methylosoma_difficile_medium

CultureMech:002904 bacterial DEFINED LIQUID
Original name: METHYLOSOMA DIFFICILE MEDIUM

Overview

External ontology
mediadive.medium:J556 (source link unavailable) — METHYLOSOMA DIFFICILE MEDIUM
Applications
  • Microbial cultivation
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=556

Composition

flowchart LR
    CultureMech_002904["methylosoma_difficile_medium"]
    ing0_NaCl["NaCl"]
    CultureMech_002904 --> ing0_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing0_NaCl -.-> CHEBI_26710
    ing1_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_002904 --> ing1_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing1_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing2_KCl["KCl"]
    CultureMech_002904 --> ing2_KCl
    CHEBI_32588["CHEBI:32588"]
    ing2_KCl -.-> CHEBI_32588
    ing3_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_002904 --> ing3_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing4_Na2SO4["Na2SO4"]
    CultureMech_002904 --> ing4_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing4_Na2SO4 -.-> CHEBI_32149
    ing5_HEPES_buffer["HEPES buffer"]
    CultureMech_002904 --> ing5_HEPES_buffer
    CHEBI_46756["CHEBI:46756"]
    ing5_HEPES_buffer -.-> CHEBI_46756
    ing6_KNO3["KNO3"]
    CultureMech_002904 --> ing6_KNO3
    CHEBI_63043["CHEBI:63043"]
    ing6_KNO3 -.-> CHEBI_63043
    ing7_Vitamin_B12["Vitamin B12"]
    CultureMech_002904 --> ing7_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing7_Vitamin_B12 -.-> CHEBI_176843
    ing8_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_002904 --> ing8_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing8_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing9_Biotin["Biotin"]
    CultureMech_002904 --> ing9_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing9_Biotin -.-> CHEBI_15956
    ing10_Nicotinic_acid["Nicotinic acid"]
    CultureMech_002904 --> ing10_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing10_Nicotinic_acid -.-> CHEBI_15940
    ing11_DL_Calcium_pantothenate["DL-Calcium pantothenate"]
    CultureMech_002904 --> ing11_DL_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing11_DL_Calcium_pantothenate -.-> CHEBI_31345
    ing12_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_002904 --> ing12_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing12_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing13_Thiamine_HCl["Thiamine HCl"]
    CultureMech_002904 --> ing13_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing13_Thiamine_HCl -.-> CHEBI_49105
    ing14_HCl["HCl"]
    CultureMech_002904 --> ing14_HCl
    CHEBI_17883["CHEBI:17883"]
    ing14_HCl -.-> CHEBI_17883
    ing15_FeCl2_x_4_H2O["FeCl2 x 4 H2O"]
    CultureMech_002904 --> ing15_FeCl2_x_4_H2O
    CHEBI_86249["CHEBI:86249"]
    ing15_FeCl2_x_4_H2O -.-> CHEBI_86249
    ing16_ZnCl2["ZnCl2"]
    CultureMech_002904 --> ing16_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing16_ZnCl2 -.-> CHEBI_49976
    ing17_MnCl2_x_4_H2O["MnCl2 x 4 H2O"]
    CultureMech_002904 --> ing17_MnCl2_x_4_H2O
    CHEBI_86368["CHEBI:86368"]
    ing17_MnCl2_x_4_H2O -.-> CHEBI_86368
    ing18_H3BO3["H3BO3"]
    CultureMech_002904 --> ing18_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing18_H3BO3 -.-> CHEBI_33118
    ing19_CoCl2_x_6_H2O["CoCl2 x 6 H2O"]
    CultureMech_002904 --> ing19_CoCl2_x_6_H2O
    CHEBI_53503["CHEBI:53503"]
    ing19_CoCl2_x_6_H2O -.-> CHEBI_53503
    ing20_CuCl2_x_2_H2O["CuCl2 x 2 H2O"]
    CultureMech_002904 --> ing20_CuCl2_x_2_H2O
    CHEBI_86318["CHEBI:86318"]
    ing20_CuCl2_x_2_H2O -.-> CHEBI_86318
    ing21_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_002904 --> ing21_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing21_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing22_Na2MoO4_x_2_H2O["Na2MoO4 x 2 H2O"]
    CultureMech_002904 --> ing22_Na2MoO4_x_2_H2O
    CHEBI_75213["CHEBI:75213"]
    ing22_Na2MoO4_x_2_H2O -.-> CHEBI_75213

Ingredients (23)

# Ingredient Concentration Ontology Notes
1 NaCl
Cl.Na 58.443 g/mol
0.0998004 G_PER_L CHEBI:26710
sodium chloride
2 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
0.0399202 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
3 KCl
Cl.K 74.551 g/mol
0.0499002 G_PER_L CHEBI:32588
potassium chloride
4 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.0149701 G_PER_L CHEBI:86158
calcium chloride dihydrate
5 Na2SO4
2Na.O4S 142.043 g/mol
0.0159681 G_PER_L CHEBI:32149
sodium sulfate
6 HEPES buffer 5 G_PER_L CHEBI:46756
HEPES
7 KNO3
K.NO3 101.102 g/mol
0.544 G_PER_L CHEBI:63043
potassium nitrate
8 Vitamin B12 0.05 G_PER_L CHEBI:176843
vitamin B12
9 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.05 G_PER_L CHEBI:30753
4-aminobenzoic acid
10 Biotin
C10H16N2O3S 244.316 g/mol
0.01 G_PER_L CHEBI:15956
biotin
11 Nicotinic acid
C6H5NO2 123.111 g/mol
0.1 G_PER_L CHEBI:15940
nicotinic acid
12 DL-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.025 G_PER_L CHEBI:31345
Calcium pantothenate
13 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.25 G_PER_L CHEBI:30961
pyridoxine hydrochloride
14 Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
0.05 G_PER_L CHEBI:49105
thiamine hydrochloride
15 HCl
HCl 36.461 g/mol
2.5 G_PER_L CHEBI:17883
hydrogen chloride
16 FeCl2 x 4 H2O
Cl2Fe.4H2O 198.811 g/mol
1.5 G_PER_L CHEBI:86249
iron dichloride tetrahydrate
17 ZnCl2
2Cl.Zn 136.296 g/mol
0.07 G_PER_L CHEBI:49976
zinc dichloride
18 MnCl2 x 4 H2O
Cl2Mn.4H2O 197.904 g/mol
0.1 G_PER_L CHEBI:86368
manganese(II) chloride tetrahydrate
19 H3BO3
H3BO3 61.833 g/mol
0.006 G_PER_L CHEBI:33118
boric acid
20 CoCl2 x 6 H2O
2Cl.Co.6H2O 237.929 g/mol
0.19 G_PER_L CHEBI:53503
cobalt chloride hexahydrate
21 CuCl2 x 2 H2O
Cl2Cu.2H2O 170.482 g/mol
0.002 G_PER_L CHEBI:86318
copper(II) chloride dihydrate
22 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
0.024 G_PER_L CHEBI:34887
nickel dichloride
23 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.036 G_PER_L CHEBI:75213
sodium molybdate dihydrate

Preparation

  1. Mix components and autoclave. After cooling, add the following solutions (autoclaved or filter-sterilized) to the medium:
  2. Distribute the culture medium into culture tubes (leave >80% volume as a gas phase) and seal with butyl rubber stoppers.
  3. Finally, replace the gas phase with 20% methane and 5% CO2 in air (by volume).
  4. Mix 28 ml of 1 M KH2PO4 and 78 ml of 1 M Na2HPO4 to prepare 100 ml of 1 M phosphate buffer.

Target organisms

No target organisms are recorded.

Provenance

Merged from 1 source record.

TimestampCuratorActionNotes
2026-06-14T05:58:58.561437+00:00 idnf-grounding-fix-v1.0 Fixed ID_NOT_FOUND term groundings Absent/obsolete CHEBI term ids fixed - 1 re-grounded to the correct CHEBI, 0 de-grounded (mixture or unverifiable).
2026-01-26T17:53:16.924035Z mediadive-import Imported from MediaDive Source: JCM, ID: J556
2026-03-13T06:19:16.465385Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002904
2026-03-17T06:29:47.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:30.019755+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "METHYLOSOMA DIFFICILE MEDIUM" to "methylosoma_difficile_medium" for consistent matching
2026-06-05T07:41:33.409277+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 21 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:37:35.579978+00:00 primary-term-regrounding-v1.0 Re-grounded wrong primary term id (OAK-verified) 1 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi.
2026-06-10T07:47:07.665208+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.
2026-08-06T03:05:45.101395+00:00 merge_recipes.py MERGED_RECIPES merged 1 source recipe(s) on fingerprint d55f4ef0c26075fa7446ee76df2545fc43c8f30449048133ef58fc8e455e19a3