Overview
- External ontology
- mediadive.medium:J1008 (source link unavailable) — MODIFIED HALOBACTERIA MEDIUM-3
- Applications
-
- Microbial cultivation
- pH
- 7.5
- Notes
- Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1008 Ingredient amounts use the exact formulation and preparation stage. Separate preparation excerpt: "Add components to distilled water and bring volume to 1.0 L.". Conditional solid option: "For preparation of solid medium, add 20.0 g/L agar.". Agar is included only in M372/M960 in this reviewed variant cohort; no step ordering is invented. JCM1008 explicitly states the modified 270 g/L NaCl and 15 g/L magnesium sulfate heptahydrate formulation, corroborated by TOGO M1065's g/L rows. The word supplemented leaves an operational ambiguity: adding magnesium to the unchanged 20 g/L base cannot lower its concentration to 15 g/L. No 35 g/L magnesium or 470 g/L sodium chloride sum is inferred, and this curation does not resolve that preparation ambiguity.
Composition
flowchart LR
CultureMech_002192["modified_halobacteria_medium_3"]
ing0_Casamino_acids["Casamino acids"]
CultureMech_002192 --> ing0_Casamino_acids
ing1_Yeast_extract["Yeast extract"]
CultureMech_002192 --> ing1_Yeast_extract
ing2_Na_glutamate["Na glutamate"]
CultureMech_002192 --> ing2_Na_glutamate
CHEBI_64220["CHEBI:64220"]
ing2_Na_glutamate -.-> CHEBI_64220
ing3_Trisodium_citrate["Trisodium citrate"]
CultureMech_002192 --> ing3_Trisodium_citrate
CHEBI_53258["CHEBI:53258"]
ing3_Trisodium_citrate -.-> CHEBI_53258
ing4_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
CultureMech_002192 --> ing4_MgSO4_x_7_H2O
CHEBI_31795["CHEBI:31795"]
ing4_MgSO4_x_7_H2O -.-> CHEBI_31795
ing5_KCl["KCl"]
CultureMech_002192 --> ing5_KCl
CHEBI_32588["CHEBI:32588"]
ing5_KCl -.-> CHEBI_32588
ing6_NaCl["NaCl"]
CultureMech_002192 --> ing6_NaCl
CHEBI_26710["CHEBI:26710"]
ing6_NaCl -.-> CHEBI_26710
ing7_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
CultureMech_002192 --> ing7_FeCl2_x_4_H2O
CHEBI_86249["CHEBI:86249"]
ing7_FeCl2_x_4_H2O -.-> CHEBI_86249
ing8_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
CultureMech_002192 --> ing8_MnCl2_x_4_H2O
CHEBI_86368["CHEBI:86368"]
ing8_MnCl2_x_4_H2O -.-> CHEBI_86368
ing9_distilled_water["distilled water"]
CultureMech_002192 --> ing9_distilled_water
Ingredients (10)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | Casamino acids | 5 G_PER_L | Copied from referenced JCM Medium 168 5.0 g in the source preparation brought to 1.0 L gives 5 G_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". | |
| 2 | Yeast extract | 5 G_PER_L | Copied from referenced JCM Medium 168 5.0 g in the source preparation brought to 1.0 L gives 5 G_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". | |
| 3 |
Na glutamate
C5H8NO4.Na 169.112 g/mol
|
1 G_PER_L |
CHEBI:64220
monosodium glutamate
|
Copied from referenced JCM Medium 168 1.0 g in the source preparation brought to 1.0 L gives 1 G_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". |
| 4 |
Trisodium citrate
C6H5O7.3Na 258.069 g/mol
|
3 G_PER_L |
CHEBI:53258
sodium citrate
|
Copied from referenced JCM Medium 168 3.0 g in the source preparation brought to 1.0 L gives 3 G_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". |
| 5 |
MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
|
15 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Copied from referenced JCM Medium 168 Use the recipe-specific final formulation, not the copied base amount. JCM1008 explicitly states the modified 270 g/L NaCl and 15 g/L magnesium sulfate heptahydrate formulation, corroborated by TOGO M1065's g/L rows. The word supplemented leaves an operational ambiguity: adding magnesium to the unchanged 20 g/L base cannot lower its concentration to 15 g/L. No 35 g/L magnesium or 470 g/L sodium chloride sum is inferred, and this curation does not resolve that preparation ambiguity. |
| 6 |
KCl
Cl.K 74.551 g/mol
|
2 G_PER_L |
CHEBI:32588
potassium chloride
|
Copied from referenced JCM Medium 168 2.0 g in the source preparation brought to 1.0 L gives 2 G_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". |
| 7 |
NaCl
Cl.Na 58.443 g/mol
|
270 G_PER_L |
CHEBI:26710
sodium chloride
|
Copied from referenced JCM Medium 168 Use the recipe-specific final formulation, not the copied base amount. JCM1008 explicitly states the modified 270 g/L NaCl and 15 g/L magnesium sulfate heptahydrate formulation, corroborated by TOGO M1065's g/L rows. The word supplemented leaves an operational ambiguity: adding magnesium to the unchanged 20 g/L base cannot lower its concentration to 15 g/L. No 35 g/L magnesium or 470 g/L sodium chloride sum is inferred, and this curation does not resolve that preparation ambiguity. |
| 8 |
FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
|
36 MG_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
Copied from referenced JCM Medium 168 36.0 mg in the source preparation brought to 1.0 L gives 36 MG_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". |
| 9 |
MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.36 MG_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Copied from referenced JCM Medium 168 0.36 mg in the source preparation brought to 1.0 L gives 0.36 MG_PER_L. Separate exact volume excerpt: "Add components to distilled water and bring volume to 1.0 L.". |
| 10 | distilled water | Water makes the preparation up to 1.0 L. Its separate input volume and mass are unspecified; neither 1 g/L nor a fixed 1 L water dose is supported. |
Preparation
- Use Medium No. 168 supplemented with 270.0 g/L NaCl (final) and 15.0 g/L MgSO4 x 7H2O. Adjust pH to 7.5.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-26T17:53:18.301275Z | mediadive-import | Imported from MediaDive | Source: JCM, ID: J1008 |
| 2026-02-03T11:26:52.545243 | quality-tagger-v1.0 | Added data quality flag | Marked as incomplete_composition due to placeholder ingredients |
| 2026-03-13T06:19:11.118644Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:002192 |
| 2026-03-17T19:45:23.870146+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "MODIFIED HALOBACTERIA MEDIUM-3" to "modified_halobacteria_medium_3" for consistent matching |
| 2026-04-04T18:49:19.145578 | copy_referenced_compositions | RESOLVED_REFERENCE | Resolved reference by copying from halobacteria_medium (CultureMech:002527) |
| 2026-05-16T08:58:09.570492+00:00 | migrate_data_quality_flags.py | MIGRATED_DATA_QUALITY_FLAGS | dict(2 keys) -> list(1 entries) |
| 2026-06-05T07:41:36.684686+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 8 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:48.808854+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 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). |
| 2026-10-09T14:23:51.976655+00:00 | codex | CURATED_HALOBACTERIA_VARIANT_CONCENTRATIONS_AND_PREPARATION_STAGES | Source-specific ingredient and variant review. Every change has an exact PURL-backed excerpt. Prepared-base quantities, unquantified water/titrant, source limitations, chemical identities and prior history are preserved; no taxa-media assertions are added. |