caldicellulosiruptor_medium_for_dsm_10319 (CultureMech:009111)

Overview

External ontology

TOGO:M2542 — Caldicellulosiruptor Medium (For DSM 10319)

Applications

Microbial cultivation

High-metal flag

True

Notes

Source: https://togomedium.org/medium/M2542 Original URL: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium640.pdf

Composition

flowchart LR
    CultureMech_009111["caldicellulosiruptor_medium_for_dsm_10319"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_009111 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_NaCl["NaCl"]
    CultureMech_009111 --> ing1_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing1_NaCl -.-> CHEBI_26710
    ing2_KH2PO4["KH2PO4"]
    CultureMech_009111 --> ing2_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing2_KH2PO4 -.-> CHEBI_63036
    ing3_NH4Cl["NH4Cl"]
    CultureMech_009111 --> ing3_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing3_NH4Cl -.-> CHEBI_31206
    ing4_K2HPO4["K2HPO4"]
    CultureMech_009111 --> ing4_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing4_K2HPO4 -.-> CHEBI_131527
    ing5_D_glucose["D-glucose"]
    CultureMech_009111 --> ing5_D_glucose
    CHEBI_17634["CHEBI:17634"]
    ing5_D_glucose -.-> CHEBI_17634
    ing6_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_009111 --> ing6_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing6_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing7_Trypticase_peptone__BD_BBL_["Trypticase peptone (BD BBL)"]
    CultureMech_009111 --> ing7_Trypticase_peptone__BD_BBL_
    ing8_L_Cysteine_HCl_x_H2O["L-Cysteine-HCl x H2O"]
    CultureMech_009111 --> ing8_L_Cysteine_HCl_x_H2O
    CHEBI_91248["CHEBI:91248"]
    ing8_L_Cysteine_HCl_x_H2O -.-> CHEBI_91248
    ing9_Yeast_extract__OXOID_["Yeast extract (OXOID)"]
    CultureMech_009111 --> ing9_Yeast_extract__OXOID_
    ing10_N2["N2"]
    CultureMech_009111 --> ing10_N2
    CHEBI_17997["CHEBI:17997"]
    ing10_N2 -.-> CHEBI_17997
    ing11_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_009111 --> ing11_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing11_Na2MoO4_x_2_H2O -.-> CHEBI_75213
    ing12_H3BO3["H3BO3"]
    CultureMech_009111 --> ing12_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing12_H3BO3 -.-> CHEBI_33118
    ing13_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_009111 --> ing13_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing13_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing14_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_009111 --> ing14_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing14_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing15_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_009111 --> ing15_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing15_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing16_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_009111 --> ing16_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing16_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing17_ZnCl2["ZnCl2"]
    CultureMech_009111 --> ing17_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing17_ZnCl2 -.-> CHEBI_49976
    ing18_HCl__25___7_7_M_["HCl (25%; 7.7 M)"]
    CultureMech_009111 --> ing18_HCl__25___7_7_M_
    ing19_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
    CultureMech_009111 --> ing19_FeCl2_x_4_H2O
    CHEBI_86249["CHEBI:86249"]
    ing19_FeCl2_x_4_H2O -.-> CHEBI_86249

Ingredients (20)

#	Ingredient	Concentration	Ontology	Notes
1	Distilled water H2O 18.015 g/mol	1990.0 G_PER_L	CHEBI:15377 water	Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 1000.0, 990.0]
2	NaCl Cl.Na 58.443 g/mol	0.9 G_PER_L	CHEBI:26710 sodium chloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
3	KH2PO4 H2O4P.K 136.084 g/mol	0.75 G_PER_L	CHEBI:63036 potassium dihydrogen phosphate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
4	NH4Cl Cl.H4N 53.492 g/mol	0.9 G_PER_L	CHEBI:31206 ammonium chloride	Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component
5	K2HPO4 HO4P.2K 174.174 g/mol	1.5 G_PER_L	CHEBI:131527 dipotassium hydrogen phosphate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
6	D-glucose C6H12O6 180.156 g/mol	5 G_PER_L	CHEBI:17634 D-glucose	Role: Carbon source; Properties: Organic compound, Defined component, Simple component
7	MgCl2 x 6 H2O 2Cl.6H2O.Mg 203.301 g/mol	0.4 G_PER_L	CHEBI:86345 magnesium dichloride hexahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
8	Trypticase peptone (BD BBL)	2 G_PER_L		Properties: Undefined component
9	L-Cysteine-HCl x H2O C3H7NO2S.H2O.HCl 175.637 g/mol	0.75 G_PER_L	CHEBI:91248 L-cysteine hydrochloride hydrate	Properties: Organic compound, Simple component, Defined component
10	Yeast extract (OXOID)	1 G_PER_L		Properties: Complex component, Undefined component
11	N2 N2 28.014 g/mol	variable VARIABLE	CHEBI:17997 dinitrogen	Properties: Gas
12	Na2MoO4 x 2 H2O 2H2O.MoO4.2Na 241.946 g/mol	36 G_PER_L	CHEBI:75213 sodium molybdate dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
13	H3BO3 H3BO3 61.833 g/mol	6 G_PER_L	CHEBI:33118 boric acid	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
14	MnCl2 x 4 H2O Cl2Mn.4H2O 197.904 g/mol	100 G_PER_L	CHEBI:86368 manganese(II) chloride tetrahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
15	CoCl2 x 6 H2O 2Cl.Co.6H2O 237.929 g/mol	190 G_PER_L	CHEBI:53503 cobalt chloride hexahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
16	NiCl2 x 6 H2O Cl2Ni 129.599 g/mol	24 G_PER_L	CHEBI:34887 nickel dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
17	CuCl2 x 2 H2O Cl2Cu.2H2O 170.482 g/mol	2 G_PER_L	CHEBI:86318 copper(II) chloride dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
18	ZnCl2 2Cl.Zn 136.296 g/mol	70 G_PER_L	CHEBI:49976 zinc dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
19	HCl (25%; 7.7 M)	10 G_PER_L		Role: Solvating media; Properties: Inorganic compound, Defined component, Solution
20	FeCl2 x 4 H2O Cl2Fe.4H2O 198.811 g/mol	1.5 G_PER_L	CHEBI:86249 iron dichloride tetrahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component

Solutions

Na-resazurin solution (0.1% w/v)

Dose: 0.5 G_PER_L

Role: pH dependent redox indicator; Properties: Defined component, Solution

FeCl3 x 6H2O solution (0.1% w/v in 0.2 N HCl)

Dose: 2.5 G_PER_L

Role: Mineral source

Trace element solution SL-10

Dose: 1 G_PER_L

See mediadive_4178_Trace_element_solution_SL-10.yaml for composition

Target organisms and growth evidence

These are curated observations and conditions for named organisms; they do not imply universal growth suitability.

Preferred term
Caldicellulosiruptor bescii
Term
Id
NCBITaxon:31899
Label
Caldicellulosiruptor bescii
Strain
DSM 6725
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; growth on the modified DSMZ 640 variant (see variant modified_dsmz_640_blumer_schuette_2010). | Identifiers: DSM 6725; INSDC CP001393
  Snippet
  Freeze-dried cells were resuspended in the recommended medium and subcultured ... into modified DSMZ medium 640 ... grown at 70C with orbital shaking; 50 ml in 125 ml serum bottle, N2 headspace, 24 h.
Preferred term
Caldicellulosiruptor saccharolyticus
Term
Id
NCBITaxon:44001
Label
Caldicellulosiruptor saccharolyticus
Strain
DSM 8903
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; grown on modified DSMZ 640 variant; 70C, N2 headspace. | Identifiers: DSM 8903; INSDC CP000679
  Snippet
  Subcultured into modified DSMZ 640; reported to grow on xylose, glucose, Avicel, pretreated switchgrass, and yeast extract control.
Preferred term
Caldicellulosiruptor hydrothermalis
Term
Id
NCBITaxon:413888
Label
Caldicellulosiruptor hydrothermalis
Strain
DSM 18901
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; 70C, N2 headspace.
  Snippet
  Subcultured into modified DSMZ 640 and included among seven species grown on selected substrates.
Preferred term
Caldicellulosiruptor kristjanssonii
Strain
DSM 12137
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; 70C, N2 headspace.
  Snippet
  Subcultured into modified DSMZ 640; explicitly noted to grow on xylose, to lower density than C. saccharolyticus.
Preferred term
Caldicellulosiruptor kronotskyensis
Term
Id
NCBITaxon:413889
Label
Caldicellulosiruptor kronotskyensis
Strain
DSM 18902
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; 70C, N2 headspace.
  Snippet
  Subcultured into modified DSMZ 640 and included among seven species grown on selected substrates.
Preferred term
Caldicellulosiruptor lactoaceticus
Strain
DSM 9545
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; 70C, N2 headspace. Note: no growth on glucose.
  Snippet
  Subcultured into modified DSMZ 640; explicitly reported as showing no growth on glucose in this comparison.
Preferred term
Caldicellulosiruptor owensensis
Term
Id
NCBITaxon:55205
Label
Caldicellulosiruptor owensensis
Strain
DSM 13100
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; 70C, N2 headspace.
  Snippet
  Subcultured into modified DSMZ 640 and included among seven species grown on selected substrates.
Preferred term
Caldicellulosiruptor acetigenus
Term
Id
NCBITaxon:301953
Label
Caldicellulosiruptor acetigenus
Strain
DSM 7040
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010; modified DSMZ 640 variant; substrate-specific growth not shown for this strain.
  Snippet
  Listed in Table 1 as available from DSMZ and stated in methods as among Caldicellulosiruptor species subcultured into modified DSMZ 640.
Preferred term
Thermoanaerobacterium calidifontis
Term
Id
NCBITaxon:715028
Label
Thermoanaerobacterium calidifontis
Strain
Rx1
Evidence
- Reference
  doi:10.1007/s00203-013-0895-5
  Supports
  SUPPORT
  Explanation
  Shang et al. 2013; strain Rx1 grown on the modified DSMZ 640 variant (see variant modified_dsmz_640_shang_2013); full recipe printed; 55C, 100% N2. | Identifiers: JCM 18270; CCTCC M 2011109; 16S rRNA AB544080
  Snippet
  All culturing of Rx1 was performed in modified DSMZ medium 640, containing (per liter) 0.9 g NH4Cl, 0.9 g NaCl, 0.4 g MgCl2.6H2O, 0.75 g KH2PO4, 1.5 g K2HPO4, 2.5 mg FeCl3.6H2O, 0.75 g cysteine-HCl.H2O, 2 g tryptone, 1 g yeast extract, 1 ml SL-10, 0.5 mg resazurin, 5 ml vitamin solution, 10.0 g substrate; pH 7.0; prepared under 100% N2.

Recipe variants

Name
modified_dsmz_640_blumer_schuette_2010
Relationship
DERIVED_FROM
Description
Modified DSMZ medium 640 used for comparative Caldicellulosiruptor physiology (Blumer-Schuette et al. 2010).
Modifications
- Trypticase, cysteine-HCl, and resazurin omitted relative to standard DSMZ 640.
- Carbon source increased to 5 g/L; Na2S.9H2O added to 0.5% final.
- Anaerobic batch cultivation under N2; 70C with orbital shaking; 50 ml in 125 ml serum bottle; 24 h.
Purpose
Reusable variant for the 8 Caldicellulosiruptor DSM strains grown in modified DSMZ 640 in this study.
Evidence
- Reference
  doi:10.1128/AEM.01400-10
  Supports
  SUPPORT
  Explanation
  Blumer-Schuette et al. 2010 methods describe the modified DSMZ 640 formulation and cultivation.
  Snippet
  subcultured ... into modified DSMZ medium 640 ... grown at 70C with orbital shaking under N2 headspace.
Name
modified_dsmz_640_shang_2013
Relationship
DERIVED_FROM
Description
Modified DSMZ medium 640 for Thermoanaerobacterium calidifontis Rx1 (Shang et al. 2013); ferric iron, added SL-10/vitamins/resazurin, variable substrate.
Modifications
- Iron source substituted: FeCl3.6H2O 2.5 mg/L (vs ferrous iron in parent).
- Added trace element solution SL-10 (1 ml/L, DSMZ medium 320) and vitamin solution (5 ml/L, DSMZ medium 141, filter-sterilized).
- Added resazurin 0.5 mg/L.
- Fixed glucose replaced by variable substrate at 10.0 g/L (e.g. oat spelt xylan, xylose, glucose).
- Per liter: 0.9 g NH4Cl, 0.9 g NaCl, 0.4 g MgCl2.6H2O, 0.75 g KH2PO4, 1.5 g K2HPO4, 0.75 g cysteine-HCl.H2O, 2 g tryptone, 1 g yeast extract; pH 7.0; prepared under 100% N2; dispensed 5 ml into 15 ml Hungate tubes; autoclaved.
Purpose
Capture the explicit modified DSMZ 640 recipe used to isolate and characterize T. calidifontis Rx1.
Evidence
- Reference
  doi:10.1007/s00203-013-0895-5
  Supports
  SUPPORT
  Explanation
  Shang et al. 2013 prints the full modified DSMZ 640 recipe with explicit deviations from the parent.
  Snippet
  All culturing of Rx1 was performed in modified DSMZ medium 640, containing (per liter distilled water) 0.9 g NH4Cl, 0.9 g NaCl, 0.4 g MgCl2 x 6 H2O, 0.75 g KH2PO4, 1.5 g K2HPO4, 2.5 mg FeCl3 x 6 H2O, 0.75 g cysteine-HCl x H2O, 2 g tryptone, 1 g yeast extract, 1 ml trace element solution SL-10, 0.5 mg resazurin, 5 ml vitamin solution, 10.0 g substrate.

Provenance

Merged from 1 source record.

caldicellulosiruptor_medium_for_dsm_10319 (CultureMech:009111)

Timestamp	Curator	Action	Notes
2026-01-27T06:35:56.665537Z	togo-import	Imported from TOGO Medium	Source: TOGO, ID: M2542
2026-01-28T19:48:17.964314Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-03T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default concentration for ingredient: N2
2026-03-09T08:04:29.745693+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 3 solution(s) from ingredients
2026-03-13T03:08:58.633780Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 1 duplicate ingredient(s)
2026-03-13T06:20:02.734350Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:009111
2026-03-14T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name; Added default solution name; Added default solution name
2026-03-17T06:30:03.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:21.479854+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "Caldicellulosiruptor Medium (For DSM 10319)" to "caldicellulosiruptor_medium_for_dsm_10319" for consistent matching
2026-05-16T09:03:26.499708+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=2
2026-05-28T06:12:21.633329+00:00	deep-research-edison-phase2	ENRICHED	Edison phase-1/phase-2: 8 Caldicellulosiruptor type strains + T. calidifontis Rx1 grown on MODIFIED DSMZ 640 (not the exact parent). NOTE: no source directly evidenced DSM 10319 itself on this medium. [added 9 organism(s), 2 variant(s)]
2026-06-05T07:40:52.082297+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 16 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:54.140312+00:00	primary-term-label-canonicalization-v1.0	Canonicalized primary term label to OBO canonical (OAK)	4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-08-06T00:58:02.710815+00:00	curate_organism_culture_type.py	SET_ORGANISM_CULTURE_TYPE	Inferred isolate: 9 specific strain(s) named, no community signal (#142)
2026-08-06T03:05:26.395459+00:00	merge_recipes.py	MERGED_RECIPES	merged 1 source recipe(s) on fingerprint 8c95e8f97e6be203eb1316cf1bc33a03a062da680c0ba10c776b38ac223e2d37