archaeoglobus_medium_dsm_399 (CultureMech:009220)

Overview

External ontology

TOGO:M2665 — Archaeoglobus medium (DSM 399)

Applications

Microbial cultivation

Notes

Source: https://togomedium.org/medium/M2665 Original URL: https://www.atcc.org/~/media/385F0331DBAE42A3B87040A1D040AC39.ashx

Composition

flowchart LR
    CultureMech_009220["archaeoglobus_medium_dsm_399"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_009220 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_MgSO4___7H2O["MgSO4 . 7H2O"]
    CultureMech_009220 --> ing1_MgSO4___7H2O
    CHEBI_31795["CHEBI:31795"]
    ing1_MgSO4___7H2O -.-> CHEBI_31795
    ing2_NaCl["NaCl"]
    CultureMech_009220 --> ing2_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing2_NaCl -.-> CHEBI_26710
    ing3_CaCl2___2H2O["CaCl2 . 2H2O"]
    CultureMech_009220 --> ing3_CaCl2___2H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2___2H2O -.-> CHEBI_86158
    ing4_NH4Cl["NH4Cl"]
    CultureMech_009220 --> ing4_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing4_NH4Cl -.-> CHEBI_31206
    ing5_K2HPO4["K2HPO4"]
    CultureMech_009220 --> ing5_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing5_K2HPO4 -.-> CHEBI_131527
    ing6_Resazurin["Resazurin"]
    CultureMech_009220 --> ing6_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing6_Resazurin -.-> CHEBI_8806
    ing7_MgCl2___6H2O["MgCl2 . 6H2O"]
    CultureMech_009220 --> ing7_MgCl2___6H2O
    CHEBI_86345["CHEBI:86345"]
    ing7_MgCl2___6H2O -.-> CHEBI_86345
    ing8_Na2S___9H2O["Na2S . 9H2O"]
    CultureMech_009220 --> ing8_Na2S___9H2O
    CHEBI_76209["CHEBI:76209"]
    ing8_Na2S___9H2O -.-> CHEBI_76209
    ing9_KCl["KCl"]
    CultureMech_009220 --> ing9_KCl
    CHEBI_32588["CHEBI:32588"]
    ing9_KCl -.-> CHEBI_32588
    ing10_NaHCO3["NaHCO3"]
    CultureMech_009220 --> ing10_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing10_NaHCO3 -.-> CHEBI_32139
    ing11_Sodium_lactate["Sodium lactate"]
    CultureMech_009220 --> ing11_Sodium_lactate
    CHEBI_75228["CHEBI:75228"]
    ing11_Sodium_lactate -.-> CHEBI_75228
    ing12_Fe_NH4_2_SO4_2___7H2O["Fe(NH4)2(SO4)2 . 7H2O"]
    CultureMech_009220 --> ing12_Fe_NH4_2_SO4_2___7H2O
    CHEBI_131378["CHEBI:131378"]
    ing12_Fe_NH4_2_SO4_2___7H2O -.-> CHEBI_131378
    ing13_Yeast_Extract__BD_212750_["Yeast Extract (BD 212750)"]
    CultureMech_009220 --> ing13_Yeast_Extract__BD_212750_
    ing14_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_009220 --> ing14_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing14_Carbon_dioxide_gas -.-> CHEBI_16526
    ing15_Nitrogen_gas["Nitrogen gas"]
    CultureMech_009220 --> ing15_Nitrogen_gas
    CHEBI_17997["CHEBI:17997"]
    ing15_Nitrogen_gas -.-> CHEBI_17997
    ing16_Na2MoO4___2H2O["Na2MoO4 . 2H2O"]
    CultureMech_009220 --> ing16_Na2MoO4___2H2O
    CHEBI_75213["CHEBI:75213"]
    ing16_Na2MoO4___2H2O -.-> CHEBI_75213
    ing17_H3BO3["H3BO3"]
    CultureMech_009220 --> ing17_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing17_H3BO3 -.-> CHEBI_33118
    ing18_FeSO4___7H2O["FeSO4 . 7H2O"]
    CultureMech_009220 --> ing18_FeSO4___7H2O
    CHEBI_75836["CHEBI:75836"]
    ing18_FeSO4___7H2O -.-> CHEBI_75836
    ing19_NiCl2___6H2O["NiCl2 . 6H2O"]
    CultureMech_009220 --> ing19_NiCl2___6H2O
    CHEBI_34887["CHEBI:34887"]
    ing19_NiCl2___6H2O -.-> CHEBI_34887
    ing20_ZnSO4___7H2O["ZnSO4 . 7H2O"]
    CultureMech_009220 --> ing20_ZnSO4___7H2O
    CHEBI_32312["CHEBI:32312"]
    ing20_ZnSO4___7H2O -.-> CHEBI_32312
    ing21_CuSO4___5H2O["CuSO4 . 5H2O"]
    CultureMech_009220 --> ing21_CuSO4___5H2O
    CHEBI_31440["CHEBI:31440"]
    ing21_CuSO4___5H2O -.-> CHEBI_31440
    ing22_Na2SeO3___5H2O["Na2SeO3 . 5H2O"]
    CultureMech_009220 --> ing22_Na2SeO3___5H2O
    CHEBI_48843["CHEBI:48843"]
    ing22_Na2SeO3___5H2O -.-> CHEBI_48843
    ing23_CoSO4___7H2O["CoSO4 . 7H2O"]
    CultureMech_009220 --> ing23_CoSO4___7H2O
    CHEBI_91244["CHEBI:91244"]
    ing23_CoSO4___7H2O -.-> CHEBI_91244
    ing24_KAl_SO4_2___12H2O["KAl(SO4)2 . 12H2O"]
    CultureMech_009220 --> ing24_KAl_SO4_2___12H2O
    CHEBI_86465["CHEBI:86465"]
    ing24_KAl_SO4_2___12H2O -.-> CHEBI_86465
    ing25_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_009220 --> ing25_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing25_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing26_MnSO4___2H2O["MnSO4 . 2H2O"]
    CultureMech_009220 --> ing26_MnSO4___2H2O
    CHEBI_86356["CHEBI:86356"]
    ing26_MnSO4___2H2O -.-> CHEBI_86356
    ing27_KOH_solusion["KOH solusion"]
    CultureMech_009220 --> ing27_KOH_solusion

Ingredients (28)

#	Ingredient	Concentration	Ontology	Notes
1	Distilled water H2O 18.015 g/mol	1.0 G_PER_L	CHEBI:15377 water	Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 2 identical duplicates: 1.0, 1.0]
2	MgSO4 . 7H2O 7H2O.Mg.O4S 246.473 g/mol	6.45 G_PER_L	CHEBI:31795 magnesium sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 3.45, 3.0]
3	NaCl Cl.Na 58.443 g/mol	19.0 G_PER_L	CHEBI:26710 sodium chloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 18.0, 1.0]
4	CaCl2 . 2H2O Ca.2Cl.2H2O 147.014 g/mol	0.24000000000000002 G_PER_L	CHEBI:86158 calcium chloride dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.14, 0.1]
5	NH4Cl Cl.H4N 53.492 g/mol	0.25 G_PER_L	CHEBI:31206 ammonium chloride	Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component
6	K2HPO4 HO4P.2K 174.174 g/mol	0.14 G_PER_L	CHEBI:131527 dipotassium hydrogen phosphate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
7	Resazurin C12H7NO4 229.191 g/mol	1 G_PER_L	CHEBI:8806 Resazurin	Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component
8	MgCl2 . 6H2O 2Cl.6H2O.Mg 203.301 g/mol	4 G_PER_L	CHEBI:86345 magnesium dichloride hexahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
9	Na2S . 9H2O 9H2O.2Na.S 240.182 g/mol	0.5 G_PER_L	CHEBI:76209 sodium sulfide nonahydrate	Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component
10	KCl Cl.K 74.551 g/mol	0.34 G_PER_L	CHEBI:32588 potassium chloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
11	NaHCO3 CHO3.Na 84.006 g/mol	5 G_PER_L	CHEBI:32139 sodium hydrogencarbonate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
12	Sodium lactate C3H5O3.Na 112.06 g/mol	1.5 G_PER_L	CHEBI:75228 sodium lactate	Role: Carbon source; Properties: Organic compound, Defined component, Simple component
13	Fe(NH4)2(SO4)2 . 7H2O Fe.7H2O.2H4N.2O4S 410.154 g/mol	2 G_PER_L	CHEBI:131378 ferrous ammonium sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
14	Yeast Extract (BD 212750)	0.5 G_PER_L		Properties: Undefined component
15	Carbon dioxide gas CO2 44.009 g/mol	variable VARIABLE	CHEBI:16526 carbon dioxide	Properties: ガス
16	Nitrogen gas N2 28.014 g/mol	variable VARIABLE	CHEBI:17997 dinitrogen	Properties: ガス
17	Na2MoO4 . 2H2O 2H2O.MoO4.2Na 241.946 g/mol	0.01 G_PER_L	CHEBI:75213 sodium molybdate dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
18	H3BO3 H3BO3 61.833 g/mol	0.01 G_PER_L	CHEBI:33118 boric acid	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
19	FeSO4 . 7H2O Fe.7H2O.O4S 278.013 g/mol	0.1 G_PER_L	CHEBI:75836 iron(2+) sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
20	NiCl2 . 6H2O Cl2Ni 129.599 g/mol	0.025 G_PER_L	CHEBI:34887 nickel dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
21	ZnSO4 . 7H2O 7H2O.O4S.Zn 287.558 g/mol	0.18 G_PER_L	CHEBI:32312 zinc sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
22	CuSO4 . 5H2O Cu.5H2O.O4S 249.684 g/mol	0.01 G_PER_L	CHEBI:31440 copper(II) sulfate pentahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
23	Na2SeO3 . 5H2O 2Na.O3Se 172.937 g/mol	0.3 G_PER_L	CHEBI:48843 disodium selenite	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
24	CoSO4 . 7H2O Co.7H2O.O4S 281.101 g/mol	0.18 G_PER_L	CHEBI:91244 cobalt(2+) sulfate heptahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
25	KAl(SO4)2 . 12H2O Al.12H2O.K.2O4S 474.386 g/mol	0.02 G_PER_L	CHEBI:86465 potassium aluminium sulfate dodecahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
26	Nitrilotriacetic acid C6H9NO6 191.139 g/mol	1.5 G_PER_L	CHEBI:44557 nitrilotriacetic acid	Role: Mineral source; Properties: Organic compound, Defined component, Simple component
27	MnSO4 . 2H2O 2H2O.Mn.O4S 187.031 g/mol	0.5 G_PER_L	CHEBI:86356 manganese(II) sulfate dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
28	KOH solusion	variable VARIABLE		Role: Mineral source; Properties: Defined component, Solution

Solutions

Trace Elements Solution

Dose: 10 G_PER_L

See mediadive_6129_Trace_elements_solution.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
Archaeoglobus fulgidus
Term
Id
NCBITaxon:2234
Label
Archaeoglobus fulgidus
Strain
DSM 4304
Evidence
- Reference
  doi:10.7888/juoeh.29.131
  Supports
  SUPPORT
  Explanation
  Tarui et al. 2007 (J UOEH) explicitly grows the A. fulgidus type strain DSM 4304 in DSM399 Archaeoglobus medium, matching this parent record. Conditions: static anaerobic, N2-CO2 4:1, 83C, 2-3 d. | Identifiers: DSM 4304; ATCC 49558; strain VC-16
  Snippet
  Cells of A. fulgidus DSM4304 (VC-16) were grown statically and anaerobically in 600 ml of DSM399 Archaeoglobus medium in a 1-L bottle with N2-CO2 (4:1) at 83C for 2 or 3 days.

Recipe variants

Name
stl_medium_archaeoglobus_variant
Relationship
DERIVED_FROM
Description
STL (sulfate-thiosulfate-lactate) medium, a recognizable Archaeoglobus-type defined/complex medium used to grow A. fulgidus VC-16, distinct in formulation from the DSM 399 record.
Modifications
- Base built from a 10x salt solution (per L of 10x: NaCl 178 g, MgSO4 74 g, MgCl2.6H2O 27.5 g, KCl 3.4 g, NH4Cl 2.5 g; Salt II CaCl2.2H2O 1.4 g; Salt III K2HPO4 1.37 g) added at 100 ml/L.
- PIPES buffer 20 ml of 1 M per L; base medium adjusted to pH 6.7 (Hartzell 1999). Reed 2001 variant uses Tris+maleic acid 20 mM each, pH 6.1.
- Carbon/electron donor: sodium lactate 7 ml of 30% (w/v) per L (Hartzell 1999); DL-sodium lactate ~22 mM (Reed 2001).
- Yeast extract 0.5 g/L (replaceable by Wolfe's vitamin mixture 10 ml/L for defined medium).
- 1000x trace element stock (1 ml/L) incl. Na2EDTA.2H2O, Mn/Co/Zn/Ni/Cu/B/Al/Mo/W/Se/V salts; (NH4)2Fe(SO4)2 1 ml of 0.2% per L.
- Reductant: Na2S 100 mM + Na2S2O3 200 mM stock added at 0.5% v/v after autoclaving (Hartzell); Na2S/Na2S2O3 ~1 mM each (Reed).
- Resazurin redox indicator; anaerobic, boiled and N2-sparged; good growth 75-82C (Hartzell), 83C in glass carboys (Reed).
Purpose
Capture the STL Archaeoglobus-type medium recipe used for A. fulgidus biofilm and enzyme studies as a variant of the DSM 399 parent rather than a duplicate medium.
Evidence
- Reference
  doi:10.1016/s0076-6879(99)10027-2
  Supports
  SUPPORT
  Explanation
  Hartzell et al. 1999 (Methods in Enzymology) prints the full STL medium recipe used to maintain A. fulgidus VC-16.
  Snippet
  A. fulgidus was grown in STL medium ... 10x salt solution 100 ml/L, PIPES buffer 20 ml of 1 M, trace element stock 1 ml of 1000x, yeast extract 0.5 g/L, sodium lactate 7 ml of 30% per L, pH 6.7; reducing agent Na2S 100 mM / Na2S2O3 200 mM added 0.5% v/v; good growth at 75-82C.
- Reference
  doi:10.1128/jb.183.24.7007-7016.2001
  Supports
  SUPPORT
  Explanation
  Reed et al. 2001 (J Bacteriol) reports a modified STL medium 3 for A. fulgidus, confirming the STL lineage and giving an alternate buffer/reductant variant.
  Snippet
  cells were grown anaerobically at 83C in glass carboys ... modified sulfate-thiosulfate-lactate (STL) medium 3 ... 20 mM Tris plus maleic acid, pH 6.1; DL-sodium lactate 22 mM; yeast extract 0.5 g/L; Na2S and Na2S2O3 1 mM; resazurin.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:56.995964Z	togo-import	Imported from TOGO Medium	Source: TOGO, ID: M2665
2026-01-28T19:48:35.559308Z	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: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: KOH solusion
2026-03-09T08:04:59.192793+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 1 solution(s) from ingredients
2026-03-13T03:09:30.925532Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 4 duplicate ingredient(s)
2026-03-13T06:20:04.305350Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:009220
2026-03-14T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name
2026-03-17T06:30:41.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:23.040131+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "Archaeoglobus medium (DSM 399)" to "archaeoglobus_medium_dsm_399" for consistent matching
2026-05-16T09:03:24.735668+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=2
2026-05-28T06:12:21.603198+00:00	deep-research-edison-phase2	ENRICHED	Edison phase-2: Archaeoglobus fulgidus DSM 4304 grows on the parent DSM 399 medium; STL medium is a recognizable Archaeoglobus-type variant. [added 1 organism(s), 1 variant(s)]
2026-06-05T07:40:49.516501+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 11 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T06:57:36.625977+00:00	mgso4-heptahydrate-term-fix-v1.0	Corrected MgSO4·7H2O primary term grounding to heptahydrate	Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched.
2026-06-10T07:46:53.457268+00:00	primary-term-label-canonicalization-v1.0	Canonicalized primary term label to OBO canonical (OAK)	3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-08-06T00:58:02.538197+00:00	curate_organism_culture_type.py	SET_ORGANISM_CULTURE_TYPE	Inferred isolate: 1 specific strain(s) named, no community signal (#142)
2026-09-02T07:37:28.500731+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.