 G_PER_L |
CHEBI:17992
sucrose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 12 |
Maltose
C12H22O11 342.297 g/mol
|
1.7 G_PER_L |
CHEBI:18167
alpha-maltose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 13 |
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, Organic compound, Simple component |
| 14 |
Na2MoO4・2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.024 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
H3BO3
H3BO3 61.833 g/mol
|
6.2 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
MnCl2・4H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.198 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
CoCl2・6H2O
2Cl.Co 129.839 g/mol
|
0.13 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
NiCl2・6H2O
Cl2Ni 129.599 g/mol
|
0.013 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
CuCl2・2H2O
Cl2Cu.2H2O 170.482 g/mol
|
1.7 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 20 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
0.136 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
AlCl3
AlCl3 133.341 g/mol
|
0.013 G_PER_L |
CHEBI:30114
aluminium trichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
FeCl2・4H2O
Cl2Fe.4H2O 198.811 g/mol
|
1.99 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
Na2SeO3・5H2O
5H2O.2Na.O3Se 263.012 g/mol
|
1.7 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 24 |
Na2WO4・2H2O
2H2O.2Na.O4W 329.846 g/mol
|
3.3 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
Biotin
C10H16N2O3S 244.316 g/mol
|
4.9 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 26 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
2.7 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 27 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
6.7 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
4.1 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 29 |
Folic acid
C19H19N7O6 441.404 g/mol
|
8.8 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 30 | Vitamin B12 | 27.1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
7.5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 32 |
Nicotinamide
C6H6N2O 122.127 g/mol
|
2.5 G_PER_L |
CHEBI:17154
nicotinamide
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 33 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
4.1 G_PER_L |
CHEBI:16494
lipoic acid
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 34 | DL--Calcium pantothenate | 9.5 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component | |
| 35 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 36 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
Solutions
Vitamin solution (see below)
Dose: 2 G_PER_L
Trace mineral solution (see below)
Dose: 1 G_PER_L
Se/W solution (see below)
Dose: 1 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.903175Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M888 |
| 2026-01-28T19:48:13.719196Z | 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 |
| 2026-03-09T08:04:22.738715+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:08:50.933378Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 3 duplicate ingredient(s) |
| 2026-03-13T06:20:12.867695Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010306 |
| 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 |
| 2026-03-17T06:29:54.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:31.814688+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Spirochaeta Medium" to "spirochaeta_medium" for consistent matching |
| 2026-05-16T09:03:21.757238+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:45.395361+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 18 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:35.136274+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24) | Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md. |
| 2026-06-10T07:46:51.952689+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-09-02T07:37:53.385983+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. |