methylotroph_medium (CultureMech:007843)

Overview

External ontology

TOGO:M1308 — Methylotroph Medium

Applications

Microbial cultivation

Notes

Source: https://togomedium.org/medium/M1308 Original source: JCM - JCM_M1219 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1219

Composition

flowchart LR
    CultureMech_007843["methylotroph_medium"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_007843 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_CaCl2_2H2O["CaCl2・2H2O"]
    CultureMech_007843 --> ing1_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing1_CaCl2_2H2O -.-> CHEBI_86158
    ing2_KH2PO4["KH2PO4"]
    CultureMech_007843 --> ing2_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing2_KH2PO4 -.-> CHEBI_63036
    ing3_MgCl2_6H2O["MgCl2・6H2O"]
    CultureMech_007843 --> ing3_MgCl2_6H2O
    CHEBI_86345["CHEBI:86345"]
    ing3_MgCl2_6H2O -.-> CHEBI_86345
    ing4_NaNO3["NaNO3"]
    CultureMech_007843 --> ing4_NaNO3
    CHEBI_63005["CHEBI:63005"]
    ing4_NaNO3 -.-> CHEBI_63005
    ing5_Na2SO4["Na2SO4"]
    CultureMech_007843 --> ing5_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing5_Na2SO4 -.-> CHEBI_32149
    ing6_HEPES["HEPES"]
    CultureMech_007843 --> ing6_HEPES
    CHEBI_46756["CHEBI:46756"]
    ing6_HEPES -.-> CHEBI_46756
    ing7_KOH["KOH"]
    CultureMech_007843 --> ing7_KOH
    CHEBI_32035["CHEBI:32035"]
    ing7_KOH -.-> CHEBI_32035
    ing8_Methanol["Methanol"]
    CultureMech_007843 --> ing8_Methanol
    CHEBI_17790["CHEBI:17790"]
    ing8_Methanol -.-> CHEBI_17790

Ingredients (9)

#	Ingredient	Concentration	Ontology	Notes
1	Distilled water H2O 18.015 g/mol	0.97 L	CHEBI:15377 water	Role: Solvating media; Properties: Defined component, Inorganic compound, Simple component
2	CaCl2・2H2O Ca.2Cl.2H2O 147.014 g/mol	0.07 G_PER_L	CHEBI:86158 calcium chloride dihydrate	Role: Mineral source; Properties: Defined component, Inorganic compound, Simple component
3	KH2PO4 H2O4P.K 136.084 g/mol	0.27 G_PER_L	CHEBI:63036 potassium dihydrogen phosphate	Role: Buffer; Properties: Defined component, Simple component, Inorganic compound
4	MgCl2・6H2O 2Cl.6H2O.Mg 203.301 g/mol	0.2 G_PER_L	CHEBI:86345 magnesium dichloride hexahydrate	Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component
5	NaNO3 NO3.Na 84.994 g/mol	0.42 G_PER_L	CHEBI:63005 sodium nitrate	Role: Nitrogen source; Properties: Simple component, Inorganic compound, Defined component
6	Na2SO4 2Na.O4S 142.043 g/mol	0.014 G_PER_L	CHEBI:32149 sodium sulfate	Role: Mineral source; Properties: Inorganic compound, Simple component, Defined component
7	HEPES	4.77 G_PER_L	CHEBI:46756 HEPES	Role: Buffer; Properties: Simple component, Organic compound, Defined component
8	KOH HO.K 56.105 g/mol	variable VARIABLE	CHEBI:32035 potassium hydroxide	Role: Mineral source; Properties: Defined component, Solution
9	Methanol CH4O 32.042 g/mol	0.00081 L	CHEBI:17790 methanol	Role: Solvating media; Properties: Organic compound, Simple component, Defined component

Preparation

Mix the main-solution components and adjust pH to 7.0 with 6 N KOH. Autoclave, then after cooling add filter-sterilized methanol, CuCl2 solution, and CeCl3 solution.

Solutions

Trace element solution (see Medium [M278])

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Nitrilotriacetic acid	12.8 G_PER_L
FeCl3 x 6 H2O	1.35 G_PER_L
MnCl2 x 4 H2O	0.1 G_PER_L
CoCl2 x 6 H2O	0.024 G_PER_L
CaCl2 x 2 H2O	0.1 G_PER_L
ZnCl2	0.1 G_PER_L
CuCl2 x 2 H2O	0.025 G_PER_L
H3BO3	0.01 G_PER_L
Na2MoO4 x 2 H2O	0.024 G_PER_L
NiCl2 x 6 H2O	0.12 G_PER_L

Se/W solution (see Medium [M278])

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Na2SeO3 x 5 H2O	4 MG_PER_L
Na2WO4 x 2 H2O	4 MG_PER_L

Trace vitamins (see Medium [M190])

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Biotin	2 MG_PER_L
Folic acid	2 MG_PER_L
Pyridoxine hydrochloride	10 MG_PER_L
Thiamine HCl	5 MG_PER_L
Riboflavin	5 MG_PER_L
Nicotinic acid	5 MG_PER_L
Calcium pantothenate	5 MG_PER_L
Vitamin B12	0.1 MG_PER_L
p-Aminobenzoic acid	5 MG_PER_L
Lipoic acid	5 MG_PER_L

10 mM CuCl2 solution

Dose: 0.002 L

Stock composition
Ingredient	Concentration	Notes
CuCl2	10 MILLIMOLAR

10 mM CeCl3 solution

Dose: 0.002 L

Stock composition
Ingredient	Concentration	Notes
CeCl3	10 MILLIMOLAR

Target organisms and growth evidence

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

Preferred term
Methylosinus sp. Ce-a6
Term
Id
NCBITaxon:2172005
Label
Methylosinus sp. Ce-a6
Genome assembly id
- GCA_009811655
- GCF_009811655
Strain
Ce-a6; JCM 32771
Growth metrics
- Temperature celsius
  30.0
  Measurement conditions
  Methanol cultures in Ca-free inorganic basal medium supplemented with 20 uM La, Ce, or Nd; source reports specific growth rates of 1.73 to 1.82 d-1 for +lanthanide cultures.
  Evidence
  Reference
  doi:10.1264/jsme2.ME19128
  Supports
  SUPPORT
  Explanation
  Kato et al. report positive growth of Methylosinus sp. Ce-a6 in methanol cultures related to the J1219 formulation, with faster growth when lanthanides were supplied.
  Is max attainment
  False
Evidence
- Reference
  doi:10.1264/jsme2.ME19128
  Supports
  SUPPORT
  Explanation
  Kato et al. identify Ce-a6 as the Methylosinus strain deposited as JCM 32771 and report positive growth experiments.
Preferred term
Methylovorus mays
Term
Id
NCBITaxon:184077
Label
Methylovorus mays
Growth metrics
- Doubling time minutes
  120.0
  Temperature celsius
  37.5
  Ph at measurement
  7.25
  Evidence
  Reference
  PMID:11315676
  Supports
  SUPPORT
  Snippet
  The optimum growth temperature is 35-40 degrees C; the optimum pH is 7.0-7.5. The doubling time is 2 h.
  Explanation
  Auto-applied from literature query: targeted: Methylovorus mays doubling time
  Is max attainment
  True

Recipe variants

Name
solid_methylotroph_medium
Description
Solidified version of JCM Medium 1219.
Modifications
- Add agar at 15.0 g/L before autoclaving.
Purpose
Solid medium preparation.
Evidence
- Reference
  DSMZ:J1219
  Supports
  SUPPORT
  Explanation
  MediaDive/JCM medium J1219 states that agar is added for solid medium preparation.
Name
ca_free_lanthanide_test_basal_medium
Description
Experimental Ca-free basal formulation used to test lanthanide effects in methanotroph cultures related to Methylotroph Medium.
Modifications
- Omit CaCl2 from the trace element solution.
- Supplement cultures with methane or methanol and defined CaCl2 or rare-earth element chlorides after autoclaving.
- Use methanol cultures to quantify lanthanide-dependent growth of strain Ce-a6.
Purpose
Experimental lanthanide-dependency growth tests.
Evidence
- Reference
  doi:10.1264/jsme2.ME19128
  Supports
  SUPPORT
  Explanation
  Kato et al. describe a Ca-free inorganic basal medium closely related to J1219 and the carbon-source/lanthanide supplements used for growth tests.

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:54.331018Z	togo-import	Imported from TOGO Medium	Source: JCM, ID: M1308
2026-01-28T19:48:07.796075Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-03T11:20:47.110320	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default concentration for ingredient: KOH
2026-03-09T08:04:12.544959+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 5 solution(s) from ingredients
2026-03-13T06:19:51.903607Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:007843
2026-03-14T21:06:48.136808	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name
2026-03-17T06:29:41.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:10.342797+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "Methylotroph Medium" to "methylotroph_medium" for consistent matching
2026-05-04T07:57:10.478117+00:00	literature_review_apply	ADDED_GROWTH_EVIDENCE	organisms_added=1 metrics_added=1 genomes_added=0 strain_mods_added=0
2026-05-05T00:00:00Z	codex-deep-literature-curation	ADDED_FORMULATION_VARIANT_AND_GROWTH_EVIDENCE	Added MediaDive/JCM J1219 formulation evidence, stock solution compositions, literature-backed lanthanide-test variant, Methylosinus sp. Ce-a6 growth evidence, and downloaded-reference manifest entries.
2026-06-05T07:40:32.243368+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 7 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:47.548697+00:00	primary-term-label-canonicalization-v1.0	Canonicalized primary term label to OBO canonical (OAK)	2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-08-06T00:58:02.647301+00:00	curate_organism_culture_type.py	SET_ORGANISM_CULTURE_TYPE	Inferred isolate: 2 specific strain(s) named, no community signal (#142)
2026-08-20T19:01:18.050006+00:00	apply_mim_groundings.py	Adopted MIM published grounding	Grounded 17 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-08-26T02:12:34.952975+00:00	apply_mim_groundings.py	Adopted MIM published grounding	Grounded 1 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-10-07T07:16:23Z	codex	CURATED_CONCENTRATION_EVIDENCE	Exact source snippets and claim-specific calculations attached in YAML. Batch volumes remain separate from stock strengths. Unresolved final-volume claims were not altered.
2026-10-07T09:45:43.849320+00:00	codex	CURATED_M1308_NESTED_STOCK_EVIDENCE	Twelve stock concentrations unchanged; exact stock and receiving-recipe evidence attached. Six main-medium denominator gaps and both variants remain unresolved.