Name: Saccharolobus shibatae B12
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16654

Type strain:

Species: Saccharolobus shibatae

Strain Designation: B12

Culture col. no.: DSM 5389, ATCC 51178, JCM 8931, IFO 15437, NBRC 15437

Strain history: DSM 5389 <-- D. W. Grogan <-- W. Zillig strain B12.

NCBI tax ID(s): 2286 (species)

SI-ID 42846

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

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

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

thermophilic
16S sequence
Archaea
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Archaea*
	Phylum	*Thermoproteota*
	Class	*Thermoprotei*
	Order	*Sulfolobales*
	Family	*Sulfolobaceae*
	Genus	*Saccharolobus*
	Species	**Saccharolobus shibatae**
	Full Scientific Name (LPSN)	Saccharolobus shibatae (Grogan et al. 1991) Sakai and Kurosawa 2018

Synonym

Sulfolobus shibatae

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2133]

Culture medium

SULFOLOBUS MEDIUM (DSMZ Medium 88)

[Ref.: #2133]

Culture medium growth

[Ref.: #2133]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2133]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2133]			growth	75 °C
[Ref.: #67770]			growth	75 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Ability of spore formation

yes Confidence in %90.7

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #2133]	Sample type/isolated from	geothermal mud hole
[Ref.: #2133]	Geographic location (country and/or sea, region)	Kiushu island, Beppu
[Ref.: #2133]	Country	Japan
[Ref.: #2133]	Country ISO 3 Code	JPN
[Ref.: #2133]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Geothermal pools and bubbling 'mud pots' in Beppu
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kyushu
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #2133]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #2133]	Sulfolobus shibatae strain B12 16S ribosomal RNA gene, partial sequence	M32504	1495	GenBank ENA	523848 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Saccharolobus shibatae B12	GCA_019175345	complete	GenBank ENA	523848 tax ID	*
[Ref.: #66792]	Saccharolobus shibatae B12	523848.4	complete	PATRIC	523848 tax ID	*

[Ref.: #2133]	GC-content	35.0 mol%
[Ref.: #67770]	GC-content	35.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	34 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	72.963	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	51.964	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	55.109	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.899	no
[Ref.: #125438]	thermophile	thermophilicⓘ	yes	73.685	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Saccharolobus shibatae B12 NCBI: GCA_019175345
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	90.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	65.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	83.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	80.7

Availability in culture collections External links

[Ref.: #2133]

Culture collection no.

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

[Ref.: #85675]

SI-ID 42846

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#85675

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID42846.1 )

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Saccharolobus shibatae in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Saccharolobus shibatae B12 B12

Saccharolobus shibatae B12

Change proposal

Change proposal