glycerol_soil_medium

CultureMech:009760 bacterial COMPLEX SOLID_AGAR
Original name: Glycerol-Soil Medium

Overview

External ontology
TOGO:M379 — Glycerol-Soil Medium
Applications
  • Microbial cultivation
pH
7.0
Notes
JCM Medium 384 Glycerol-Soil Medium lists, per liter, 5.0 g Bacto peptone (BD-Difco), 3.0 g Beef extract (BD-Difco), 20.0 g Glycerol, 150 ml Soil extract, 850 ml Tap water, and 15.0 g Agar. The final pH is 7.0. Soil extract is prepared by autoclaving 400 g air-dried garden soil in 960 ml tap water at 121 C for 1 hr, cooling and settling the slurry, decanting and paper-filtering the supernatant, then autoclaving and storing it at room temperature until cleared by sedimentation.

Composition

flowchart LR
    CultureMech_009760["glycerol_soil_medium"]
    ing0_Bacto_peptone__BD_Difco_["Bacto peptone (BD-Difco)"]
    CultureMech_009760 --> ing0_Bacto_peptone__BD_Difco_
    ing1_Beef_extract__BD_Difco_["Beef extract (BD-Difco)"]
    CultureMech_009760 --> ing1_Beef_extract__BD_Difco_
    ing2_Glycerol["Glycerol"]
    CultureMech_009760 --> ing2_Glycerol
    CHEBI_17754["CHEBI:17754"]
    ing2_Glycerol -.-> CHEBI_17754
    ing3_Tap_water["Tap water"]
    CultureMech_009760 --> ing3_Tap_water
    CHEBI_15377["CHEBI:15377"]
    ing3_Tap_water -.-> CHEBI_15377
    ing4_Agar["Agar"]
    CultureMech_009760 --> ing4_Agar
    CHEBI_2509["CHEBI:2509"]
    ing4_Agar -.-> CHEBI_2509

Ingredients (5)

# Ingredient Concentration Ontology Notes
1 Bacto peptone (BD-Difco) 5.0 G_PER_L TOGO M379 / JCM Medium 384 lists 5.0 g/L Bacto peptone (BD-Difco).
2 Beef extract (BD-Difco) 3.0 G_PER_L TOGO M379 / JCM Medium 384 lists 3.0 g/L Beef extract (BD-Difco).
3 Glycerol
C3H8O3 92.094 g/mol
20.0 G_PER_L CHEBI:17754
glycerol
 TOGO M379 / JCM Medium 384 lists 20.0 g/L Glycerol.
4 Tap water
H2O 18.015 g/mol
850.0 ML_PER_L CHEBI:15377
water
 TOGO M379 / JCM Medium 384 lists 850.0 ml/L Tap water.
5 Agar 15.0 G_PER_L CHEBI:2509
agar
 TOGO M379 / JCM Medium 384 lists 15.0 g/L Agar.

Preparation

  1. Suspend 400 g air-dried garden soil in 960 ml tap water and autoclave at 121 C for 1 hr to prepare Soil extract.
  2. After the soil slurry is cooled and settled, decant the supernatant and filter it through paper.
  3. Autoclave the filtered Soil extract and store it at room temperature until cleared by sedimentation.
  4. Prepare the main liter with Bacto peptone, Beef extract, Glycerol, 150 ml Soil extract, 850 ml Tap water, and Agar.
  5. Adjust pH to 7.0.

Solutions

Soil extract

Dose: 150.0 ML_PER_L

Stock composition
IngredientConcentrationNotes
Tap water 960.0 ML_PER_L TOGO M379 / JCM Medium 384 prepares Soil extract from 960 ml Tap water with 400 g air-dried garden soil.
Air-dried garden soil 400.0 G_PER_L TOGO M379 / JCM Medium 384 prepares Soil extract from 400 g air-dried garden soil in 960 ml Tap water.
TOGO M379 / JCM Medium 384 adds 150 ml/L Soil extract to the main liter.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-27T06:35:54.947617Z togo-import Imported from TOGO Medium Source: JCM, ID: M379
2026-01-28T19:48:34.878401Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-13T03:09:29.549828Z data-quality-cleanup-v1.0 Data quality fixes Merged 1 duplicate ingredient(s)
2026-03-13T06:20:08.673872Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:009760
2026-03-17T06:30:39.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:27.668445+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Glycerol-Soil Medium" to "glycerol_soil_medium" for consistent matching
2026-06-05T07:40:40.892161+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 3 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:34.177911+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).
2026-09-11T00:00:00-07:00 repair_togo_m379_score15.py RESOLVED_TOGO_M379_SCORE15 JCM Medium 384 Glycerol-Soil Medium lists, per liter, 5.0 g Bacto peptone (BD-Difco), 3.0 g Beef extract (BD-Difco), 20.0 g Glycerol, 150 ml Soil extract, 850 ml Tap water, and 15.0 g Agar. The final pH is 7.0. Soil extract is prepared by autoclaving 400 g air-dried garden soil in 960 ml tap water at 121 C for 1 hr, cooling and settling the slurry, decanting and paper-filtering the supernatant, then autoclaving and storing it at room temperature until cleared by sedimentation. Corrected the imported water merge and ml-to-g/L artifacts, moved Soil extract to a 150 ml/L nested solution, and retained source-disclosed Bacto peptone and Beef extract as intentionally ungrounded products.