desulfovibrio_piger_medium

CultureMech:002756 bacterial COMPLEX LIQUID
Original name: DESULFOVIBRIO PIGER MEDIUM

Overview

External ontology
mediadive.medium:J400 (source link unavailable) — DESULFOVIBRIO PIGER MEDIUM
Applications
  • Microbial cultivation
pH range
{'min': 7.0, 'max': 7.2}
Notes
TOGO M396 preserves a JCM Medium J400 snapshot for Desulfovibrio Piger Medium. The JCM formula lists 1 L distilled water, 1 g MgSO4・7H2O, 1 g yeast extract, 0.1 g CaCl2・2H2O, 0.5 g KH2PO4, 1 g NH4Cl, 0.5 mg resazurin, 75 mg Na2S・9H2O, 2 g NaHCO3, 2 g Na2SO4, 2.5 g sodium lactate, 1 g Na2S2O3・5H2O, and referenced trace-minerals, trace-element, and trace-vitamins stocks from JCM media M151, M187, and M197. The preparation text specifies an N2 gas stream and N2 atmosphere, and states to check the final pH to be 7.0-7.2.

Composition

flowchart LR
    CultureMech_002756["desulfovibrio_piger_medium"]
    ing0_Distilled_water["Distilled water"]
    CultureMech_002756 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_MgSO4_7H2O["MgSO4・7H2O"]
    CultureMech_002756 --> ing1_MgSO4_7H2O
    CHEBI_31795["CHEBI:31795"]
    ing1_MgSO4_7H2O -.-> CHEBI_31795
    ing2_Yeast_extract["Yeast extract"]
    CultureMech_002756 --> ing2_Yeast_extract
    ing3_CaCl2_2H2O["CaCl2・2H2O"]
    CultureMech_002756 --> ing3_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing3_CaCl2_2H2O -.-> CHEBI_86158
    ing4_KH2PO4["KH2PO4"]
    CultureMech_002756 --> ing4_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing4_KH2PO4 -.-> CHEBI_63036
    ing5_NH4Cl["NH4Cl"]
    CultureMech_002756 --> ing5_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing5_NH4Cl -.-> CHEBI_31206
    ing6_Resazurin["Resazurin"]
    CultureMech_002756 --> ing6_Resazurin
    CHEBI_8806["CHEBI:8806"]
    ing6_Resazurin -.-> CHEBI_8806
    ing7_Na2S_9H2O["Na2S・9H2O"]
    CultureMech_002756 --> ing7_Na2S_9H2O
    CHEBI_76209["CHEBI:76209"]
    ing7_Na2S_9H2O -.-> CHEBI_76209
    ing8_NaHCO3["NaHCO3"]
    CultureMech_002756 --> ing8_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing8_NaHCO3 -.-> CHEBI_32139
    ing9_Na2SO4["Na2SO4"]
    CultureMech_002756 --> ing9_Na2SO4
    CHEBI_32149["CHEBI:32149"]
    ing9_Na2SO4 -.-> CHEBI_32149
    ing10_Sodium_lactate["Sodium lactate"]
    CultureMech_002756 --> ing10_Sodium_lactate
    CHEBI_75228["CHEBI:75228"]
    ing10_Sodium_lactate -.-> CHEBI_75228
    ing11_Na2S2O3_5H2O["Na2S2O3・5H2O"]
    CultureMech_002756 --> ing11_Na2S2O3_5H2O
    CHEBI_32150["CHEBI:32150"]
    ing11_Na2S2O3_5H2O -.-> CHEBI_32150

Ingredients (12)

# Ingredient Concentration Ontology Notes
1 Distilled water
H2O 18.015 g/mol
1.0 L CHEBI:15377
water
 TOGO M396 lists 1 L distilled water.
2 MgSO4・7H2O
7H2O.Mg.O4S 246.473 g/mol
1.0 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 TOGO M396 lists 1 g/L MgSO4・7H2O.
3 Yeast extract 1.0 G_PER_L FOODON:03315426
yeast extract
 TOGO M396 lists 1 g/L yeast extract.
4 CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
0.1 G_PER_L CHEBI:86158
calcium chloride dihydrate
 TOGO M396 lists 0.1 g/L CaCl2・2H2O.
5 KH2PO4
H2O4P.K 136.084 g/mol
0.5 G_PER_L CHEBI:63036
potassium dihydrogen phosphate
 TOGO M396 lists 0.5 g/L KH2PO4.
6 NH4Cl
Cl.H4N 53.492 g/mol
1.0 G_PER_L CHEBI:31206
ammonium chloride
 TOGO M396 lists 1 g/L NH4Cl.
7 Resazurin
C12H7NO4 229.191 g/mol
0.5 MG_PER_L CHEBI:8806
Resazurin
 TOGO M396 lists 0.5 mg/L resazurin.
8 Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
75.0 MG_PER_L CHEBI:76209
sodium sulfide nonahydrate
 TOGO M396 lists 75 mg/L Na2S・9H2O.
9 NaHCO3
CHO3.Na 84.006 g/mol
2.0 G_PER_L CHEBI:32139
sodium hydrogencarbonate
 TOGO M396 lists 2 g/L NaHCO3.
10 Na2SO4
2Na.O4S 142.043 g/mol
2.0 G_PER_L CHEBI:32149
sodium sulfate
 TOGO M396 lists 2 g/L Na2SO4.
11 Sodium lactate
C3H5O3.Na 112.06 g/mol
2.5 G_PER_L CHEBI:75228
sodium lactate
 TOGO M396 lists 2.5 g/L sodium lactate.
12 Na2S2O3・5H2O
5H2O.2Na.O3S2 248.186 g/mol
1.0 G_PER_L CHEBI:32150
sodium thiosulfate pentahydrate
 TOGO M396 lists 1 g/L Na2S2O3・5H2O.

Preparation

  1. Mix ingredients, except sodium lactate, NaHCO3 and Na2S・9H2O, bring to aboil, and cool down to room temperature under a N2 gas stream. Dispense themedium into culture vessels under a N2 atmosphere, seal with butyl rubber stoppers and autoclave. Separately autoclave sodium lactate, NaHCO3 and Na2S・9H2O solutions (10, 8 and 0.75%, respectively) under a N2 atmosphere,and add to the medium. Check final pH to be 7.0 -- 7.2.
  2. Use Medium No. [388] with 2.5 g/L (final) sodium lactate. Add Trace minerals of Medium No. [151], instead of FeCl2 solution, and Trace element solution of Medium No. [230].

Solutions

Trace minerals (see Medium [M142])

Dose: 1 ML_PER_L

Defined in TOGO medium M142.

Trace element solution (see Medium [M180])

Dose: 1 ML_PER_L

Defined in TOGO medium M180.

Trace vitamins (see Medium [M190])

Dose: 10 ML_PER_L

Defined in TOGO medium M190.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:16.510493Z mediadive-import Imported from MediaDive Source: JCM, ID: J400
2026-02-03T11:26:54.810481 quality-tagger-v1.0 Added data quality flag Marked as incomplete_composition due to placeholder ingredients
2026-03-13T06:19:15.508205Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:002756
2026-03-17T19:45:28.915113+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "DESULFOVIBRIO PIGER MEDIUM" to "desulfovibrio_piger_medium" for consistent matching
2026-04-05T17:20:25.578036 mark_unavailable_media MARKED_UNAVAILABLE Source database has no composition data. Category: EMPTY. JCM page returns "Nothing found"
2026-05-16T08:57:28.841191+00:00 migrate_data_quality_flags.py MIGRATED_DATA_QUALITY_FLAGS dict(2 keys) -> list(2 entries)
2026-08-06T07:56:36.092888+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 J400 from source-equivalent TOGO M396. Preserved final ingredients and stock-solution boundaries; did not flatten referenced media or stocks.
2026-08-26T02:12:53.862982+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 7 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-09-11T00:00:00-07:00 repair_jcm_j400_desulfovibrio_piger_score15.py RESOLVED_JCM_J400_DESULFOVIBRIO_PIGER_SCORE15 TOGO M396 preserves a JCM Medium J400 snapshot for Desulfovibrio Piger Medium. The JCM formula lists 1 L distilled water, 1 g MgSO4・7H2O, 1 g yeast extract, 0.1 g CaCl2・2H2O, 0.5 g KH2PO4, 1 g NH4Cl, 0.5 mg resazurin, 75 mg Na2S・9H2O, 2 g NaHCO3, 2 g Na2SO4, 2.5 g sodium lactate, 1 g Na2S2O3・5H2O, and referenced trace-minerals, trace-element, and trace-vitamins stocks from JCM media M151, M187, and M197. The preparation text specifies an N2 gas stream and N2 atmosphere, and states to check the final pH to be 7.0-7.2. Added the TOGO M396 pH range and grounded the main JCM J400 salt, yeast extract, redox indicator, and carbon-source rows.