ignicoccus_medium_for_dsm_18386 (CultureMech:009166)

Overview

External ontology

TOGO:M2599 — Ignicoccus Medium (for DSM 18386)

Applications

Microbial cultivation

Notes

Source: https://togomedium.org/medium/M2599 Original URL: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium897.pdf

Composition

flowchart LR
    CultureMech_009166["ignicoccus_medium_for_dsm_18386"]
    ing0_Sodium_resazurin__0_1__w_v_["Sodium resazurin (0.1% w/v)"]
    CultureMech_009166 --> ing0_Sodium_resazurin__0_1__w_v_
    ing1_Distilled_water["Distilled water"]
    CultureMech_009166 --> ing1_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing1_Distilled_water -.-> CHEBI_15377
    ing2_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_009166 --> ing2_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing2_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing3_NaCl["NaCl"]
    CultureMech_009166 --> ing3_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing3_NaCl -.-> CHEBI_26710
    ing4_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_009166 --> ing4_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing4_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing5_KH2PO4["KH2PO4"]
    CultureMech_009166 --> ing5_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing5_KH2PO4 -.-> CHEBI_63036
    ing6_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_009166 --> ing6_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing6_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing7_Na2S_x_9_H2O["Na2S x 9 H2O"]
    CultureMech_009166 --> ing7_Na2S_x_9_H2O
    CHEBI_76209["CHEBI:76209"]
    ing7_Na2S_x_9_H2O -.-> CHEBI_76209
    ing8_H3BO3["H3BO3"]
    CultureMech_009166 --> ing8_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing8_H3BO3 -.-> CHEBI_33118
    ing9_KCl["KCl"]
    CultureMech_009166 --> ing9_KCl
    CHEBI_32588["CHEBI:32588"]
    ing9_KCl -.-> CHEBI_32588
    ing10__NH4_2SO4["(NH4)2SO4"]
    CultureMech_009166 --> ing10__NH4_2SO4
    CHEBI_62946["CHEBI:62946"]
    ing10__NH4_2SO4 -.-> CHEBI_62946
    ing11_Sulfur__powdered_["Sulfur (powdered)"]
    CultureMech_009166 --> ing11_Sulfur__powdered_
    ing12_NaBr["NaBr"]
    CultureMech_009166 --> ing12_NaBr
    CHEBI_63004["CHEBI:63004"]
    ing12_NaBr -.-> CHEBI_63004
    ing13_2_N_H2SO4["2 N H2SO4"]
    CultureMech_009166 --> ing13_2_N_H2SO4
    ing14_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_009166 --> ing14_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing14_Carbon_dioxide_gas -.-> CHEBI_16526
    ing15_N2["N2"]
    CultureMech_009166 --> ing15_N2
    CHEBI_17997["CHEBI:17997"]
    ing15_N2 -.-> CHEBI_17997
    ing16_Hydrogen_gas["Hydrogen gas"]
    CultureMech_009166 --> ing16_Hydrogen_gas
    CHEBI_18276["CHEBI:18276"]
    ing16_Hydrogen_gas -.-> CHEBI_18276

Ingredients (17)

#	Ingredient	Concentration	Ontology	Notes
1	Sodium resazurin (0.1% w/v)	0.5 G_PER_L		Role: pH dependent redox indicator; Properties: Solution, Defined component
2	Distilled water H2O 18.015 g/mol	1000 G_PER_L	CHEBI:15377 water	Role: Solvating media; Properties: Simple component, Inorganic compound, Defined component
3	MgSO4 x 7 H2O 7H2O.Mg.O4S 246.473 g/mol	3.5 G_PER_L	CHEBI:31795 magnesium sulfate heptahydrate	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
4	NaCl Cl.Na 58.443 g/mol	13.65 G_PER_L	CHEBI:26710 sodium chloride	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
5	CaCl2 x 2 H2O Ca.2Cl.2H2O 147.014 g/mol	0.38 G_PER_L	CHEBI:86158 calcium chloride dihydrate	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
6	KH2PO4 H2O4P.K 136.084 g/mol	0.5 G_PER_L	CHEBI:63036 potassium dihydrogen phosphate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
7	MgCl2 x 6 H2O 2Cl.6H2O.Mg 203.301 g/mol	2.75 G_PER_L	CHEBI:86345 magnesium dichloride hexahydrate	Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component
8	Na2S x 9 H2O 9H2O.2Na.S 240.182 g/mol	0.2 G_PER_L	CHEBI:76209 sodium sulfide nonahydrate	Role: Reducing agent; Properties: Defined component, Inorganic compound, Simple component
9	H3BO3 H3BO3 61.833 g/mol	15 G_PER_L	CHEBI:33118 boric acid	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
10	KCl Cl.K 74.551 g/mol	0.33 G_PER_L	CHEBI:32588 potassium chloride	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
11	(NH4)2SO4 2H4N.O4S 132.141 g/mol	0.25 G_PER_L	CHEBI:62946 ammonium sulfate	Role: Nitrogen source; Properties: Inorganic compound, Simple component, Defined component
12	Sulfur (powdered)	5 G_PER_L		Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component
13	NaBr Br.Na 102.894 g/mol	0.05 G_PER_L	CHEBI:63004 sodium bromide	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
14	2 N H2SO4	variable VARIABLE		Role: Mineral source; Properties: Defined component, Inorganic compound, Solution
15	Carbon dioxide gas CO2 44.009 g/mol	variable VARIABLE	CHEBI:16526 carbon dioxide	Properties: ガス
16	N2 N2 28.014 g/mol	variable VARIABLE	CHEBI:17997 dinitrogen	Properties: ガス
17	Hydrogen gas H2 2.016 g/mol	variable VARIABLE	CHEBI:18276 dihydrogen	Properties: ガス

Solutions

SrCl2 x 6 H2O solution (0.1% w/v)

Dose: 7 G_PER_L

Role: Mineral source; Properties: Solution, Defined component

KI solution (0.01% w/v)

Dose: 0.5 G_PER_L

Role: Mineral source; Properties: Solution, Defined component, Inorganic compound

Target organisms and growth evidence

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

Preferred term
Ignicoccus hospitalis
Term
Id
NCBITaxon:160233
Label
Ignicoccus hospitalis
Strain
KIN4/I (= KIN4/IT), DSM 18386T
Genome assembly id
- GCA_000017945.1
Evidence
- Reference
  doi:10.1128/JB.06130-11
  Supports
  SUPPORT
  Explanation
  Mayer et al. 2012 explicitly cultivates the DSM 18386 type strain in 1/2 SME-Ignicoccus medium, the medium this record represents. Ingredient-level recipe is cited transitively (Paper et al. 2007), so parent-formulation identity is strong by name but not printed in this source. | Identifiers: DSM 18386T; RefSeq NC_009776.1; 16S Gene ID 5562932
  Snippet
  I. hospitalis KIN4/IT (DSM 18386) was grown in 1/2 SME-Ignicoccus medium at 90C under H2/CO2 (80:20, v/v) at 250 kPa, H2 as electron donor and elemental sulfur as electron acceptor.
Preferred term
Ignicoccus islandicus
Term
Id
NCBITaxon:54259
Label
Ignicoccus islandicus
Strain
Kol8, DSM 13165T
Genome assembly id
- GCA_001481685.1
Evidence
- Reference
  doi:10.5283/epub.34741
  Supports
  SUPPORT
  Explanation
  Growth supported on the 1/2 SME+S0 variant of the Ignicoccus medium family (extra NaHCO3, SrCl2.6H2O, KI and different S0/Na2S vs parent). Curate against the half_sme_s0_ignicoccus variant rather than asserting identity with the parent. | Identifiers: DSM 13165T; NZ_CP006867
  Snippet
  Ignicoccus pacificus LPC33, DSM 13166T • Ignicoccus islandicus Kol8, DSM 13165T
Preferred term
Ignicoccus pacificus
Term
Id
NCBITaxon:114376
Label
Ignicoccus pacificus
Strain
LPC33, DSM 13166T
Evidence
- Reference
  doi:10.5283/epub.34741
  Supports
  SUPPORT
  Explanation
  Growth supported on the 1/2 SME+S0 variant. Phase-2 flagged that this formulation differs from the parent (KI, SrCl2.6H2O, NaHCO3, different boric acid level); treat as variant-scoped evidence, not parent identity. | Identifiers: DSM 13166T

Recipe variants

Name
half_sme_s0_ignicoccus
Relationship
DERIVED_FROM
Description
Half-strength SME (synthetic seawater) medium supplemented with elemental sulfur and reduced with Na2S, used by Koschnitzki 2017 for all Ignicoccus representatives. Recognizable variant of the parent Ignicoccus medium.
Modifications
- Half-strength SME synthetic-seawater base
- Add elemental sulfur (S0) as electron acceptor
- Reduce with Na2S
- Additional/trace components vs parent: explicit NaHCO3, SrCl2.6H2O, KI
- H2/CO2 (80:20) headspace, ~1.5 bar; pH 5.5-6.0; 90C
Purpose
Routine cultivation of Ignicoccus representatives (I. hospitalis DSM 18386T, I. islandicus DSM 13165T, I. pacificus DSM 13166T) under sulfur-reducing chemolithoautotrophic conditions.
Evidence
- Reference
  doi:10.5283/epub.34741
  Supports
  SUPPORT
  Explanation
  Koschnitzki 2017 prints the formulation and strain list.
  Snippet
  ½ SME+S0 medium for all Ignicoccus representatives (Paper et al., 2007) Substance Amount Concentration SME 500 ml ½ x KH2PO4 0.5 g 3.7 mM (NH4)2SO4 0.25 g 1.9 mM NaHCO3 0.16 g 1.9 mM Resazurin (0.1 %) 1 ml 0.0001 % Na2S x 7-9 H2O 0.5 g 2.1 mM ddH2O ad 1000 ml
Name
half_sme_ignicoccus_plus_0_1pct_yeast_extract
Relationship
SUPPLEMENTED_VARIANT
Description
Mixotrophic version of 1/2 SME-Ignicoccus medium with 0.1% (w/v) yeast extract added, used by Mayer 2012 to compare autotrophic vs mixotrophic growth of I. hospitalis DSM 18386.
Modifications
- Add yeast extract to 0.1% (w/v)
Purpose
Mixotrophic growth / physiology comparison vs the autotrophic baseline.
Evidence
- Reference
  doi:10.1128/JB.06130-11
  Supports
  SUPPORT
  Explanation
  Mayer et al. 2012 describes the yeast-extract supplementation explicitly.
  Snippet
  Comparison of autotrophic growth with mixotrophic growth where 0.1% yeast extract was added to the normal culture medium of I. hospitalis DSM 18386.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:56.831971Z	togo-import	Imported from TOGO Medium	Source: TOGO, ID: M2599
2026-01-28T19:48:33.568051Z	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: 2 N H2SO4; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: Hydrogen gas
2026-03-09T08:04:55.653355+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 2 solution(s) from ingredients
2026-03-13T06:20:03.512450Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:009166
2026-03-14T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name; Added default solution name
2026-03-17T06:30:36.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:22.238533+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "Ignicoccus Medium (for DSM 18386)" to "ignicoccus_medium_for_dsm_18386" for consistent matching
2026-05-16T09:03:37.720366+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=2
2026-06-05T07:41:09.294319+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.
2026-06-10T06:57:49.327627+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.
2026-06-10T07:47:00.018762+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.
2026-06-02T06:47:50.241127+00:00	deep-research-edison-phase2	ENRICHED	Phase-2: I. hospitalis DSM 18386T (the type strain named in the record) is cultivated in '1/2 SME-Ignicoccus medium'; I. islandicus DSM 13165T and I. pacificus DSM 13166T grow in the closely related '1/2 SME+S0' formulation (Koschnitzki 2017, explicit recipe). The ingredient-level recipe of the parent (TOGO M2599 / DSMZ 897) is cited transitively (Paper 2007 / Huber 2000), so exact recipe identity is unverified; organism links are to the recognizable Ignicoccus-medium family. [added 3 organism(s), 2 variant(s)]
2026-08-06T00:58:02.548599+00:00	curate_organism_culture_type.py	SET_ORGANISM_CULTURE_TYPE	Inferred isolate: 3 specific strain(s) named, no community signal (#142)