for_dsm_16632_and_dsm_16643 (CultureMech:003918)

Overview

External ontology

komodo.medium:119.1 (source link unavailable) — For DSM 16632 and DSM 16643

Applications

Microbial cultivation

pH

7.5

Notes

pH buffer: NaOH | Source: KOMODO ModelSEED | ID: 119.1 | DSMZ Medium: 119 (mediadive.medium:119) | Aerobic: Yes Superseded historical provenance (not a current formulation claim): Commercial Product: LB Medium (Luria-Bertani, Miller formulation) Supplier: Multiple suppliers (Difco,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. Provider aerobic=true and pH=7.5 metadata disagree with the linked DSMZ anoxic preparation and complete-medium pH 6.8-7.0. Retain provider scope without asserting a resolved oxygen requirement. The linked original uses anoxic preparation; its individual stock inputs and strain instructions must not silently replace this provider's reported medium rates. Linked original instruction (For DSM 1093, DSM 1125, DSM 11977, DSM 11978, DSM 11995, DSM 16643): Supplement medium after autoclaving with 1 ml/l Wolin's vitamin solution (10x, see medium 120), 0.30 g/l DL-dithiothreitol, and 0.15 g/l coenzyme M (2-mercaptoethanesulfonic acid) from anoxic stock solutions sterilized by filtration. Omit Na2S x 9 H2O and L-Cysteine HCl x H2O. This is a separate source/strain prescription, not an overwrite of the KOMODO table or new growth evidence. Any disagreement remains explicit. Linked original instruction (For DSM 16632): Replace sludge fluid with the same volume of clarified rumen fluid (see medium 1310) and supplement medium with 2.00 g/l Trypticase peptone and 10.00 ml/l of Wolin's vitamin solution (see medium 141). This is a separate source/strain prescription, not an overwrite of the KOMODO table or new growth evidence. Any disagreement remains explicit. Archive all prior ingredient nodes, including false LB expansion, combined yeast amounts and copied or chemically inexact annotations, in append-only history. New nodes follow this exact source's stage and label; other unchanged chemical annotations are preserved, not recertified. Source-scoped recipe inputs supersede unsupported flattened concentrations and false LB identities. All prior history and permanent IDs remain unchanged; unquantified quantities remain unknown. No taxa-media association is added.

Composition

flowchart LR
    CultureMech_003918["for_dsm_16632_and_dsm_16643"]
    ing0_NaHCO3["NaHCO3"]
    CultureMech_003918 --> ing0_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing0_NaHCO3 -.-> CHEBI_32139
    ing1_D_Ca_pantothenate["D-Ca-pantothenate"]
    CultureMech_003918 --> ing1_D_Ca_pantothenate
    ing2_Lipoic_acid["Lipoic acid"]
    CultureMech_003918 --> ing2_Lipoic_acid
    ing3_Na2S_x_9_H2O["Na2S x 9 H2O"]
    CultureMech_003918 --> ing3_Na2S_x_9_H2O
    CHEBI_76209["CHEBI:76209"]
    ing3_Na2S_x_9_H2O -.-> CHEBI_76209
    ing4_Cysteine_HCl_x_H2O["Cysteine-HCl x H2O"]
    CultureMech_003918 --> ing4_Cysteine_HCl_x_H2O
    ing5_Isovaleric_acid["Isovaleric acid"]
    CultureMech_003918 --> ing5_Isovaleric_acid
    CHEBI_28484["CHEBI:28484"]
    ing5_Isovaleric_acid -.-> CHEBI_28484
    ing6_CO2["CO2"]
    CultureMech_003918 --> ing6_CO2
    ing7_Nicotinic_acid["Nicotinic acid"]
    CultureMech_003918 --> ing7_Nicotinic_acid
    ing8_Riboflavin["Riboflavin"]
    CultureMech_003918 --> ing8_Riboflavin
    ing9_NaOH["NaOH"]
    CultureMech_003918 --> ing9_NaOH
    CHEBI_32145["CHEBI:32145"]
    ing9_NaOH -.-> CHEBI_32145
    ing10_KH2PO4["KH2PO4"]
    CultureMech_003918 --> ing10_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing10_KH2PO4 -.-> CHEBI_63036
    ing11_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_003918 --> ing11_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing11_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing12_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_003918 --> ing12_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing12_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing13_Vitamin_B12["Vitamin B12"]
    CultureMech_003918 --> ing13_Vitamin_B12
    ing14_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
    CultureMech_003918 --> ing14_FeCl2_x_4_H2O
    CHEBI_86249["CHEBI:86249"]
    ing14_FeCl2_x_4_H2O -.-> CHEBI_86249
    ing15_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_003918 --> ing15_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing15_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing16_Folic_acid["Folic acid"]
    CultureMech_003918 --> ing16_Folic_acid
    ing17_Thiamine_HCl_x_2_H2O["Thiamine-HCl x 2 H2O"]
    CultureMech_003918 --> ing17_Thiamine_HCl_x_2_H2O
    ing18_HCl["HCl"]
    CultureMech_003918 --> ing18_HCl
    CHEBI_17883["CHEBI:17883"]
    ing18_HCl -.-> CHEBI_17883
    ing19_ZnCl2["ZnCl2"]
    CultureMech_003918 --> ing19_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing19_ZnCl2 -.-> CHEBI_49976
    ing20_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_003918 --> ing20_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing20_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing21_Yeast_extract["Yeast extract"]
    CultureMech_003918 --> ing21_Yeast_extract
    ing22_Pyridoxine_HCl["Pyridoxine HCl"]
    CultureMech_003918 --> ing22_Pyridoxine_HCl
    ing23_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_003918 --> ing23_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing23_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing24_Na_formate["Na-formate"]
    CultureMech_003918 --> ing24_Na_formate
    CHEBI_62965["CHEBI:62965"]
    ing24_Na_formate -.-> CHEBI_62965
    ing25_Resazurin["Resazurin"]
    CultureMech_003918 --> ing25_Resazurin
    ing26_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_003918 --> ing26_p_Aminobenzoic_acid
    ing27_H2O["H2O"]
    CultureMech_003918 --> ing27_H2O
    ing28_2_Methylbutyric_acid["2-Methylbutyric acid"]
    CultureMech_003918 --> ing28_2_Methylbutyric_acid
    ing29_rumen_fluid["rumen fluid"]
    CultureMech_003918 --> ing29_rumen_fluid
    CultureMech_003918 --> more["...13 more"]

Ingredients (43)

#	Ingredient	Concentration	Ontology	Notes
1	NaHCO3 CHO3.Na 84.006 g/mol	3.92 G_PER_L	CHEBI:32139 sodium hydrogencarbonate	Provider-reported rate: 3.92 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
2	D-Ca-pantothenate	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
3	Lipoic acid	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
4	Na2S x 9 H2O 9H2O.2Na.S 240.182 g/mol	0.49 G_PER_L	CHEBI:76209 sodium sulfide nonahydrate	Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
5	Cysteine-HCl x H2O	0.49 G_PER_L		Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted. Copied annotations do not establish the source's exact chemical form; withdraw them, preserve the literal source name, and archive the prior node. No replacement ontology identifier is inferred.
6	Isovaleric acid C5H10O2 102.133 g/mol	0.49 G_PER_L	CHEBI:28484 isovaleric acid	Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
7	CO2			Provider Gram Amount is null; no fixed amount is asserted and missing is not zero. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
8	Nicotinic acid	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
9	Riboflavin	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
10	NaOH HO.Na 39.997 g/mol		CHEBI:32145 sodium hydroxide	Provider Gram Amount is null; no fixed amount is asserted and missing is not zero. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
11	KH2PO4 H2O4P.K 136.084 g/mol	0.49 G_PER_L	CHEBI:63036 potassium dihydrogen phosphate	Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
12	CoCl2 x 6 H2O 2Cl.Co.6H2O 237.929 g/mol	1.86E-4 G_PER_L	CHEBI:53503 cobalt chloride hexahydrate	Provider-reported rate: 1.86E-4 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
13	CuCl2 x 2 H2O Cl2Cu.2H2O 170.482 g/mol	1.95E-6 G_PER_L	CHEBI:86318 copper(II) chloride dihydrate	Provider-reported rate: 1.95E-6 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
14	Vitamin B12	9.79E-7 G_PER_L		Provider-reported rate: 9.79E-7 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
15	FeCl2 x 4 H2O Cl2Fe.4H2O 198.811 g/mol	1.47E-3 G_PER_L	CHEBI:86249 iron dichloride tetrahydrate	Provider-reported rate: 1.47E-3 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
16	MgSO4 x 7 H2O 7H2O.Mg.O4S 246.473 g/mol	0.39 G_PER_L	CHEBI:31795 magnesium sulfate heptahydrate	Provider-reported rate: 0.39 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
17	Folic acid	1.96E-5 G_PER_L		Provider-reported rate: 1.96E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
18	Thiamine-HCl x 2 H2O	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
19	HCl HCl 36.461 g/mol	6.58E-4 G_PER_L	CHEBI:17883 hydrogen chloride	Provider-reported rate: 6.58E-4 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
20	ZnCl2 2Cl.Zn 136.296 g/mol	6.84E-5 G_PER_L	CHEBI:49976 zinc dichloride	Provider-reported rate: 6.84E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
21	MnCl2 x 4 H2O Cl2Mn.4H2O 197.904 g/mol	9.77E-5 G_PER_L	CHEBI:86368 manganese(II) chloride tetrahydrate	Provider-reported rate: 9.77E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
22	Yeast extract	0.98 G_PER_L		Superseded flattening history, not a current amount: [Merged 2 duplicates: 0.996016, 4.0] Provider-reported rate: 0.98 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
23	Pyridoxine HCl	9.79E-5 G_PER_L		Provider-reported rate: 9.79E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
24	Na2MoO4 x 2 H2O 2H2O.MoO4.2Na 241.946 g/mol	3.52E-5 G_PER_L	CHEBI:75213 sodium molybdate dihydrate	Provider-reported rate: 3.52E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
25	Na-formate CHO2.Na 68.007 g/mol	1.96 G_PER_L	CHEBI:62965 sodium formate	Provider-reported rate: 1.96 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
26	Resazurin	9.79E-4 G_PER_L		Provider-reported rate: 9.79E-4 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted. Copied annotations do not establish the source's exact chemical form; withdraw them, preserve the literal source name, and archive the prior node. No replacement ontology identifier is inferred.
27	p-Aminobenzoic acid	4.90E-5 G_PER_L		Provider-reported rate: 4.90E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
28	H2O			Provider Gram Amount is null; no fixed amount is asserted and missing is not zero. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
29	2-Methylbutyric acid	0.49 G_PER_L		Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
30	rumen fluid	48.97 G_PER_L		Provider-reported rate: 48.97 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
31	Distilled water			Provider Gram Amount is null; no fixed amount is asserted and missing is not zero. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
32	Biotin	1.96E-5 G_PER_L		Provider-reported rate: 1.96E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
33	H2			Provider Gram Amount is null; no fixed amount is asserted and missing is not zero. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
34	FeSO4 x 7 H2O Fe.7H2O.O4S 278.013 g/mol	1.96E-3 G_PER_L	CHEBI:75836 iron(2+) sulfate heptahydrate	Provider-reported rate: 1.96E-3 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
35	NH4Cl Cl.H4N 53.492 g/mol	0.39 G_PER_L	CHEBI:31206 ammonium chloride	Provider-reported rate: 0.39 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
36	Isobutyric acid C4H8O2 88.106 g/mol	0.49 G_PER_L	CHEBI:16135 isobutyric acid	Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
37	Valeric acid C5H10O2 102.133 g/mol	0.49 G_PER_L	CHEBI:17418 valeric acid	Provider-reported rate: 0.49 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
38	CaCl2 x 2 H2O Ca.2Cl.2H2O 147.014 g/mol	0.05 G_PER_L	CHEBI:86158 calcium chloride dihydrate	Provider-reported rate: 0.05 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
39	Na-acetate C2H3O2.Na 82.034 g/mol	0.98 G_PER_L	CHEBI:32954 sodium acetate	Provider-reported rate: 0.98 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
40	NiCl2 x 6 H2O	2.34E-5 G_PER_L		Provider-reported rate: 2.34E-5 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted. Copied annotations do not establish the source's exact chemical form; withdraw them, preserve the literal source name, and archive the prior node. No replacement ontology identifier is inferred.
41	H3BO3 H3BO3 61.833 g/mol	5.86E-6 G_PER_L	CHEBI:33118 boric acid	Provider-reported rate: 5.86E-6 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
42	NaCl Cl.Na 58.443 g/mol	0.39 G_PER_L	CHEBI:26710 sodium chloride	Provider-reported rate: 0.39 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.
43	Trypticase Peptone	1.96 G_PER_L		Provider-reported rate: 1.96 g/L, preserving the displayed precision. This table reports medium rates, not stock inputs or stock addition volumes. No Mol Amount, SEED aggregate identity, density or linked DSMZ normalization is adopted.

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T01:15:01.fZ	komodo-web-import	Imported from KOMODO web table	Source: KOMODO, ID: 119.1
2026-02-03T11:19:00.148574	dsmz-resolver-v1.0	Enriched with DSMZ composition	Copied ingredients from DSMZ Medium 119
2026-03-13T03:08:52.134455Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 1 duplicate ingredient(s)
2026-03-13T06:19:23.274893Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:003918
2026-03-17T06:29:56.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:37.794835+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "For DSM 16632 and DSM 16643" to "for_dsm_16632_and_dsm_16643" for consistent matching
2026-06-05T07:41:02.586293+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 28 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:57.691155+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.
2026-10-09T03:06:56.858381+00:00	codex	RESTORED_MEDIUM_119_SOURCE_FORMULATIONS_AND_STOCK_SCOPES_WITH_EVIDENCE	Restore exact-source medium-119 ingredients, liquid inputs, stock strengths/doses and preparation scopes; preserve source-specific variants, quantity limits and disagreements, and repair reciprocal family references without inferring growth.