medium_for_co_culture_of_strain_jt_with_methanospirillum_hungatei_nbrc_100397 (CultureMech:008179)

Overview

External ontology

TOGO:M1624 — Medium for Co-culture of Strain JT with Methanospirillum hungatei NBRC 100397

Applications

Microbial cultivation

Notes

Source: https://togomedium.org/medium/M1624 Original source: NBRC - NBRC_M824 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=824

Composition

flowchart LR
    CultureMech_008179["medium_for_co_culture_of_strain_jt_with_methanospirillum_hungatei_n..."]
    ing0_Distilled_water["Distilled water"]
    CultureMech_008179 --> ing0_Distilled_water
    CHEBI_15377["CHEBI:15377"]
    ing0_Distilled_water -.-> CHEBI_15377
    ing1_Yeast_extract["Yeast extract"]
    CultureMech_008179 --> ing1_Yeast_extract
    ing2_CaCl2_2H2O["CaCl2·2H2O"]
    CultureMech_008179 --> ing2_CaCl2_2H2O
    CHEBI_86158["CHEBI:86158"]
    ing2_CaCl2_2H2O -.-> CHEBI_86158
    ing3_KH2PO4["KH2PO4"]
    CultureMech_008179 --> ing3_KH2PO4
    CHEBI_63036["CHEBI:63036"]
    ing3_KH2PO4 -.-> CHEBI_63036
    ing4_NH4Cl["NH4Cl"]
    CultureMech_008179 --> ing4_NH4Cl
    CHEBI_31206["CHEBI:31206"]
    ing4_NH4Cl -.-> CHEBI_31206
    ing5_Na2S_9H2O["Na2S·9H2O"]
    CultureMech_008179 --> ing5_Na2S_9H2O
    CHEBI_76209["CHEBI:76209"]
    ing5_Na2S_9H2O -.-> CHEBI_76209
    ing6_NaHCO3["NaHCO3"]
    CultureMech_008179 --> ing6_NaHCO3
    CHEBI_32139["CHEBI:32139"]
    ing6_NaHCO3 -.-> CHEBI_32139
    ing7_MgCl2_H2O["MgCl2·H2O"]
    CultureMech_008179 --> ing7_MgCl2_H2O
    CHEBI_86355["CHEBI:86355"]
    ing7_MgCl2_H2O -.-> CHEBI_86355
    ing8_Na_terephthalate["Na-terephthalate"]
    CultureMech_008179 --> ing8_Na_terephthalate
    ing9_Cysteine_HCl["Cysteine-HCl"]
    CultureMech_008179 --> ing9_Cysteine_HCl
    CHEBI_91247["CHEBI:91247"]
    ing9_Cysteine_HCl -.-> CHEBI_91247
    ing10_Carbon_dioxide_gas["Carbon dioxide gas"]
    CultureMech_008179 --> ing10_Carbon_dioxide_gas
    CHEBI_16526["CHEBI:16526"]
    ing10_Carbon_dioxide_gas -.-> CHEBI_16526
    ing11_Nitrogen_gas["Nitrogen gas"]
    CultureMech_008179 --> ing11_Nitrogen_gas
    CHEBI_17997["CHEBI:17997"]
    ing11_Nitrogen_gas -.-> CHEBI_17997
    ing12_Biotin["Biotin"]
    CultureMech_008179 --> ing12_Biotin
    CHEBI_15956["CHEBI:15956"]
    ing12_Biotin -.-> CHEBI_15956
    ing13_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
    CultureMech_008179 --> ing13_p_Aminobenzoic_acid
    CHEBI_30753["CHEBI:30753"]
    ing13_p_Aminobenzoic_acid -.-> CHEBI_30753
    ing14_Thiamine_HCl["Thiamine-HCl"]
    CultureMech_008179 --> ing14_Thiamine_HCl
    CHEBI_49105["CHEBI:49105"]
    ing14_Thiamine_HCl -.-> CHEBI_49105
    ing15_Ca_pantothenate["Ca-pantothenate"]
    CultureMech_008179 --> ing15_Ca_pantothenate
    CHEBI_29032["CHEBI:29032"]
    ing15_Ca_pantothenate -.-> CHEBI_29032
    ing16_Pyridoxine_HCl["Pyridoxine-HCl"]
    CultureMech_008179 --> ing16_Pyridoxine_HCl
    CHEBI_30961["CHEBI:30961"]
    ing16_Pyridoxine_HCl -.-> CHEBI_30961
    ing17_Folic_acid["Folic acid"]
    CultureMech_008179 --> ing17_Folic_acid
    CHEBI_27470["CHEBI:27470"]
    ing17_Folic_acid -.-> CHEBI_27470
    ing18_Vitamin_B12["Vitamin B12"]
    CultureMech_008179 --> ing18_Vitamin_B12
    CHEBI_176843["CHEBI:176843"]
    ing18_Vitamin_B12 -.-> CHEBI_176843
    ing19_Riboflavin["Riboflavin"]
    CultureMech_008179 --> ing19_Riboflavin
    CHEBI_17015["CHEBI:17015"]
    ing19_Riboflavin -.-> CHEBI_17015
    ing20_Nicotinic_acid["Nicotinic acid"]
    CultureMech_008179 --> ing20_Nicotinic_acid
    CHEBI_15940["CHEBI:15940"]
    ing20_Nicotinic_acid -.-> CHEBI_15940
    ing21_Lipoic_acid["Lipoic acid"]
    CultureMech_008179 --> ing21_Lipoic_acid
    CHEBI_16494["CHEBI:16494"]
    ing21_Lipoic_acid -.-> CHEBI_16494
    ing22_Na2MoO4_2H2O["Na2MoO4·2H2O"]
    CultureMech_008179 --> ing22_Na2MoO4_2H2O
    CHEBI_75213["CHEBI:75213"]
    ing22_Na2MoO4_2H2O -.-> CHEBI_75213
    ing23_H3BO3["H3BO3"]
    CultureMech_008179 --> ing23_H3BO3
    CHEBI_33118["CHEBI:33118"]
    ing23_H3BO3 -.-> CHEBI_33118
    ing24_MnCl2_4H2O["MnCl2·4H2O"]
    CultureMech_008179 --> ing24_MnCl2_4H2O
    CHEBI_86368["CHEBI:86368"]
    ing24_MnCl2_4H2O -.-> CHEBI_86368
    ing25_CoCl2_6H2O["CoCl2·6H2O"]
    CultureMech_008179 --> ing25_CoCl2_6H2O
    CHEBI_35696["CHEBI:35696"]
    ing25_CoCl2_6H2O -.-> CHEBI_35696
    ing26_NiCl2_6H2O["NiCl2·6H2O"]
    CultureMech_008179 --> ing26_NiCl2_6H2O
    CHEBI_34887["CHEBI:34887"]
    ing26_NiCl2_6H2O -.-> CHEBI_34887
    ing27_CuCl2_2H2O["CuCl2·2H2O"]
    CultureMech_008179 --> ing27_CuCl2_2H2O
    CHEBI_86318["CHEBI:86318"]
    ing27_CuCl2_2H2O -.-> CHEBI_86318
    ing28_ZnCl2["ZnCl2"]
    CultureMech_008179 --> ing28_ZnCl2
    CHEBI_49976["CHEBI:49976"]
    ing28_ZnCl2 -.-> CHEBI_49976
    ing29_FeCl3_6H2O["FeCl3·6H2O"]
    CultureMech_008179 --> ing29_FeCl3_6H2O
    CHEBI_86254["CHEBI:86254"]
    ing29_FeCl3_6H2O -.-> CHEBI_86254
    CultureMech_008179 --> more["...5 more"]

Ingredients (35)

#	Ingredient	Concentration	Ontology	Notes
1	Distilled water H2O 18.015 g/mol	1.0 G_PER_L	CHEBI:15377 water	Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 4 identical duplicates: 1.0, 1.0, 1.0, 1.0]
2	Yeast extract	0.2 G_PER_L		Role: Nutrient source; Properties: Undefined component
3	CaCl2·2H2O Ca.2Cl.2H2O 147.014 g/mol	0.25 G_PER_L	CHEBI:86158 calcium chloride dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.15, 0.1]
4	KH2PO4 H2O4P.K 136.084 g/mol	0.14 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	0.54 G_PER_L	CHEBI:31206 ammonium chloride	Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component
6	Na2S·9H2O 9H2O.2Na.S 240.182 g/mol	0.3 G_PER_L	CHEBI:76209 sodium sulfide nonahydrate	Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component
7	NaHCO3 CHO3.Na 84.006 g/mol	2.5 G_PER_L	CHEBI:32139 sodium hydrogencarbonate	Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
8	MgCl2·H2O 2Cl.H2O.Mg 113.226 g/mol	0.2 G_PER_L	CHEBI:86355 magnesium dichloride monohydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
9	Na-terephthalate	0.42 G_PER_L		Role: Carbon source; Properties: Organic compound, Defined component, Simple component
10	Cysteine-HCl C3H7NO2S.HCl 157.622 g/mol	0.3 G_PER_L	CHEBI:91247 L-cysteine hydrochloride	Properties: Defined component, Organic compound, Simple component
11	Carbon dioxide gas CO2 44.009 g/mol	variable VARIABLE	CHEBI:16526 carbon dioxide	Properties: ガス
12	Nitrogen gas N2 28.014 g/mol	variable VARIABLE	CHEBI:17997 dinitrogen	Properties: ガス
13	Biotin C10H16N2O3S 244.316 g/mol	0.5 G_PER_L	CHEBI:15956 biotin	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
14	p-Aminobenzoic acid C7H7NO2 137.138 g/mol	0.3 G_PER_L	CHEBI:30753 4-aminobenzoic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
15	Thiamine-HCl C12H17N4OS.Cl.HCl 337.276 g/mol	0.7 G_PER_L	CHEBI:49105 thiamine hydrochloride	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
16	Ca-pantothenate C9H16NO5 218.229 g/mol	0.5 G_PER_L	CHEBI:29032 (R)-pantothenate	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
17	Pyridoxine-HCl C8H11NO3.HCl 205.641 g/mol	0.4 G_PER_L	CHEBI:30961 pyridoxine hydrochloride	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
18	Folic acid C19H19N7O6 441.404 g/mol	0.9 G_PER_L	CHEBI:27470 folic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
19	Vitamin B12	2.7 G_PER_L	CHEBI:176843 vitamin B12	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
20	Riboflavin C17H20N4O6 376.369 g/mol	0.8 G_PER_L	CHEBI:17015 riboflavin	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
21	Nicotinic acid C6H5NO2 123.111 g/mol	0.2 G_PER_L	CHEBI:15940 nicotinic acid	Role: Vitamin; Properties: Organic compound, Defined component, Simple component
22	Lipoic acid C8H14O2S2 206.332 g/mol	0.4 G_PER_L	CHEBI:16494 lipoic acid	Role: Growth factor; Properties: Organic compound, Defined component, Simple component
23	Na2MoO4·2H2O 2H2O.MoO4.2Na 241.946 g/mol	24 G_PER_L	CHEBI:75213 sodium molybdate dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
24	H3BO3 H3BO3 61.833 g/mol	10 G_PER_L	CHEBI:33118 boric acid	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
25	MnCl2·4H2O Cl2Mn.4H2O 197.904 g/mol	0.1 G_PER_L	CHEBI:86368 manganese(II) chloride tetrahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
26	CoCl2·6H2O 2Cl.Co 129.839 g/mol	24 G_PER_L	CHEBI:35696 cobalt dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
27	NiCl2·6H2O Cl2Ni 129.599 g/mol	0.12 G_PER_L	CHEBI:34887 nickel dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
28	CuCl2·2H2O Cl2Cu.2H2O 170.482 g/mol	25 G_PER_L	CHEBI:86318 copper(II) chloride dihydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
29	ZnCl2 2Cl.Zn 136.296 g/mol	0.1 G_PER_L	CHEBI:49976 zinc dichloride	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
30	FeCl3·6H2O Cl3Fe.6H2O 270.294 g/mol	1.35 G_PER_L	CHEBI:86254 iron trichloride hexahydrate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
31	Nitrilotriacetic acid (NTA) C6H9NO6 191.139 g/mol	12.8 G_PER_L	CHEBI:44557 nitrilotriacetic acid	Role: Mineral source; Properties: Organic compound, Defined component, Simple component
32	KOH HO.K 56.105 g/mol	variable VARIABLE	CHEBI:32035 potassium hydroxide	Role: Mineral source; Properties: Defined component, Solution
33	Na2WO4 2Na.O4W 293.816 g/mol	4 G_PER_L	CHEBI:63940 sodium tungstate	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
34	Na2SeO3 2Na.O3Se 172.937 g/mol	4 G_PER_L	CHEBI:48843 disodium selenite	Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component
35	Resazurin C12H7NO4 229.191 g/mol	1 G_PER_L	CHEBI:8806 Resazurin	Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component

Solutions

Vitamin solution*

Dose: 3 G_PER_L

See mediadive_6241_Vitamin_solution.yaml for composition

Trace element solution**

Dose: 1 G_PER_L

See mediadive_6187_Trace_element_solution.yaml for composition

Se/W solution***

Dose: 1 G_PER_L

See mediadive_4826_Se_W_solution.yaml for composition

Resazurin solution****

Dose: 1 G_PER_L

See mediadive_30_Resazurin_solution.yaml for composition

Target organisms and growth evidence

These are curated observations and conditions for named organisms; they do not imply universal growth suitability.

Preferred term
Pelotomaculum sp.
Term
Id
NCBITaxon:2053590
Label
Pelotomaculum sp.
Strain
strain JT
Evidence
- Reference
  doi:10.1128/AEM.70.3.1617-1626.2004
  Supports
  SUPPORT
  Explanation
  Qiu et al. 2004 is the defining study for strain JT, the organism this co-culture medium is named for. Basal-medium recipe is cited transitively (Sekiguchi et al. 2000), so the exact match to the TOGO/NBRC M1624 formulation is not text-verified in this source. | Identifiers: 16S rRNA GenBank AB091329 (set AB091323-AB091329); no culture-collection ID reported
Preferred term
Methanospirillum hungatei
Term
Id
NCBITaxon:2203
Label
Methanospirillum hungatei
Strain
NBRC 100397T (= DSM 864T = ATCC 27890T), JF-1T
Evidence
- Reference
  doi:10.1128/AEM.70.3.1617-1626.2004
  Supports
  SUPPORT
  Explanation
  M. hungatei NBRC 100397 is named in this medium record. Qiu 2004 identifies the partner as DSM 864 (type strain equivalent to NBRC 100397T) but does not print the co-culture basal recipe; curate as the named co-culture partner with recipe-identity flagged uncertain. | Identifiers: NBRC 100397T; DSM 864; ATCC 27890T; genome CP000254

Provenance

Timestamp	Curator	Action	Notes
2026-01-27T06:35:57.978992Z	togo-import	Imported from TOGO Medium	Source: NBRC, ID: M1624
2026-01-28T19:48:34.162298Z	chebi-enrichment	Added CHEBI ontology terms to ingredients	Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-02-03T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: KOH
2026-03-09T08:04:56.688341+00:00	solution-migrator-v1.0	Migrated solutions from ingredients to solutions array	Moved 4 solution(s) from ingredients
2026-03-13T03:09:28.266117Z	data-quality-cleanup-v1.0	Data quality fixes	Merged 4 duplicate ingredient(s)
2026-03-13T06:19:54.189765Z	culturemech-id-assigner-v1.0	Assigned CultureMech ID	Assigned stable identifier: CultureMech:008179
2026-03-14T00:00:00+00:00	schema-defaulter-v1.0	Applied schema defaults and normalizations	Added default solution name; Added default solution name; Added default solution name; Added default solution name
2026-03-17T06:30:37.000000Z	mediaingredientmech-enrichment-v1.0	Added MediaIngredientMech links	Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:12.767484+00:00	normalize_media_names_to_snake_case.py	NAME_NORMALIZED	Normalized name from "Medium for Co-culture of Strain JT with Methanospirillum hungatei NBRC 100397" to "medium_for_co_culture_of_strain_jt_with_methanospirillum_hungatei_nbrc_100397" for consistent matching
2026-05-16T09:04:19.938421+00:00	migrate_legacy_fields.py	MIGRATED_LEGACY_FIELDS	curation_history.date->timestamp=2
2026-06-05T07:41:28.989734+00:00	mim-legacy-to-chebi-migration-v1.0	Refreshed legacy MediaIngredientMech links to CHEBI keying	Replaced 27 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-06-08T23:19:46.921439+00:00	chebi-regrounding-v1.0	Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24)	Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md.
2026-06-10T07:47:06.026168+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.
2026-06-02T06:47:50.262641+00:00	deep-research-edison-phase2	ENRICHED	Phase-2: this record is by definition the medium for syntrophic co-culture of 'strain JT' with M. hungatei NBRC 100397. Strain JT (a Pelotomaculum sp.) and M. hungatei are both named in the record and both are supported as the intended organisms (Qiu et al. 2004). CAVEAT: the basal-medium recipe is not printed in Qiu 2004 (cited to Sekiguchi et al. 2000), and Qiu names the methanogen as DSM 864 rather than NBRC 100397; treat both as evidence-backed but recipe-unverified. [added 2 organism(s), 0 variant(s)]
2026-08-06T06:01:46.226804+00:00	coculture-community-curation-v1.0	SET_ORGANISM_CULTURE_TYPE	Set community: syntrophic co-culture of Pelotomaculum sp. + Methanospirillum hungatei grown together. Deferred from #142 (script does not guess community from a keyword); resolved manually per #223.
2026-09-02T07:37:29.298380+00:00	repair_merged_duplicates.py	REPAIRED_SUMMED_DUPLICATE_MERGE	Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched.