Overview
- External ontology
- TOGO:M689 — Spirochaeta Caldaria Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M689 Original source: JCM - JCM_M670 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=670
Composition
flowchart LR
CultureMech_010094["spirochaeta_caldaria_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010094 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Resazurin["Resazurin"]
CultureMech_010094 --> ing1_Resazurin
CHEBI_8806["CHEBI:8806"]
ing1_Resazurin -.-> CHEBI_8806
ing2_Glucose["Glucose"]
CultureMech_010094 --> ing2_Glucose
CHEBI_17234["CHEBI:17234"]
ing2_Glucose -.-> CHEBI_17234
ing3_Tryptone__BD_Difco_["Tryptone (BD-Difco)"]
CultureMech_010094 --> ing3_Tryptone__BD_Difco_
ing4_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
CultureMech_010094 --> ing4_L__Cysteine_HCl_H2O
CHEBI_91248["CHEBI:91248"]
ing4_L__Cysteine_HCl_H2O -.-> CHEBI_91248
ing5_N2["N2"]
CultureMech_010094 --> ing5_N2
CHEBI_17997["CHEBI:17997"]
ing5_N2 -.-> CHEBI_17997
ing6_NaOH["NaOH"]
CultureMech_010094 --> ing6_NaOH
CHEBI_32145["CHEBI:32145"]
ing6_NaOH -.-> CHEBI_32145
Ingredients (7)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component Source water batch input: 1 L = 1 L. This is not a measured final volume. |
| 2 |
Resazurin
C12H7NO4 229.191 g/mol
|
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Defined component, Organic compound, Simple component Source batch input: 0.5 mg. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 3 |
Glucose
C6H12O6 180.156 g/mol
|
CHEBI:17234
glucose
|
Role: Carbon source; Properties: Simple component, Organic compound, Defined component Source batch input: 2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 4 | Tryptone (BD-Difco) | Properties: Undefined component Source batch input: 2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | ||
| 5 |
L--Cysteine・HCl・H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
|
CHEBI:91248
L-cysteine hydrochloride hydrate
|
Properties: Defined component, Simple component, Organic compound Source batch input: 0.25 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 6 |
N2
N2 28.014 g/mol
|
CHEBI:17997
dinitrogen
|
Properties: Gas Source specifies an N2 atmosphere, not a fixed gas input or dissolved concentration. The unsupported VARIABLE quantity placeholder is removed. | |
| 7 |
NaOH
HO.Na 39.997 g/mol
|
CHEBI:32145
sodium hydroxide
|
Properties: Defined component, Inorganic compound, Solution pH-adjustment reagent; no fixed dose is specified. Normality is not converted to molarity. |
Preparation
- Mix ingredients and distribute into culture vessels under a N2 atmosphere, seal with butyl rubber stoppers, and autoclave. Separately autoclave or *filter--sterilize the following solutions under a N2 atmosphere and add to the medium (per liter):
- Adjust pH of the medium to 7.0 with sterile NaOH, if necessary.
Solutions
FeCl2 solution (see Medium [M180])
Dose: 10 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 0.99 L | Source water batch input: 990 ml = 0.99 L. This is not a measured final volume. |
| FeCl2・4H2O | Source batch input: 1.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M180
Explicit receiving-medium addition: 10 ml per liter, not grams per liter. Expand only the referenced FeCl2 solution stock definition.
HCl reagent (7.7 M)
Dose: 0.01 L
| Ingredient | Concentration | Notes |
|---|---|---|
| 25% HCl (7.7 M) | 7.7 MOLAR | Explicit HCl reagent strength 7.7 M, not a final-medium concentration. The 25% basis is unspecified; the enclosing stock holds the 10 ml batch dose. |
FeCl2-stock-only acid input: 10 ml = 0.01 L per stock batch. The reagent is explicitly 7.7 M; the 25% basis is unspecified. This is not a dose per liter of receiving medium.
Trace element solution (see Medium [M180])
Dose: 10 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Source water batch input: 1 L = 1 L. This is not a measured final volume. |
| Na2MoO4・2H2O | Source batch input: 36 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| H3BO3 | Source batch input: 6 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| MnCl2・4H2O | Source batch input: 100 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CoCl2・6H2O | Source batch input: 190 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| NiCl2・6H2O | Source batch input: 24 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CuCl2・2H2O | Source batch input: 2 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| ZnCl2 | Source batch input: 70 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M180
Explicit receiving-medium addition: 10 ml per liter, not grams per liter. Expand only the referenced Trace element solution stock definition.
Trace minerals (see Medium [M142])
Dose: 25 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Source water batch input: 1 L = 1 L. This is not a measured final volume. |
| MgSO4・7H2O | Source batch input: 3 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| NaCl | Source batch input: 1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CaCl2・2H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Na2MoO4・2H2O | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| H3BO3 | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| FeSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| ZnSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CuSO4・5H2O | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| CoSO4・7H2O | Source batch input: 0.1 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Nitrilotriacetic acid | Source batch input: 1.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| MnSO4・xH2O | Source batch input: 0.5 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| AlK(SO4)2 | Source batch input: 0.01 g. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M142
Explicit receiving-medium addition: 25 ml per liter, not grams per liter. Expand only the referenced Trace minerals stock definition.
KOH solution
Stock pH-adjustment reagent with no fixed dose or numeric strength.
Trace vitamins (see Medium [M190])
Dose: 10 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Source water batch input: 1 L = 1 L. This is not a measured final volume. |
| Biotin | Source batch input: 2 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| p--Aminobenzoic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Thiamine・HCl | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Calcium pantothenate | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Pyridoxine・HCl | Source batch input: 10 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Folic acid | Source batch input: 2 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Vitamin B12 | Source batch input: 0.1 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Riboflavin | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Nicotinic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. | |
| Lipoic acid | Source batch input: 5 mg. Final preparation volume is not independently established; the source batch amount is retained without asserting a final concentration. |
Cross-reference to Medium M190
Explicit receiving-medium addition: 10 ml per liter, not grams per liter. Expand only the referenced Trace vitamins stock definition.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.530487Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M689 |
| 2026-01-28T19:48:20.152398Z | 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: NaOH |
| 2026-03-09T08:04:33.418082+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 4 solution(s) from ingredients |
| 2026-03-13T06:20:11.245911Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010094 |
| 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 |
| 2026-03-17T06:30:08.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:30.174113+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Spirochaeta Caldaria Medium" to "spirochaeta_caldaria_medium" for consistent matching |
| 2026-05-16T09:03:20.043601+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:43.562348+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 4 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-10-08T17:18:41.548273+00:00 | codex | RESTORED_M689_STOCK_DOSES_AND_COMPOSITIONS_WITH_EVIDENCE | Corrected four stock addition units, expanded the four named stocks at their own preparation stages, and withdrew unsupported batch-to-final concentration assertions. Preserved annotations/history and source batch quantities. Replaced the N2 quantity placeholder with source atmosphere context; chemical groundings remain unverified. |