Overview
- External ontology
- komodo.medium:829.3 (source link unavailable) — For DSM 21157
- Applications
-
- Microbial cultivation
- pH
- 6.0
- Notes
- Source: KOMODO ModelSEED | ID: 829.3 | DSMZ Medium: 829 (mediadive.medium:829) | Aerobic: Yes Superseded historical provenance, not a current formulation claim: Commercial Product: LB Medium (Luria-Bertani, Miller formulation) Supplier: Multiple suppliers (Difco, Sigma, etc.) Catalog: Multiple (L3522 Sigma, 244520 BD) Source: https://www.laboratorynotes.com/preparation-of-luria-bertani-lb-miller-broth/ Accessed: 2026-03-28 Constituent composition researched from product specification. Preserve the provider's aerobic metadata as a source assertion, not a biological growth claim. Its linked original specifies anoxic preparation; any disagreement remains unresolved rather than silently overriding either source. The original's anoxic instructions and stock preparations are separate source context; they do not override the provider's exact reported table rates and nulls. This source reports sodium bicarbonate, whereas original DSMZ829 lists sodium carbonate. Preserve exact source chemical identity; do not rename or average the two formulations. Original DSMZ829 lists 0.50 g sodium carbonate per basal batch; this is source comparison, not permission to replace the provider's bicarbonate rate. The provider's displayed dithionite rate remains distinct from the original's 1 ml addition of 5% w/v stock; do not replace a source-specific rate with a different formulation's dilution. Original DSMZ829's dithionite stock strength and receiving input are separate from the KOMODO rate; the formulations are not certified identical. Original DSMZ829 separately instructs DSM16661 and DSM21157 to omit growth factors and use 2 bar after inoculation. The provider tables retain their own quantities; notably K829_16661 still lists the acids. Source/version disagreement is explicit, not silently resolved. Full exact-source recipe and stock/preparation tables were inspected. Reconstructed nodes retain explicit source scope; complete prior ingredient/stock assertions, including copied LB mappings and stage conflations, are archived in append-only history. A title alone is not the basis for removal. Unchanged annotations are preserved, not recertified; no new organism-growth association is added. Full exact-source recipe and stock/preparation tables were inspected. Reconstructed nodes retain explicit source scope; complete prior ingredient/stock assertions, including copied LB mappings and stage conflations, are archived in append-only history. A title alone is not the basis for removal. Unchanged annotations are preserved, not recertified; no new organism-growth association is added.
Composition
flowchart LR
CultureMech_006563["for_dsm_21157"]
ing0_NaHCO3["NaHCO3"]
CultureMech_006563 --> ing0_NaHCO3
ing1_D____Biotin["D(+)-Biotin"]
CultureMech_006563 --> ing1_D____Biotin
CHEBI_15956["CHEBI:15956"]
ing1_D____Biotin -.-> CHEBI_15956
ing2_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_006563 --> ing2_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing2_Calcium_pantothenate -.-> CHEBI_31345
ing3_CO2["CO2"]
CultureMech_006563 --> ing3_CO2
ing4_Nicotinic_acid["Nicotinic acid"]
CultureMech_006563 --> ing4_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing4_Nicotinic_acid -.-> CHEBI_15940
ing5_NaOH["NaOH"]
CultureMech_006563 --> ing5_NaOH
CHEBI_32145["CHEBI:32145"]
ing5_NaOH -.-> CHEBI_32145
ing6_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
CultureMech_006563 --> ing6_CoCl2_x_6_H2O
CHEBI_53503["CHEBI:53503"]
ing6_CoCl2_x_6_H2O -.-> CHEBI_53503
ing7_KH2PO4["KH2PO4"]
CultureMech_006563 --> ing7_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing7_KH2PO4 -.-> CHEBI_63036
ing8_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
CultureMech_006563 --> ing8_CuCl2_x_2_H2O
CHEBI_86318["CHEBI:86318"]
ing8_CuCl2_x_2_H2O -.-> CHEBI_86318
ing9_Vitamin_B12["Vitamin B12"]
CultureMech_006563 --> ing9_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing9_Vitamin_B12 -.-> CHEBI_176843
ing10_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
CultureMech_006563 --> ing10_FeCl2_x_4_H2O
CHEBI_86249["CHEBI:86249"]
ing10_FeCl2_x_4_H2O -.-> CHEBI_86249
ing11_Thiamine_HCl_x_2_H2O["Thiamine-HCl x 2 H2O"]
CultureMech_006563 --> ing11_Thiamine_HCl_x_2_H2O
CHEBI_132751["CHEBI:132751"]
ing11_Thiamine_HCl_x_2_H2O -.-> CHEBI_132751
ing12_HCl["HCl"]
CultureMech_006563 --> ing12_HCl
CHEBI_17883["CHEBI:17883"]
ing12_HCl -.-> CHEBI_17883
ing13_ZnCl2["ZnCl2"]
CultureMech_006563 --> ing13_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing13_ZnCl2 -.-> CHEBI_49976
ing14_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
CultureMech_006563 --> ing14_MnCl2_x_4_H2O
CHEBI_86368["CHEBI:86368"]
ing14_MnCl2_x_4_H2O -.-> CHEBI_86368
ing15_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_006563 --> ing15_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing15_Pyridoxine_HCl -.-> CHEBI_30961
ing16_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
CultureMech_006563 --> ing16_Na2MoO4_x_2_H2O
CHEBI_75213["CHEBI:75213"]
ing16_Na2MoO4_x_2_H2O -.-> CHEBI_75213
ing17_Resazurin["Resazurin"]
CultureMech_006563 --> ing17_Resazurin
ing18_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_006563 --> ing18_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing18_p_Aminobenzoic_acid -.-> CHEBI_30753
ing19_Sulfur["Sulfur"]
CultureMech_006563 --> ing19_Sulfur
CHEBI_26833["CHEBI:26833"]
ing19_Sulfur -.-> CHEBI_26833
ing20_Na2WO4_x_2_H2O["Na2WO4 x 2 H2O"]
CultureMech_006563 --> ing20_Na2WO4_x_2_H2O
CHEBI_63939["CHEBI:63939"]
ing20_Na2WO4_x_2_H2O -.-> CHEBI_63939
ing21_H2O["H2O"]
CultureMech_006563 --> ing21_H2O
ing22_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
CultureMech_006563 --> ing22_Na2SeO3_x_5_H2O
CHEBI_131361["CHEBI:131361"]
ing22_Na2SeO3_x_5_H2O -.-> CHEBI_131361
ing23_H2["H2"]
CultureMech_006563 --> ing23_H2
ing24_NH4Cl["NH4Cl"]
CultureMech_006563 --> ing24_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing24_NH4Cl -.-> CHEBI_31206
ing25_Sea_salt["Sea salt"]
CultureMech_006563 --> ing25_Sea_salt
ing26_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
CultureMech_006563 --> ing26_NiCl2_x_6_H2O
ing27_Na2_dithionite["Na2-dithionite"]
CultureMech_006563 --> ing27_Na2_dithionite
CHEBI_66870["CHEBI:66870"]
ing27_Na2_dithionite -.-> CHEBI_66870
ing28_H3BO3["H3BO3"]
CultureMech_006563 --> ing28_H3BO3
CHEBI_33118["CHEBI:33118"]
ing28_H3BO3 -.-> CHEBI_33118
ing29_MES["MES"]
CultureMech_006563 --> ing29_MES
CHEBI_39005["CHEBI:39005"]
ing29_MES -.-> CHEBI_39005
Ingredients (30)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | NaHCO3 | 1.00 G_PER_L | Exact-accession provider medium Gram Amount: 1.00 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | |
| 2 |
D(+)-Biotin
C10H16N2O3S 244.316 g/mol
|
2.00E-5 G_PER_L |
CHEBI:15956
biotin
|
Exact-accession provider medium Gram Amount: 2.00E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 3 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
1.00E-4 G_PER_L |
CHEBI:31345
Calcium pantothenate
|
Exact-accession provider medium Gram Amount: 1.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 4 | CO2 | Exact-accession provider medium Gram Amount is null; no fixed amount is asserted. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | ||
| 5 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
2.00E-4 G_PER_L |
CHEBI:15940
nicotinic acid
|
Exact-accession provider medium Gram Amount: 2.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 6 |
NaOH
HO.Na 39.997 g/mol
|
5.00E-4 G_PER_L |
CHEBI:32145
sodium hydroxide
|
Superseded flattening history, not a current quantity: [Collapsed 2 identical duplicates: 0.5, 0.5] Exact-accession provider medium Gram Amount: 5.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 7 |
CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
|
1.90E-4 G_PER_L |
CHEBI:53503
cobalt chloride hexahydrate
|
Exact-accession provider medium Gram Amount: 1.90E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 8 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.35 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Exact-accession provider medium Gram Amount: 0.35 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 9 |
CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
|
2.00E-6 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Exact-accession provider medium Gram Amount: 2.00E-6 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 10 | Vitamin B12 | 1.00E-4 G_PER_L |
CHEBI:176843
vitamin B12
|
Exact-accession provider medium Gram Amount: 1.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 11 |
FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
|
1.50E-3 G_PER_L |
CHEBI:86249
iron dichloride tetrahydrate
|
Exact-accession provider medium Gram Amount: 1.50E-3 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 12 |
Thiamine-HCl x 2 H2O
C12H18N4OS.2Cl.2H2O 373.306 g/mol
|
2.00E-4 G_PER_L |
CHEBI:132751
thiamine hydrochloride dihydrate
|
Exact-accession provider medium Gram Amount: 2.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 13 |
HCl
HCl 36.461 g/mol
|
6.72E-4 G_PER_L |
CHEBI:17883
hydrogen chloride
|
Exact-accession provider medium Gram Amount: 6.72E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 14 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
6.98E-5 G_PER_L |
CHEBI:49976
zinc dichloride
|
Exact-accession provider medium Gram Amount: 6.98E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 15 |
MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
|
9.98E-5 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Exact-accession provider medium Gram Amount: 9.98E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 16 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
3.00E-4 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Exact-accession provider medium Gram Amount: 3.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 17 |
Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
|
3.59E-5 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Exact-accession provider medium Gram Amount: 3.59E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 18 | Resazurin | 5.00E-4 G_PER_L | Exact-accession provider medium Gram Amount: 5.00E-4 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | |
| 19 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
8.00E-5 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Exact-accession provider medium Gram Amount: 8.00E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 20 |
Sulfur
S 32.067 g/mol
|
10.00 G_PER_L |
CHEBI:26833
sulfur atom
|
(powdered) Exact-accession provider medium Gram Amount: 10.00 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 21 |
Na2WO4 x 2 H2O
2H2O.2Na.O4W 329.846 g/mol
|
4.00E-6 G_PER_L |
CHEBI:63939
sodium tungstate dihydrate
|
Exact-accession provider medium Gram Amount: 4.00E-6 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 22 | H2O | Exact-accession provider medium Gram Amount is null; no fixed amount is asserted. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | ||
| 23 |
Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
|
3.00E-6 G_PER_L |
CHEBI:131361
disodium selenite pentahydrate
|
Exact-accession provider medium Gram Amount: 3.00E-6 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 24 | H2 | Exact-accession provider medium Gram Amount is null; no fixed amount is asserted. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | ||
| 25 |
NH4Cl
Cl.H4N 53.492 g/mol
|
1.00 G_PER_L |
CHEBI:31206
ammonium chloride
|
Exact-accession provider medium Gram Amount: 1.00 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 26 | Sea salt | 30.00 G_PER_L | Exact-accession provider medium Gram Amount: 30.00 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. | |
| 27 | NiCl2 x 6 H2O | 2.39E-5 G_PER_L | Exact-accession provider medium Gram Amount: 2.39E-5 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. Copied annotations do not establish this exact salt, hydrate or stereochemical form; archive them without inventing replacement identifiers. | |
| 28 |
Na2-dithionite
2Na.O4S2 174.11 g/mol
|
0.02 G_PER_L |
CHEBI:66870
sodium dithionite
|
Exact-accession provider medium Gram Amount: 0.02 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 29 |
H3BO3
H3BO3 61.833 g/mol
|
5.99E-6 G_PER_L |
CHEBI:33118
boric acid
|
Exact-accession provider medium Gram Amount: 5.99E-6 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
| 30 |
MES
C6H13NO4S 195.24 g/mol
|
1.95 G_PER_L |
CHEBI:39005
2-(N-morpholino)ethanesulfonic acid
|
Exact-accession provider medium Gram Amount: 1.95 g/L, preserving displayed precision. This is a source-reported rate or null, not an inferred stock dose or a normalization from the linked DSMZ recipe. Mol Amount and SEED aggregates are not adopted. |
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T01:15:03.fZ | komodo-web-import | Imported from KOMODO web table | Source: KOMODO, ID: 829.3 |
| 2026-02-03T11:19:16.583010 | dsmz-resolver-v1.0 | Enriched with DSMZ composition | Copied ingredients from DSMZ Medium 829 |
| 2026-03-13T03:09:35.717224Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:41.945775Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:006563 |
| 2026-03-17T06:30:46.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:45:59.477610+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "For DSM 21157" to "for_dsm_21157" for consistent matching |
| 2026-06-05T07:41:03.501796+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 29 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:58.043190+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 5 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-15T00:17:30.394828+00:00 | apply_cocktail_nesting.py | NESTED_FLATTENED_COCKTAIL | Moved 5 stock-strength component(s) out of ingredients into 2 solution(s): 1 -> 'Trace element solution SL-10' @ 1 ml/l; 4 -> 'Seven vitamins solution' @ 1 ml/l. Each moved component matched the MediaDive stock by name AND value; bulk ingredients sharing a name were left in place (#150). |
| 2026-08-15T20:08:01.494270+00:00 | dedupe_identical_ingredients.py | REMOVED_DUPLICATE_INGREDIENT_ROWS | Removed 3 ingredient row(s) that were identical in every field to another row in this record, which made the recipe read as double-strength in those components (#263): Sodium chloride, Tryptone, Yeast extract. |
| 2026-09-02T07:38:07.214880+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |
| 2026-09-13T00:00:00-07:00 | repair_komodo_829_desulfurobacterium_ph_score10.py | RESOLVED_KOMODO_829_DESULFUROBACTERIUM_STRAIN_VARIANT | KOMODO Medium 829.3 preserves DESULFUROBACTERIUM MEDIUM components and pH 6 but applies the recipe for DSM 21157. |
| 2026-10-09T04:52:49.323535+00:00 | codex | RESTORED_MEDIUM_829_SOURCE_FORMULATIONS_AND_STOCK_SCOPES_WITH_EVIDENCE | Restore exact-source medium-829 formulations and stock boundaries, preserve provider rates/nulls and source conflicts, repair quantity units and family scope, and retain prior evidence/history. Each scientific change is linked to an inspected source excerpt; no growth association inferred. |