methanocaldococcus_indiensis_medium

CultureMech:002720 archaea COMPLEX LIQUID
Original name: METHANOCALDOCOCCUS INDIENSIS MEDIUM

Overview

External ontology
mediadive.medium:J361 (source link unavailable) — METHANOCALDOCOCCUS INDIENSIS MEDIUM
Applications
  • Microbial cultivation
Notes
Source: JCM | Link: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=361 Composition recovery source: https://togomedium.org/medium/M355 (TOGO snapshot of JCM medium J361).

Composition

flowchart LR
    CultureMech_002720["methanocaldococcus_indiensis_medium"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_002720 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_NaCl["NaCl"]
    CultureMech_002720 --> ing1_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing1_NaCl -.-> CHEBI_26710
    ing2_CaCl2_2H2O["CaCl2・2H2O"]
    CultureMech_002720 --> ing2_CaCl2_2H2O
    ing3_KH2PO4["KH2PO4"]
    CultureMech_002720 --> ing3_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing3_KH2PO4 -.-> CHEBI_63036
    ing4_NH4Cl["NH4Cl"]
    CultureMech_002720 --> ing4_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing4_NH4Cl -.-> CHEBI_31206
    ing5_Resazurin["Resazurin"]
    CultureMech_002720 --> ing5_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing5_Resazurin -.-> CHEBI_8806
    ing6_MgCl2_6H2O["MgCl2・6H2O"]
    CultureMech_002720 --> ing6_MgCl2_6H2O
    ing7_Na2S_9H2O["Na2S・9H2O"]
    CultureMech_002720 --> ing7_Na2S_9H2O
    ing8_KCl["KCl"]
    CultureMech_002720 --> ing8_KCl
    CHEBI_32588["CHEBI:32588"]
    ing8_KCl -.-> CHEBI_32588
    ing9_Vitamin_B12["Vitamin B12"]
    CultureMech_002720 --> ing9_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing9_Vitamin_B12 -.-> CHEBI_176843
    ing10_Na2SO4["Na2SO4"]
    CultureMech_002720 --> ing10_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing10_Na2SO4 -.-> CHEBI_32149
    ing11_Na2WO4_2H2O["Na2WO4・2H2O"]
    CultureMech_002720 --> ing11_Na2WO4_2H2O
    ing12_PIPES["PIPES"]
    CultureMech_002720 --> ing12_PIPES
    CHEBI_39033["CHEBI:39033"]
    ing12_PIPES -.-> CHEBI_39033
    ing13_Na2SeO4["Na2SeO4"]
    CultureMech_002720 --> ing13_Na2SeO4
    CHEBI_77775["CHEBI:77775"]
    ing13_Na2SeO4 -.-> CHEBI_77775
    ing14_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
    CultureMech_002720 --> ing14_Yeast_extract__BD_Difco_
    ing15_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_002720 --> ing15_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing15_Carbon_dioxide_gas -.-> CHEBI_16526
    ing16_N2["N2"]
    CultureMech_002720 --> ing16_N2
    ing17_Hydrogen_gas["Hydrogen gas"]
    CultureMech_002720 --> ing17_Hydrogen_gas
    CHEBI_18276["CHEBI:18276"]
    ing17_Hydrogen_gas -.-> CHEBI_18276

Ingredients (18)

# Ingredient Concentration Ontology Notes
1 Distilled water
H2O 18.015 g/mol
1 L CHEBI:15377
water
 Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component
2 NaCl
Cl.Na 58.443 g/mol
30 G_PER_L CHEBI:26710
sodium chloride
 Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
3 CaCl2・2H2O 0.15 G_PER_L Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
4 KH2PO4
H2O4P.K 136.084 g/mol
0.2 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
5 NH4Cl
Cl.H4N 53.492 g/mol
0.25 G_PER_L CHEBI:31206
ammonium chloride
 Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component
6 Resazurin
C12H7NO4 229.191 g/mol
1 MG_PER_L CHEBI:8806
Resazurin
 Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component
7 MgCl2・6H2O 3 G_PER_L Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
8 Na2S・9H2O 0.5 G_PER_L Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component
9 KCl
Cl.K 74.551 g/mol
0.5 G_PER_L CHEBI:32588
potassium chloride
 Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
10 Vitamin B12 0.05 MG_PER_L CHEBI:176843
vitamin B12
 Role: Vitamin; Properties: Organic compound, Defined component, Simple component
11 Na2SO4
2Na.O4S 142.043 g/mol
4 G_PER_L CHEBI:32149
sodium sulfate
 Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
12 Na2WO4・2H2O 0.2 MG_PER_L Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
13 PIPES 3.46 G_PER_L CHEBI:39033
PIPES
 Role: Buffer; Properties: Organic compound, Defined component, Simple component
14 Na2SeO4
2Na.O4Se 188.936 g/mol
0.05 MG_PER_L CHEBI:77775
sodium selenate
 Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
15 Yeast extract (BD-Difco) 0.5 G_PER_L Properties: Undefined component
16 Carbon dioxide gas
CO2 44.009 g/mol
variable VARIABLE CHEBI:16526
carbon dioxide
 Properties: ガス
17 N2 variable VARIABLE Properties: ガス
18 Hydrogen gas
H2 2.016 g/mol
variable VARIABLE CHEBI:18276
dihydrogen
 Properties: ガス

Preparation

  1. Mix ingredients, except Na2S・9H2O, and adjust pH to 6.5 with HCl. Distribute the medium into culture vessels (e.g., 20 ml of the medium in 120 ml serum bottles) under a stream of H2--CO2 (4:1, v/v) gas mixture and seal with butyl rubber stoppers, and autoclave. Neutralize Na2S・9H2O as a 5% solution, and autoclave under a N2 atmosphere. Add the sterile Na2S solution to the medium, and pressurize the bottles to 200 kPa H2--CO2 (4:1, v/v). After incubation at 70C for 1 hr, readjust pH to 6.5 with a sterile and anaerobic NaHCO3 stock solution.
  2. Use Medium No. [301] without sodium acetate.

Solutions

Trace element solution (see Medium [M296])

Dose: 1 ML_PER_L

Defined in TOGO medium M296.

Trace vitamins (see Medium [M190])

Dose: 10 ML_PER_L

Defined in TOGO medium M190.

Growth stimulating factors (see Medium [M296])

Dose: 1 ML_PER_L

Defined in TOGO medium M296.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:16.398074Z mediadive-import Imported from MediaDive Source: JCM, ID: J361
2026-02-03T11:26:54.667692 quality-tagger-v1.0 Added data quality flag Marked as incomplete_composition due to placeholder ingredients
2026-03-13T06:19:15.250457Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002720
2026-03-17T19:45:28.621643+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "METHANOCALDOCOCCUS INDIENSIS MEDIUM" to "methanocaldococcus_indiensis_medium" for consistent matching
2026-04-05T17:20:25.546358 mark_unavailable_media MARKED_UNAVAILABLE Source database has no composition data. Category: EMPTY. JCM page returns "Nothing found"
2026-05-16T08:58:06.146667+00:00 migrate_data_quality_flags.py MIGRATED_DATA_QUALITY_FLAGS dict(2 keys) -> list(2 entries)
2026-08-06T07:56:36.073536+00:00 curate_placeholder_composition.py REMOVED_PLACEHOLDER_INGREDIENT Removed the 'See source for composition' placeholder ingredient; the record carries no imported composition and is flagged incomplete (#175).
2026-08-25T00:00:00-07:00 repair_jcm_missing_from_togo.py RECOVERED_JCM_COMPOSITION_FROM_TOGO Recovered JCM J361 from source-equivalent TOGO M355. Preserved final ingredients and stock-solution boundaries; did not flatten referenced media or stocks.
2026-08-26T02:12:20.646915+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 12 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).