Overview
- External ontology
- TOGO:M260 — MJ/YPGS Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M260 Original source: JCM - JCM_M268 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=268
Composition
flowchart LR
CultureMech_009177["mj_ypgs_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009177 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Sodium_succinate["Sodium succinate"]
CultureMech_009177 --> ing1_Sodium_succinate
CHEBI_63675["CHEBI:63675"]
ing1_Sodium_succinate -.-> CHEBI_63675
ing2_Na2SiO3_9H2O["Na2SiO3・9H2O"]
CultureMech_009177 --> ing2_Na2SiO3_9H2O
CHEBI_132108["CHEBI:132108"]
ing2_Na2SiO3_9H2O -.-> CHEBI_132108
ing3_Glucose["Glucose"]
CultureMech_009177 --> ing3_Glucose
CHEBI_17234["CHEBI:17234"]
ing3_Glucose -.-> CHEBI_17234
ing4_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_009177 --> ing4_Yeast_extract__BD_Difco_
ing5_Na2S2O3_5H2O["Na2S2O3・5H2O"]
CultureMech_009177 --> ing5_Na2S2O3_5H2O
CHEBI_32150["CHEBI:32150"]
ing5_Na2S2O3_5H2O -.-> CHEBI_32150
ing6_Bacto_peptone__BD_Difco_["Bacto peptone (BD-Difco)"]
CultureMech_009177 --> ing6_Bacto_peptone__BD_Difco_
Ingredients (7)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
0.9 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 900.0, 1.0] Source water batch input: 900 ml = 0.9 L. This is not a measured final volume. The earlier duplicate-summing note is superseded: it combined separate preparation scopes and source units. This node carries only the batch input at the cited source row; other occurrences are separate scoped ingredients. |
| 2 |
Sodium succinate
C4H4O4.2Na 162.052 g/mol
|
CHEBI:63675
sodium succinate (anhydrous)
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component Source batch input: 0.2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 3 |
Na2SiO3・9H2O
9H2O.2Na.O3Si 284.198 g/mol
|
CHEBI:132108
sodium silicate nonahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 4 |
Glucose
C6H12O6 180.156 g/mol
|
CHEBI:17234
glucose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component Source batch input: 0.2 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 5 | Yeast extract (BD-Difco) | Properties: Undefined component Source batch input: 1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | ||
| 6 |
Na2S2O3・5H2O
5H2O.2Na.O3S2 248.186 g/mol
|
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Inorganic compound, Simple component, Defined component Source batch input: 2.48 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| 7 | Bacto peptone (BD-Difco) | Properties: Undefined component Source batch input: 1 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. |
Preparation
- Adjust pH to 7.5.
Solutions
MJ(-N) synthetic seawater (see below)
Dose: 0.1 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 900.0, 1.0] Source water batch input: 1 L = 1 L. This is not a measured final volume. The earlier duplicate-summing note is superseded: it combined separate preparation scopes and source units. This node carries only the batch input at the cited source row; other occurrences are separate scoped ingredients. |
| MgSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 3.4 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NaCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 30 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| CaCl2・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.14 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| K2HPO4 | Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.14 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| MgCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 4.18 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| KCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.33 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. | |
| NiCl2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, 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. | |
| Na2SeO3・5H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, 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. | |
| Fe(NH4)2(SO4)2・6H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Source batch input: 0.01 g. Final preparation volume is not independently established; the unsupported g/L assertion is withdrawn, not replaced by an assumed one-liter concentration. |
Source stock addition: 100 ml = 0.1 L per receiving batch, not grams per liter or a dose per final liter.
Expand only this named preparation, not the complete referenced medium. Water input does not establish final stock volume; no final-medium rate is inferred.
Trace minerals (see Medium [M142])
Dose: 0.01 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
Source stock addition: 10 ml = 0.01 L per receiving batch, not grams per liter or a dose per final liter. This dose belongs to the enclosing stock preparation, not directly to the final medium.
Expand only this named preparation, not the complete referenced medium. Water input does not establish final stock volume; no final-medium rate is inferred.
KOH solution
Stock pH-adjustment reagent with no fixed dose or numeric strength.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.720054Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M260 |
| 2026-01-28T19:48:20.097996Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-03-09T08:04:33.342402+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 1 solution(s) from ingredients |
| 2026-03-13T03:09:02.759348Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:20:03.668112Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009177 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name |
| 2026-03-17T06:30:08.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:22.398497+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "MJ/YPGS Medium" to "mj_ypgs_medium" for consistent matching |
| 2026-05-16T09:03:14.633545+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=1 |
| 2026-06-05T07:40:37.905913+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 6 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T06:57:27.526236+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:46:49.408380+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 1 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-10-08T20:12:07.152932+00:00 | codex | REPAIRED_M258_IDENTITY_AND_M260_NESTED_STOCK_WITH_EVIDENCE | Corrected stock boundaries and unsupported quantity assertions with exact batch-amount evidence. M258 supersedes its erroneous LB expansion and restores alpha-methylbutyric acid, rumen/fatty-acid preparations and separate reducing agents. M260 nests the trace-mineral dose inside MJ(-N) seawater. Preserved unrelated annotations and append-only history. No final volume, percent basis or chemical grounding inferred. |