Overview
- External ontology
- TOGO:M2313 — minimal media
- Applications
-
- Microbial cultivation
- pH
- 7.8
- Notes
- TOGO M2313 describes minimal media containing 2.3% w/v sea salts, 0.05% w/v yeast extract, 0.05% w/v NH4Cl, and 50 mM Tris-HCl at pH 7.8, with a final concentration of 0.2% w/v of one listed carbon source.
Composition
flowchart LR
CultureMech_008900["minimal_media"]
ing0_yeast_extract["yeast extract"]
CultureMech_008900 --> ing0_yeast_extract
ing1_NH4Cl["NH4Cl"]
CultureMech_008900 --> ing1_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing1_NH4Cl -.-> CHEBI_31206
ing2_D_glucose["D-glucose"]
CultureMech_008900 --> ing2_D_glucose
CHEBI_17634["CHEBI:17634"]
ing2_D_glucose -.-> CHEBI_17634
ing3_N_acetyl_D_glucosamine["N-acetyl-D-glucosamine"]
CultureMech_008900 --> ing3_N_acetyl_D_glucosamine
CHEBI_8006["CHEBI:8006"]
ing3_N_acetyl_D_glucosamine -.-> CHEBI_8006
ing4_Tris_HCl["Tris-HCl"]
CultureMech_008900 --> ing4_Tris_HCl
ing5_D_galactose["D-galactose"]
CultureMech_008900 --> ing5_D_galactose
CHEBI_12936["CHEBI:12936"]
ing5_D_galactose -.-> CHEBI_12936
ing6_D_xylose["D-xylose"]
CultureMech_008900 --> ing6_D_xylose
CHEBI_65327["CHEBI:65327"]
ing6_D_xylose -.-> CHEBI_65327
ing7_D_galacturonic_acid["D-galacturonic acid"]
CultureMech_008900 --> ing7_D_galacturonic_acid
CHEBI_18024["CHEBI:18024"]
ing7_D_galacturonic_acid -.-> CHEBI_18024
ing8_L_arabinose["L-arabinose"]
CultureMech_008900 --> ing8_L_arabinose
CHEBI_30849["CHEBI:30849"]
ing8_L_arabinose -.-> CHEBI_30849
ing9_L_rhamnose["L-rhamnose"]
CultureMech_008900 --> ing9_L_rhamnose
CHEBI_62345["CHEBI:62345"]
ing9_L_rhamnose -.-> CHEBI_62345
ing10_D_mannose["D-mannose"]
CultureMech_008900 --> ing10_D_mannose
CHEBI_16024["CHEBI:16024"]
ing10_D_mannose -.-> CHEBI_16024
ing11_D_trehalose["D-trehalose"]
CultureMech_008900 --> ing11_D_trehalose
CHEBI_27082["CHEBI:27082"]
ing11_D_trehalose -.-> CHEBI_27082
ing12_xylan__oat_spelts_["xylan (oat spelts)"]
CultureMech_008900 --> ing12_xylan__oat_spelts_
ing13_pectin__apple_["pectin (apple)"]
CultureMech_008900 --> ing13_pectin__apple_
ing14_pectin__citrus_peel_["pectin (citrus peel)"]
CultureMech_008900 --> ing14_pectin__citrus_peel_
ing15_galatcomannan__Ceratonia_siliqua_["galatcomannan (Ceratonia siliqua)"]
CultureMech_008900 --> ing15_galatcomannan__Ceratonia_siliqua_
ing16_mannan__Saccharomyces_cerevisiae_["mannan (Saccharomyces cerevisiae)"]
CultureMech_008900 --> ing16_mannan__Saccharomyces_cerevisiae_
ing17_arabinan__sugar_beet_["arabinan (sugar beet)"]
CultureMech_008900 --> ing17_arabinan__sugar_beet_
ing18_arabinogalactan__larch_["arabinogalactan (larch)"]
CultureMech_008900 --> ing18_arabinogalactan__larch_
ing19_laminarin__brown_algae_["laminarin (brown algae)"]
CultureMech_008900 --> ing19_laminarin__brown_algae_
ing20_chitin__shrimp_shells_["chitin (shrimp shells)"]
CultureMech_008900 --> ing20_chitin__shrimp_shells_
ing21_sea_salts["sea salts"]
CultureMech_008900 --> ing21_sea_salts
ing22_alginate__brown_algae_["alginate (brown algae)"]
CultureMech_008900 --> ing22_alginate__brown_algae_
Ingredients (23)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | yeast extract | 0.05 PERCENT_W_V |
FOODON:03315426
Yeast extract
|
TOGO M2313 lists 0.05% w/v yeast extract in the shared sea-salts/Tris minimal-media base. |
| 2 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.05 PERCENT_W_V |
CHEBI:31206
ammonium chloride
|
TOGO M2313 lists 0.05% w/v NH4Cl in the shared sea-salts/Tris minimal-media base. |
| 3 |
D-glucose
C6H12O6 180.156 g/mol
|
0.2 PERCENT_W_V |
CHEBI:17634
D-glucose
|
TOGO M2313 lists D-glucose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 4 |
N-acetyl-D-glucosamine
C34H60N8O18 868.892 g/mol
|
0.2 PERCENT_W_V |
CHEBI:8006
Peptidoglycan(N-acetyl-D-glucosamine)
|
TOGO M2313 lists N-acetyl-D-glucosamine as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 5 | Tris-HCl | 50.0 MILLIMOLAR | TOGO M2313 lists 50 mM Tris-HCl at pH 7.8 in the shared minimal-media base; this pH-specific buffer is retained without a single-molecule ontology grounding and remains intentionally unmapped. | |
| 6 |
D-galactose
C6H12O6 180.156 g/mol
|
0.2 PERCENT_W_V |
CHEBI:12936
D-galactose
|
TOGO M2313 lists D-galactose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 7 |
D-xylose
C5H10O5 150.13 g/mol
|
0.2 PERCENT_W_V |
CHEBI:65327
D-xylose
|
TOGO M2313 lists D-xylose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 8 |
D-galacturonic acid
C6H10O7 194.14 g/mol
|
0.2 PERCENT_W_V |
CHEBI:18024
D-galacturonic acid
|
TOGO M2313 lists D-galacturonic acid as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 9 |
L-arabinose
C5H10O5 150.13 g/mol
|
0.2 PERCENT_W_V |
CHEBI:30849
L-arabinose
|
TOGO M2313 lists L-arabinose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 10 | L-rhamnose | 0.2 PERCENT_W_V |
CHEBI:62345
L-rhamnose
|
TOGO M2313 lists L-rhamnose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 11 |
D-mannose
C6H12O6 180.156 g/mol
|
0.2 PERCENT_W_V |
CHEBI:16024
D-mannose
|
TOGO M2313 lists D-mannose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 12 |
D-trehalose
C12H22O11 342.297 g/mol
|
0.2 PERCENT_W_V |
CHEBI:27082
trehalose
|
TOGO M2313 lists D-trehalose as one of the alternative carbon sources tested at a final concentration of 0.2% w/v. |
| 13 | xylan (oat spelts) | 0.2 PERCENT_W_V | TOGO M2313 lists xylan from oat spelts as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. | |
| 14 | pectin (apple) | 0.2 PERCENT_W_V | TOGO M2313 lists pectin from apple as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. | |
| 15 | pectin (citrus peel) | 0.2 PERCENT_W_V | TOGO M2313 lists pectin from citrus peel as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. | |
| 16 | galatcomannan (Ceratonia siliqua) | 0.2 PERCENT_W_V | TOGO M2313 lists galatcomannan from Ceratonia siliqua as an alternative carbon source; this source-qualified locust-bean gum remains intentionally unmapped. | |
| 17 | mannan (Saccharomyces cerevisiae) | 0.2 PERCENT_W_V | TOGO M2313 lists mannan from Saccharomyces cerevisiae as an alternative carbon source; this source-qualified yeast mannan remains intentionally unmapped. | |
| 18 | arabinan (sugar beet) | 0.2 PERCENT_W_V | TOGO M2313 lists arabinan from sugar beet as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. | |
| 19 | arabinogalactan (larch) | 0.2 PERCENT_W_V | TOGO M2313 lists arabinogalactan from larch as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. | |
| 20 | laminarin (brown algae) | 0.2 PERCENT_W_V | TOGO M2313 lists laminarin from brown algae at 0.2% w/v; this source-qualified polysaccharide remains intentionally unmapped. | |
| 21 | chitin (shrimp shells) | 0.2 PERCENT_W_V | TOGO M2313 lists chitin from shrimp shells as an alternative carbon source; this source-qualified chitin remains intentionally unmapped. | |
| 22 | sea salts | 2.3 PERCENT_W_V | TOGO M2313 lists 2.3% w/v sea salts; this heterogeneous salt mixture remains intentionally unmapped. | |
| 23 | alginate (brown algae) | 0.2 PERCENT_W_V | TOGO M2313 lists alginate from brown algae as an alternative carbon source; this source-qualified polysaccharide remains intentionally unmapped. |
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:56.326504Z | togo-import | Imported from TOGO Medium | Source: TOGO, ID: M2313 |
| 2026-01-28T19:48:17.980480Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:25.566835Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:20:01.158811Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008900 |
| 2026-03-17T06:30:03.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:19.863510+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "minimal media" to "minimal_media" for consistent matching |
| 2026-06-05T07:41:34.639615+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 9 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:47:08.058554+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. |
| 2026-08-20T19:02:54.583252+00:00 | apply_mim_groundings.py | Adopted MIM published grounding | Grounded 1 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308). |
| 2026-09-12T00:00:00-07:00 | repair_togo_m2313_minimal_media_score15.py | RESOLVED_TOGO_M2313_SCORE15 | TOGO M2313 describes minimal media containing 2.3% w/v sea salts, 0.05% w/v yeast extract, 0.05% w/v NH4Cl, and 50 mM Tris-HCl at pH 7.8, with a final concentration of 0.2% w/v of one listed carbon source. Added the source pH, grounded yeast extract, and kept the disclosed source-qualified polysaccharides, Tris-HCl, and sea salts intentionally unmapped. |