methanomethylovorans_uponensis_medium (CultureMech:003334)

Overview

External ontology

mediadive.medium:J985 (source link unavailable) — METHANOMETHYLOVORANS UPONENSIS MEDIUM

Applications

Microbial cultivation

Notes

Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=985

Composition

flowchart LR
    CultureMech_003334["methanomethylovorans_uponensis_medium"]
    ing0_NaCl["NaCl"]
    CultureMech_003334 --> ing0_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing0_NaCl -.-> CHEBI_26710
    ing1_KCl["KCl"]
    CultureMech_003334 --> ing1_KCl
    CHEBI_32588["CHEBI:32588"]
    ing1_KCl -.-> CHEBI_32588
    ing2_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_003334 --> ing2_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing2_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing3_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_003334 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_KH2PO4["KH2PO4"]
    CultureMech_003334 --> ing4_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing4_KH2PO4 -.-> CHEBI_63036
    ing5_NH4Cl["NH4Cl"]
    CultureMech_003334 --> ing5_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing5_NH4Cl -.-> CHEBI_31206
    ing6_Resazurin["Resazurin"]
    CultureMech_003334 --> ing6_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing6_Resazurin -.-> CHEBI_8806
    ing7_Distilled_water["Distilled water"]
    CultureMech_003334 --> ing7_Distilled_water

Ingredients (8)

#	Ingredient	Concentration	Ontology	Notes
1	NaCl Cl.Na 58.443 g/mol		CHEBI:26710 sodium chloride	Source batch input: 1 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
2	KCl Cl.K 74.551 g/mol		CHEBI:32588 potassium chloride	Source batch input: 0.5 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
3	MgCl2 x 6 H2O 2Cl.6H2O.Mg 203.301 g/mol		CHEBI:86345 magnesium dichloride hexahydrate	Source batch input: 0.4 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
4	CaCl2 x 2 H2O Ca.2Cl.2H2O 147.014 g/mol		CHEBI:86158 calcium chloride dihydrate	Source batch input: 0.1 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
5	KH2PO4 H2O4P.K 136.084 g/mol		CHEBI:63036 potassium dihydrogen phosphate	Source batch input: 0.2 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
6	NH4Cl Cl.H4N 53.492 g/mol		CHEBI:31206 ammonium chloride	Source batch input: 0.5 g. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
7	Resazurin C12H7NO4 229.191 g/mol		CHEBI:8806 Resazurin	Source batch input: 1 mg. The former g/L assertion is withdrawn because final preparation volume is not independently established. Evidence supports this batch-amount note, not a calculated concentration.
8	Distilled water	0.96 L		Water batch input: 960 ml / 1000 ml per L = 0.96 L, not a measured final volume.

Preparation

Mix components thoroughly and autoclave under a N2-CO2 (80:20, v/v) gas atmosphere. After cooling, add the following solutions (autoclaved or *filter-sterilized):
Aseptically and anaerobically distribute the medium into culture vessels under a N2-CO2 (80:20, v/v) gas mixture and seal with butyl rubber stoppers. Finally, add per liter the following solution from an anaerobic stock (autoclaved and stored under a N2 atmosphere):

Solutions

Trace vitamins

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Biotin	0.002 G_PER_L	Source stock input: 2 mg. Retain only the provider-declared stock g_l=0.002 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Folic acid	0.002 G_PER_L	Source stock input: 2 mg. Retain only the provider-declared stock g_l=0.002 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Pyridoxine hydrochloride	0.01 G_PER_L	Source stock input: 10 mg. Retain only the provider-declared stock g_l=0.01 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Thiamine HCl	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Riboflavin	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Nicotinic acid	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Calcium pantothenate	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Vitamin B12	0.0001 G_PER_L	Source stock input: 0.1 mg. Retain only the provider-declared stock g_l=0.0001 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
p-Aminobenzoic acid	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Lipoic acid	0.005 G_PER_L	Source stock input: 5 mg. Retain only the provider-declared stock g_l=0.005 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Distilled water	1 L	Water batch input: 1000 ml / 1000 ml per L = 1 L, not a measured final volume.

Source batch stock input: 10 ml = 0.01 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

FeCl2 solution

Dose: 0.001 L

Stock composition
Ingredient	Concentration	Notes
FeCl2 x 4 H2O	1.5 G_PER_L	Source stock input: 1.5 g. Retain only the provider-declared stock g_l=1.5 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Distilled water	0.99 L	Water batch input: 990 ml / 1000 ml per L = 0.99 L, not a measured final volume.

Source batch stock input: 1 ml = 0.001 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

HCl stock (7.7 M)

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
HCl	7.7 MOLAR	Rebase HCl to the explicit 7.7 M reagent strength, not its provider-derived 2.5 g/L in the FeCl2 stock. The 25% label has unspecified basis; the batch dose is stored on the enclosing HCl solution.

Source batch stock input: 10 ml = 0.01 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Trace element solution

Dose: 0.001 L

Stock composition
Ingredient	Concentration	Notes
ZnCl2	0.07 G_PER_L	Source stock input: 70 mg. Retain only the provider-declared stock g_l=0.07 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
MnCl2 x 4 H2O	0.1 G_PER_L	Source stock input: 100 mg. Retain only the provider-declared stock g_l=0.1 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
H3BO3	0.006 G_PER_L	Source stock input: 6 mg. Retain only the provider-declared stock g_l=0.006 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
CoCl2 x 6 H2O	0.19 G_PER_L	Source stock input: 190 mg. Retain only the provider-declared stock g_l=0.19 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
CuCl2 x 2 H2O	0.002 G_PER_L	Source stock input: 2 mg. Retain only the provider-declared stock g_l=0.002 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
NiCl2 x 6 H2O	0.024 G_PER_L	Source stock input: 24 mg. Retain only the provider-declared stock g_l=0.024 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Na2MoO4 x 2 H2O	0.036 G_PER_L	Source stock input: 36 mg. Retain only the provider-declared stock g_l=0.036 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Distilled water	1 L	Water batch input: 1000 ml / 1000 ml per L = 1 L, not a measured final volume.

Source batch stock input: 1 ml = 0.001 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Selenite-tungstate solution

Dose: 0.001 L

Stock composition
Ingredient	Concentration	Notes
NaOH	0.4 G_PER_L	Source stock input: 0.4 g. Retain only the provider-declared stock g_l=0.4 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Na2SeO3 x 5 H2O	0.006 G_PER_L	Source stock input: 6 mg. Retain only the provider-declared stock g_l=0.006 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Na2WO4 x 2 H2O	0.008 G_PER_L	Source stock input: 8 mg. Retain only the provider-declared stock g_l=0.008 (source volume field=1000 ml), not a receiving-medium concentration or independently measured final stock volume. This restores the preparation boundary; any prior merged-duplicate note describes the superseded flattened record.
Distilled water	1 L	Water batch input: 1000 ml / 1000 ml per L = 1 L, not a measured final volume.

Source batch stock input: 1 ml = 0.001 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Trimethylamine-HCl stock

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
Trimethylamine-HCl		Source reagent label: *, 30%. The former 10 g/L encodes a liquid addition as mass concentration and is withdrawn. Stock percentage basis is unspecified; the supported volume dose is on the enclosing solution. Unresolved source disagreement: MediaDive labels this reagent 30%, while TOGO M1038 labels it 3%. Both lack percentage basis; neither is selected as a numeric strength and the original JCM985 page returns Nothing found. This is not evidence that the two versions are identical.

Source batch stock input: 10 ml = 0.01 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

NaHCO3 stock

Dose: 0.02 L

Stock composition
Ingredient	Concentration	Notes
NaHCO3		Source reagent label: *, 8%. The former 20 g/L encodes a liquid addition as mass concentration and is withdrawn. Stock percentage basis is unspecified; the supported volume dose is on the enclosing solution.

Source batch stock input: 20 ml = 0.02 L, not a dose per final liter. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Na2S x 9 H2O stock

Dose: 8 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
Na2S x 9 H2O		Source reagent label: 5%. The former 8 g/L encodes a liquid addition as mass concentration and is withdrawn. Stock percentage basis is unspecified; the supported volume dose is on the enclosing solution.

The preparation explicitly prescribes 8 ml per liter at this stage, not 8 g/L or an absolute batch dose. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-26T17:53:18.220518Z	mediadive-import	Imported from MediaDive	Source: JCM, ID: J985
2026-01-28T19:48:31.542150Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-13T06:19:19.588360Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:003334
2026-03-17T06:30:32.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:33.613695+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "METHANOMETHYLOVORANS UPONENSIS MEDIUM" to "methanomethylovorans_uponensis_medium" for consistent matching
2026-06-05T07:41:32.016078+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 32 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:47:07.155589+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.
2026-10-08T13:12:36.691952+00:00	codex	RESTORED_METHANOGEN_STOCK_BOUNDARIES_AND_DOSE_BASES_WITH_EVIDENCE	Restored preparation boundaries and explicit stock-dose bases. Preserved source-specific conflicts, chemical annotations and earlier history. Batch-mass notes do not assert final concentrations; provider-declared stock rates remain qualified. No growth or identity equivalence claim inferred.