Thermosipho japonicus (DSM 13481, JCM 10495, IHB1)

Name: Thermosipho japonicus (DSM 13481, JCM 10495, IHB1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17056

Type strain

Strain Designation IHB1

Culture col. no. DSM 13481 JCM 10495 IHB1

NCBI tax ID(s) 90323

Special Collections DSMZ JCM

History DSMZ <- JCM <- K. Takai, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Yokosuka; IHB1 JCM <-- K. Takai IHB1.

Links

Thermosipho japonicus IHB1 is an anaerobe bacterium that was isolated from deep-sea hydrothermal vent chimney, 972 m depth.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49474

DSM 13481,JCM 10495

@ref 20215

Last LPSN update 2026-05-29 08:28:55

Domain Bacteria

Phylum Thermotogota

Class Thermotogae

Order Thermotogales

Family Fervidobacteriaceae

Genus Thermosipho

Species Thermosipho japonicus

Full scientific name Thermosipho japonicus Takai and Horikoshi 2000

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5058	PYROCOCCUS MEDIUM (DSMZ Medium 377)		Medium recipe at MediaDive	Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5058	positive	growth	70
67770	positive	growth	70

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5058	anaerobe
125438	anaerobe	93.772
125439	anaerobe	99.514

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5058	deep-sea hydrothermal vent chimney, 972 m depth	Okinawa area, Ilheya Basin hydrothermal field	Japan	JPN	Asia
67770	Deep-sea hydrothermal vent chimney	Iheya Basin in the Okinawa area	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB024932 (>99% sequence identity) for Thermosipho from Microbeatlas

Aquatic Samples	5
Soil Samples	1
Animal Samples	0
Plant Samples	0
Total Samples	6

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5058	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420165v1 assembly for Thermosipho japonicus DSM 13481	scaffold	GCA_014201655	90323.3	2861242185	90323	73.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5058	Thermosipho japonicus gene for 16S rRNA, partial sequence	AB024932	1503		90323

GC content

@ref	GC-content (mol%)	Method
5058	31.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1420165v1 assembly for Thermosipho japonicus DSM 13481
NCBI: GCA_014201655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	66.97	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.51	no
125439	motility	BacteriaNetⓘ	no	62.83	no
125439	spore_formation	BacteriaNetⓘ	no	88.16	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermosipho japonicus DSM 13481
NCBI: GCA_014201655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	64.50	no
125438	anaerobic	anaerobicⓘ	yes	93.77	yes
125438	aerobic	aerobicⓘ	no	97.05	no
125438	spore-forming	spore-formingⓘ	no	71.35	no
125438	thermophilic	thermophileⓘ	yes	77.75	yes
125438	flagellated	motile2+ⓘ	yes	60.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan.	Takai K, Horikoshi K	Extremophiles	10.1007/s007920050002	2000

References

#5058	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13481
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Thermosipho japonicus (DSM 13481, JCM 10495, IHB1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014201655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media