Saccharolobus shibatae (DSM 5389, ATCC 51178, B12)

Name: Saccharolobus shibatae (DSM 5389, ATCC 51178, B12)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16654

Type strain

Strain Designation B12

Culture col. no. DSM 5389 ATCC 51178 B12 JCM 8931 IFO 15437 1 more

NCBI tax ID(s) 2286

Special Collections DSMZ JCM

History <- D.W. Grogan <- W. Zillig, B12 (Sulfolobus acidocaldarius) DSM 5389 <-- D. W. Grogan <-- W. Zillig strain B12.

Links

Saccharolobus shibatae B12 is an archaeon that was isolated from geothermal mud hole.

genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 42846

ATCC 51178,DSM 5389,JCM 8931,IFO 15437,NBRC 15437

@ref 20215

Last LPSN update 2026-02-09 11:22:01

Domain Archaea

Phylum Thermoproteota

Class Thermoprotei

Order Sulfolobales

Family Sulfolobaceae

Genus Saccharolobus

Species Saccharolobus shibatae

Full scientific name Saccharolobus shibatae (Grogan et al. 1991) Sakai and Kurosawa 2018

Synonyms (1)

Sulfolobus shibatae

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2133	SULFOLOBUS MEDIUM (DSMZ Medium 88)		Medium recipe at MediaDive	Name: SULFOLOBUS MEDIUM (DSMZ Medium 88) Composition: (NH4)2SO4 1.28713 g/l Yeast extract 0.990099 g/l KH2PO4 0.277228 g/l MgSO4 x 7 H2O 0.247525 g/l CaCl2 x 2 H2O 0.0693069 g/l FeCl3 x 6 H2O 0.019802 g/l Na2B4O7 x 10 H2O 0.00445545 g/l MnCl2 x 4 H2O 0.00178218 g/l ZnSO4 x 7 H2O 0.000217822 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Na2MoO4 x 2 H2O 2.9703e-05 g/l VOSO4 x 2 H2O 2.9703e-05 g/l CoSO4 x 7 H2O 9.90099e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2133	positive	growth	75
67770	positive	growth	75

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		90.7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2133	geothermal mud hole	Kiushu island, Beppu	Japan	JPN	Asia
67770	Geothermal pools and bubbling 'mud pots' in Beppu	Kyushu	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence M32504 (>99% sequence identity) for Sulfolobaceae from Microbeatlas

Aquatic Samples	131
Soil Samples	5
Animal Samples	3
Plant Samples
Total Samples	139

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2133	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	ASM1917534v1 assembly for Saccharolobus shibatae B12	complete	GCA_019175345	523848.4	8047903996	523848	98.19

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2133	Sulfolobus shibatae strain B12 16S ribosomal RNA gene, partial sequence	M32504	1495		523848

GC content

@ref	GC-content (mol%)	Method
2133	35.0
67770	35.2	high performance liquid chromatography (HPLC)
67770	34	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Saccharolobus shibatae B12
NCBI: GCA_019175345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.70	no
125439	motility	BacteriaNetⓘ	yes	65.20	no
125439	gram_stain	BacteriaNetⓘ	variable	83.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	80.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Saccharolobus shibatae B12 B12
NCBI: GCA_019175345.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	72.96	no
125438	anaerobic	anaerobicⓘ	yes	51.96	no
125438	aerobic	aerobicⓘ	yes	55.11	no
125438	spore-forming	spore-formingⓘ	no	87.90	no
125438	thermophilic	thermophileⓘ	yes	73.69	no
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA.	Fusco S, Aulitto M, Iacobucci I, Crocamo G, Pucci P, Bartolucci S, Monti M, Contursi P.	Biochim Biophys Acta Gene Regul Mech	10.1016/j.bbagrm.2020.194493	2020
	Isolation of archaeal viruses with lipid membrane from Tengchong acidic hot springs.	Feng X, Li Y, Tian C, Yang W, Liu X, Zhang C, Zeng Z.	Front Microbiol	10.3389/fmicb.2023.1134935	2023
Pathogenicity	Novel Sulfolobus Fuselloviruses with Extensive Genomic Variations.	Zhang J, Zheng X, Wang H, Jiang H, Dong H, Huang L.	J Virol	10.1128/jvi.01624-19	2020
Enzymology	Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases.	Ohara K, Unno H, Oshima Y, Hosoya M, Fujino N, Hirooka K, Takahashi S, Yamashita S, Kusunoki M, Nakayama T	J Biol Chem	10.1074/jbc.M113.521856	2014
Enzymology	Molecular cloning and characterization of a thermostable carboxylesterase from an archaeon, Sulfolobus shibatae DSM5389: non-linear kinetic behavior of a hormone-sensitive lipase family enzyme.	Ejima K, Liu J, Oshima Y, Hirooka K, Shimanuki S, Yokota Y, Hemmi H, Nakayama T, Nishino T	J Biosci Bioeng	10.1016/S1389-1723(05)00310-5	2004
Metabolism	Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389.	Okazaki N, Blaber M, Kuroki R, Tamada T	Acta Crystallogr F Struct Biol Commun	10.1107/S2053230X1801453X	2018
Enzymology	Highly enantioselective stereo-inverting sec-alkylsulfatase activity of hyperthermophilic Archaea.	Wallner SR, Nestl BM, Faber K	Org Biomol Chem	10.1039/b504883d	2005

References

#2133	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5389
#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 )

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Saccharolobus shibatae (DSM 5389, ATCC 51178, B12)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_019175345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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