methanogenium_medium (CultureMech:000295)

Overview

External ontology

mediadive.medium:J265 (source link unavailable) — METHANOGENIUM MEDIUM

Applications

Microbial cultivation

pH

6.5

Notes

Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=265

Composition

flowchart LR
    CultureMech_000295["methanogenium_medium"]
    ing0_KCl["KCl"]
    CultureMech_000295 --> ing0_KCl
    CHEBI_32588["CHEBI:32588"]
    ing0_KCl -.-> CHEBI_32588
    ing1_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_000295 --> ing1_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing1_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing2_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_000295 --> ing2_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing2_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing3_NH4Cl["NH4Cl"]
    CultureMech_000295 --> ing3_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing3_NH4Cl -.-> CHEBI_31206
    ing4_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_000295 --> ing4_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing4_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing5_KH2PO4["KH2PO4"]
    CultureMech_000295 --> ing5_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing5_KH2PO4 -.-> CHEBI_63036
    ing6_NaCl["NaCl"]
    CultureMech_000295 --> ing6_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing6_NaCl -.-> CHEBI_26710
    ing7_Fe_NH4_2_SO4_2_x_6_H2O["Fe(NH4)2(SO4)2 x 6 H2O"]
    CultureMech_000295 --> ing7_Fe_NH4_2_SO4_2_x_6_H2O
    CHEBI_76181["CHEBI:76181"]
    ing7_Fe_NH4_2_SO4_2_x_6_H2O -.-> CHEBI_76181
    ing8_NaHCO3["NaHCO3"]
    CultureMech_000295 --> ing8_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing8_NaHCO3 -.-> CHEBI_32139
    ing9_Sodium_acetate["Sodium acetate"]
    CultureMech_000295 --> ing9_Sodium_acetate
    CHEBI_32954["CHEBI:32954"]
    ing9_Sodium_acetate -.-> CHEBI_32954
    ing10_Yeast_extract["Yeast extract"]
    CultureMech_000295 --> ing10_Yeast_extract
    ing11_Trypticase_peptone["Trypticase peptone"]
    CultureMech_000295 --> ing11_Trypticase_peptone
    ing12_Resazurin["Resazurin"]
    CultureMech_000295 --> ing12_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing12_Resazurin -.-> CHEBI_8806
    ing13_Distilled_water["Distilled water"]
    CultureMech_000295 --> ing13_Distilled_water

Ingredients (14)

#	Ingredient	Concentration	Ontology	Notes
1	KCl Cl.K 74.551 g/mol		CHEBI:32588 potassium chloride	Source batch input: 0.355 g. The former g/L assertion is withdrawn because final preparation volume is not independently established.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	MgCl2 x 6 H2O 2Cl.6H2O.Mg 203.301 g/mol		CHEBI:86345 magnesium dichloride hexahydrate	Source batch input: 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.
3	MgSO4 x 7 H2O 7H2O.Mg.O4S 246.473 g/mol		CHEBI:31795 magnesium sulfate heptahydrate	[Merged 2 duplicates: 3.38235, 3.0] Source batch input: 3.45 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	NH4Cl Cl.H4N 53.492 g/mol		CHEBI:31206 ammonium chloride	Source batch input: 0.25 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	CaCl2 x 2 H2O Ca.2Cl.2H2O 147.014 g/mol		CHEBI:86158 calcium chloride dihydrate	[Merged 2 duplicates: 0.137255, 0.1] Source batch input: 0.14 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	KH2PO4 H2O4P.K 136.084 g/mol		CHEBI:63036 potassium dihydrogen phosphate	Source batch input: 0.14 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	NaCl Cl.Na 58.443 g/mol		CHEBI:26710 sodium chloride	[Merged 2 duplicates: 17.6471, 1.0] Source batch input: 18 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.
8	Fe(NH4)2(SO4)2 x 6 H2O Fe.6H2O.2H4N.2O4S 392.139 g/mol		CHEBI:76181 ferrous ammonium sulfate hexahydrate	Source batch input: 2 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.
9	NaHCO3 CHO3.Na 84.006 g/mol		CHEBI:32139 sodium hydrogencarbonate	Source batch input: 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.
10	Sodium acetate C2H3O2.Na 82.034 g/mol		CHEBI:32954 sodium acetate	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.
11	Yeast extract			Source batch input: 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. Source material qualifier: BD-Difco.
12	Trypticase peptone			Source batch input: 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. Source material qualifier: BD-BBL.
13	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.
14	Distilled water	0.98 L		Water batch input: 980 ml / 1000 ml per L = 0.98 L, not a measured final volume.

Preparation

Mix components thoroughly, except NaHCO3, and adjust pH to 6.5. Bring to a boil for 5-10 sec, then, cool down under a stream of H2-CO2 (80:20, v/v) and add NaHCO3 to the medium. Dispense the medium into suitable culture vessels (e.g., 5 ml medium in Hungate tubes) under the same gas mixture and seal with butyl rubber stoppers. After autoclaving, stand the medium overnight. Aseptically and anaerobically add per liter the following solutions (autoclaved and stored under a N2 atmosphere):
Pressurize the inoculated bottles to 200 kPa H2:CO2 (80:20, v/v).

Solutions

Wolfe's mineral solution

Dose: 0.01 L

Stock composition
Ingredient	Concentration	Notes
NiCl2 x 6 H2O	0.02 G_PER_L	Source stock input: 0.02 g. Retain only the provider-declared stock g_l=0.02 (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	0.001 G_PER_L	Source stock input: 1 mg. Retain only the provider-declared stock g_l=0.001 (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	0.01 G_PER_L	Source stock input: 0.01 g. 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.

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 minerals

Dose: 1 L

Stock composition
Ingredient	Concentration	Notes
Nitrilotriacetic acid	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.
MgSO4 x 7 H2O	3 G_PER_L	[Merged 2 duplicates: 3.38235, 3.0] Source stock input: 3 g. Retain only the provider-declared stock g_l=3 (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.
MnSO4 x n H2O	0.5 G_PER_L	Source stock input: 0.5 g. Retain only the provider-declared stock g_l=0.5 (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.
NaCl	1 G_PER_L	[Merged 2 duplicates: 17.6471, 1.0] Source stock input: 1 g. Retain only the provider-declared stock g_l=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.
FeSO4 x 7 H2O	0.1 G_PER_L	Source stock input: 0.1 g. 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.
CoSO4 x 7 H2O	0.1 G_PER_L	Source stock input: 0.1 g. 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.
CaCl2 x 2 H2O	0.1 G_PER_L	[Merged 2 duplicates: 0.137255, 0.1] Source stock input: 0.1 g. 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.
ZnSO4 x 7 H2O	0.1 G_PER_L	Source stock input: 0.1 g. 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.
CuSO4 x 5 H2O	0.01 G_PER_L	Source stock input: 0.01 g. 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.
AlK(SO4)2	0.01 G_PER_L	Source stock input: 0.01 g. 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.
H3BO3	0.01 G_PER_L	Source stock input: 0.01 g. 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.
Na2MoO4 x 2 H2O	0.01 G_PER_L	Source stock input: 0.01 g. 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.
Distilled water	1 L	Water batch input: 1000 ml / 1000 ml per L = 1 L, not a measured final volume.
KOH solution		Add to adjust trace-mineral preparation pH; the source gives no fixed amount or stock strength.

Source batch stock input: 1000 ml = 1 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 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.

L-Cysteine HCl x H2O stock

Dose: 10 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
L-Cysteine HCl x H2O		Source reagent label: 5%. 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.

The preparation explicitly prescribes 10 ml per liter at this stage, not 10 g/L or an absolute batch dose. Stock composition, where given, belongs to this preparation and is not a direct receiving-medium ingredient list.

Na2S x 9 H2O stock

Dose: 10 ML_PER_L

Stock composition
Ingredient	Concentration	Notes
Na2S x 9 H2O		Source reagent label: 5%. 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.

Target organisms

No target organisms are recorded.

Provenance

Timestamp	Curator	Action	Notes
2026-01-26T17:53:16.117967Z	mediadive-import	Imported from MediaDive	Source: JCM, ID: J265
2026-01-28T19:48:44.697304Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-13T03:09:46.961528Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 3 duplicate ingredient(s)
2026-03-13T06:18:54.238893Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:000295
2026-03-17T17:06:12.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:05.193001+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "METHANOGENIUM MEDIUM" to "methanogenium_medium" for consistent matching
2026-05-16T09:02:57.447158+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	category->lowercase=1
2026-06-05T07:40:14.730956+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 34 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:42.244964+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.
2026-10-08T13:12:36.691952+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.