hydrogenivirga_okinawensis_medium

CultureMech:000567 bacterial DEFINED LIQUID
Original name: HYDROGENIVIRGA OKINAWENSIS MEDIUM

Overview

External ontology
mediadive.medium:1131 (source link unavailable) — HYDROGENIVIRGA OKINAWENSIS MEDIUM
Applications
  • Microbial cultivation
pH
7.0
Notes
Source: DSMZ | Link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1131.pdf

Composition

flowchart LR
    CultureMech_000567["hydrogenivirga_okinawensis_medium"]
    ing0_Sulfur["Sulfur"]
    CultureMech_000567 --> ing0_Sulfur
    CHEBI_26833["CHEBI:26833"]
    ing0_Sulfur -.-> CHEBI_26833
    ing1_NaNO3["NaNO3"]
    CultureMech_000567 --> ing1_NaNO3
    CHEBI_63005["CHEBI:63005"]
    ing1_NaNO3 -.-> CHEBI_63005
    ing2_NaHCO3["NaHCO3"]
    CultureMech_000567 --> ing2_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing2_NaHCO3 -.-> CHEBI_32139
    ing3_NaCl["NaCl"]
    CultureMech_000567 --> ing3_NaCl
    CHEBI_26710["CHEBI:26710"]
    ing3_NaCl -.-> CHEBI_26710
    ing4_K2HPO4["K2HPO4"]
    CultureMech_000567 --> ing4_K2HPO4
    CHEBI_131527["CHEBI:131527"]
    ing4_K2HPO4 -.-> CHEBI_131527
    ing5_CaCl2_x_2_H2O["CaCl2 x 2 H2O"]
    CultureMech_000567 --> ing5_CaCl2_x_2_H2O
    CHEBI_86158["CHEBI:86158"]
    ing5_CaCl2_x_2_H2O -.-> CHEBI_86158
    ing6_NH4Cl["NH4Cl"]
    CultureMech_000567 --> ing6_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing6_NH4Cl -.-> CHEBI_31206
    ing7_MgSO4_x_7_H2O["MgSO4 x 7 H2O"]
    CultureMech_000567 --> ing7_MgSO4_x_7_H2O
    CHEBI_31795["CHEBI:31795"]
    ing7_MgSO4_x_7_H2O -.-> CHEBI_31795
    ing8_MgCl2_x_6_H2O["MgCl2 x 6 H2O"]
    CultureMech_000567 --> ing8_MgCl2_x_6_H2O
    CHEBI_86345["CHEBI:86345"]
    ing8_MgCl2_x_6_H2O -.-> CHEBI_86345
    ing9_KCl["KCl"]
    CultureMech_000567 --> ing9_KCl
    CHEBI_32588["CHEBI:32588"]
    ing9_KCl -.-> CHEBI_32588
    ing10_FeSO4_x_7_H2O["FeSO4 x 7 H2O"]
    CultureMech_000567 --> ing10_FeSO4_x_7_H2O
    CHEBI_75836["CHEBI:75836"]
    ing10_FeSO4_x_7_H2O -.-> CHEBI_75836
    ing11_NiCl2_x_6_H2O["NiCl2 x 6 H2O"]
    CultureMech_000567 --> ing11_NiCl2_x_6_H2O
    CHEBI_34887["CHEBI:34887"]
    ing11_NiCl2_x_6_H2O -.-> CHEBI_34887
    ing12_Na2SeO3_x_5_H2O["Na2SeO3 x 5 H2O"]
    CultureMech_000567 --> ing12_Na2SeO3_x_5_H2O
    CHEBI_131361["CHEBI:131361"]
    ing12_Na2SeO3_x_5_H2O -.-> CHEBI_131361
    ing13_Biotin["Biotin"]
    CultureMech_000567 --> ing13_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing13_Biotin -.-> CHEBI_15956
    ing14_Folic_acid["Folic acid"]
    CultureMech_000567 --> ing14_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing14_Folic_acid -.-> CHEBI_27470
    ing15_Pyridoxine_hydrochloride["Pyridoxine hydrochloride"]
    CultureMech_000567 --> ing15_Pyridoxine_hydrochloride
    CHEBI_30961["CHEBI:30961"]
    ing15_Pyridoxine_hydrochloride -.-> CHEBI_30961
    ing16_Thiamine_HCl_x_2_H2O["Thiamine-HCl x 2 H2O"]
    CultureMech_000567 --> ing16_Thiamine_HCl_x_2_H2O
    CHEBI_132751["CHEBI:132751"]
    ing16_Thiamine_HCl_x_2_H2O -.-> CHEBI_132751
    ing17_Riboflavin["Riboflavin"]
    CultureMech_000567 --> ing17_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing17_Riboflavin -.-> CHEBI_17015
    ing18_Nicotinic_acid["Nicotinic acid"]
    CultureMech_000567 --> ing18_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing18_Nicotinic_acid -.-> CHEBI_15940
    ing19_D_Calcium_pantothenate["D-Calcium pantothenate"]
    CultureMech_000567 --> ing19_D_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing19_D_Calcium_pantothenate -.-> CHEBI_31345
    ing20_Vitamin_B12["Vitamin B12"]
    CultureMech_000567 --> ing20_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing20_Vitamin_B12 -.-> CHEBI_176843
    ing21_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_000567 --> ing21_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing21_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing22_Lipoic_acid["Lipoic acid"]
    CultureMech_000567 --> ing22_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing22_Lipoic_acid -.-> CHEBI_16494
    ing23_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
    CultureMech_000567 --> ing23_Nitrilotriacetic_acid
    CHEBI_44557["CHEBI:44557"]
    ing23_Nitrilotriacetic_acid -.-> CHEBI_44557
    ing24_MnSO4_x_H2O["MnSO4 x H2O"]
    CultureMech_000567 --> ing24_MnSO4_x_H2O
    CHEBI_86364["CHEBI:86364"]
    ing24_MnSO4_x_H2O -.-> CHEBI_86364
    ing25_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
    CultureMech_000567 --> ing25_CoSO4_x_7_H2O
    CHEBI_91244["CHEBI:91244"]
    ing25_CoSO4_x_7_H2O -.-> CHEBI_91244
    ing26_ZnSO4_x_7_H2O["ZnSO4 x 7 H2O"]
    CultureMech_000567 --> ing26_ZnSO4_x_7_H2O
    CHEBI_32312["CHEBI:32312"]
    ing26_ZnSO4_x_7_H2O -.-> CHEBI_32312
    ing27_CuSO4_x_5_H2O["CuSO4 x 5 H2O"]
    CultureMech_000567 --> ing27_CuSO4_x_5_H2O
    CHEBI_31440["CHEBI:31440"]
    ing27_CuSO4_x_5_H2O -.-> CHEBI_31440
    ing28_AlK_SO4_2_x_12_H2O["AlK(SO4)2 x 12 H2O"]
    CultureMech_000567 --> ing28_AlK_SO4_2_x_12_H2O
    CHEBI_86465["CHEBI:86465"]
    ing28_AlK_SO4_2_x_12_H2O -.-> CHEBI_86465
    ing29_H3BO3["H3BO3"]
    CultureMech_000567 --> ing29_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing29_H3BO3 -.-> CHEBI_33118
    CultureMech_000567 --> more["...1 more"]

Ingredients (31)

# Ingredient Concentration Ontology Notes
1 Sulfur
S 32.067 g/mol
3 G_PER_L CHEBI:26833
sulfur atom
2 NaNO3
NO3.Na 84.994 g/mol
1 G_PER_L CHEBI:63005
sodium nitrate
3 NaHCO3
CHO3.Na 84.006 g/mol
1 G_PER_L CHEBI:32139
sodium hydrogencarbonate
4 NaCl
Cl.Na 58.443 g/mol
31.0 G_PER_L CHEBI:26710
sodium chloride
 [Merged 2 duplicates: 30.0, 1.0]
5 K2HPO4
HO4P.2K 174.174 g/mol
0.14 G_PER_L CHEBI:131527
dipotassium hydrogen phosphate
6 CaCl2 x 2 H2O
Ca.2Cl.2H2O 147.014 g/mol
0.6 G_PER_L CHEBI:86158
calcium chloride dihydrate
 [Merged 2 duplicates: 0.5, 0.1]
7 NH4Cl
Cl.H4N 53.492 g/mol
0.5 G_PER_L CHEBI:31206
ammonium chloride
8 MgSO4 x 7 H2O
7H2O.Mg.O4S 246.473 g/mol
6.4 G_PER_L CHEBI:31795
magnesium sulfate heptahydrate
 [Merged 2 duplicates: 3.4, 3.0]
9 MgCl2 x 6 H2O
2Cl.6H2O.Mg 203.301 g/mol
4.18 G_PER_L CHEBI:86345
magnesium dichloride hexahydrate
10 KCl
Cl.K 74.551 g/mol
0.33 G_PER_L CHEBI:32588
potassium chloride
11 FeSO4 x 7 H2O
Fe.7H2O.O4S 278.013 g/mol
0.11 G_PER_L CHEBI:75836
iron(2+) sulfate heptahydrate
 [Merged 2 duplicates: 0.01, 0.1]
12 NiCl2 x 6 H2O
Cl2Ni 129.599 g/mol
1 MG_PER_L CHEBI:34887
nickel dichloride
 [Unit conflict resolved: assumed G_PER_L was data entry error, kept MG_PER_L]
13 Na2SeO3 x 5 H2O
5H2O.2Na.O3Se 263.012 g/mol
1 MG_PER_L CHEBI:131361
disodium selenite pentahydrate
 [WARNING: 2 duplicates with conflicting units]
14 Biotin
C10H16N2O3S 244.316 g/mol
0.002 G_PER_L CHEBI:15956
biotin
15 Folic acid
C19H19N7O6 441.404 g/mol
0.002 G_PER_L CHEBI:27470
folic acid
16 Pyridoxine hydrochloride
C8H11NO3.HCl 205.641 g/mol
0.01 G_PER_L CHEBI:30961
pyridoxine hydrochloride
17 Thiamine-HCl x 2 H2O
C12H18N4OS.2Cl.2H2O 373.306 g/mol
0.005 G_PER_L CHEBI:132751
thiamine hydrochloride dihydrate
18 Riboflavin
C17H20N4O6 376.369 g/mol
0.005 G_PER_L CHEBI:17015
riboflavin
19 Nicotinic acid
C6H5NO2 123.111 g/mol
0.005 G_PER_L CHEBI:15940
nicotinic acid
20 D-Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.005 G_PER_L CHEBI:31345
Calcium pantothenate
21 Vitamin B12 0.0001 G_PER_L CHEBI:176843
vitamin B12
22 p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
0.005 G_PER_L CHEBI:30753
4-aminobenzoic acid
23 Lipoic acid
C8H14O2S2 206.332 g/mol
0.005 G_PER_L CHEBI:16494
lipoic acid
24 Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
1.5 G_PER_L CHEBI:44557
nitrilotriacetic acid
25 MnSO4 x H2O
H2O.Mn.O4S 169.016 g/mol
0.5 G_PER_L CHEBI:86364
manganese(II) sulfate monohydrate
26 CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
0.18 G_PER_L CHEBI:91244
cobalt(2+) sulfate heptahydrate
27 ZnSO4 x 7 H2O
7H2O.O4S.Zn 287.558 g/mol
0.18 G_PER_L CHEBI:32312
zinc sulfate heptahydrate
28 CuSO4 x 5 H2O
Cu.5H2O.O4S 249.684 g/mol
0.01 G_PER_L CHEBI:31440
copper(II) sulfate pentahydrate
29 AlK(SO4)2 x 12 H2O
Al.12H2O.K.2O4S 474.386 g/mol
0.02 G_PER_L CHEBI:86465
potassium aluminium sulfate dodecahydrate
30 H3BO3
H3BO3 61.833 g/mol
0.01 G_PER_L CHEBI:33118
boric acid
31 Na2MoO4 x 2 H2O
2H2O.MoO4.2Na 241.946 g/mol
0.01 G_PER_L CHEBI:75213
sodium molybdate dihydrate

Preparation

  1. Sparge medium with 100% N2 gas mixture for 10 min to make anoxic.
  2. Adjust pH to 7.0 with NaOH.
  3. Sparge medium with 80% N2 and 20% CO2 gas mixture for 10 min.
  4. Dispense the medium (10 mL) into 100 mL serum bottles, containing 0,03g sulfur (powder) under a stream of H2/CO2 (80:20) and seal with butyl rubber stoppers.
  5. Autoclave at 121 °C for 20 min.
  6. Prior to inoculation, add vitamins, NaNO3, and NaHCO3 (from filter sterilized stock solutions under a N2 gas atmosphere) to the medium.
  7. First dissolve nitrilotriacetic acid and adjust pH to 6.5 with KOH, then add minerals. Adjust final to pH 7.0 with KOH.

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-01-26T17:53:13.467775Z mediadive-import Imported from MediaDive Source: DSMZ, ID: 1131
2026-01-28T19:48:22.110456Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-13T03:09:06.442561Z data-quality-cleanup-v1.0 Data quality fixes Merged 6 duplicate ingredient(s); WARNING: Duplicate 'NiCl2 x 6 H2O' with different units: {'MG_PER_L', 'G_PER_L'}; WARNING: Duplicate 'Na2SeO3 x 5 H2O' with different units: {'MG_PER_L', 'G_PER_L'}
2026-03-13T04:23:43.767987Z unit-conflict-resolver-v1.0 Resolved unit conflicts Resolved trace metal unit conflict for NiCl2 x 6 H2O
2026-03-13T06:18:56.435535Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:000567
2026-03-17T06:30:12.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:45:07.520230+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "HYDROGENIVIRGA OKINAWENSIS MEDIUM" to "hydrogenivirga_okinawensis_medium" for consistent matching
2026-06-05T07:41:08.992225+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 30 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-10T07:46:59.906823+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.