Shimazuella kribbensis A9500 | Type strain | DSM 45090, JCM 14729, KCCM 41585, KCTC 9933 | BacDiveID:16785

Strain identifier

BacDive ID: 16785

Type strain:

Species: Shimazuella kribbensis

Strain Designation: A9500

Culture col. no.: DSM 45090, JCM 14729, KCCM 41585, KCTC 9933

Strain history: C.-J. Kim A 9500.

NCBI tax ID(s): 1123252 (strain), 139808 (species)

SI-ID 107666

KCTC 9933, DSM 45090, JCM 14729

Section

Shimazuella kribbensis A9500 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from forest soil.

Gram-positive
spore-forming
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Thermoactinomycetaceae*
	Genus	*Shimazuella*
	Species	**Shimazuella kribbensis**
	Full Scientific Name (LPSN)	Shimazuella kribbensis Park et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

Multimedia content

Caption:

Medium 65 28°C

Intellectual property rights:

© Leibniz-Institut DSMZ

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #12332]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #12332]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

Observation

quinones: MK-9, MK-10

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

[Ref.: #12332]	Sample type/isolated from	forest soil
[Ref.: #12332]	Geographic location (country and/or sea, region)	Sobaek Mountain
[Ref.: #12332]	Country	Republic of Korea
[Ref.: #12332]	Country ISO 3 Code	KOR
[Ref.: #12332]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from Sobaek mountain
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

Global distribution of 16S sequence AB049939 (>99% sequence identity) for Shimazuella kribbensis subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	119
Animal Samples	7
Plant Samples	5
Total Samples	138

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

Biosafety level

1

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.: #12332]	Shimazuella kribbensis gene for 16S rRNA, partial sequence	AB049939	1459	ENA	139808 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Shimazuella kribbensis DSM 45090	GCA_000428065	scaffold	GenBank	1123252 tax ID
[Ref.: #66792]	Shimazuella kribbensis DSM 45090	1123252.3	wgs	PATRIC	1123252 tax ID	*
[Ref.: #66792]	Shimazuella kribbensis DSM 45090	2515154144	draft	JGI IMG/M	1123252 tax ID	*

GC-content

39.4 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Shimazuella kribbensis DSM 45090 DSM 45090 NCBI: GCA_000428065.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shimazuella kribbensis DSM 45090 PATRIC: 1123252.3
[Ref.: #69480]	motile	no	80.818	no
[Ref.: #69480]	flagellated	no	86.478	no
[Ref.: #69480]	gram-positive	yes	91.567	no
[Ref.: #69480]	anaerobic	no	98.791	no
[Ref.: #69480]	aerobic	yes	92.97	no
[Ref.: #69480]	halophile	no	91.679	no
[Ref.: #69480]	spore-forming	yes	90.559	no
[Ref.: #69480]	thermophile	no	95.412	yes
[Ref.: #69480]	glucose-util	yes	84.766	no
[Ref.: #69480]	glucose-ferment	no	91.786	no

Availability in culture collections External links

Culture collection no.

DSM 45090, JCM 14729, KCCM 41585, KCTC 9933

SI-ID 107666

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shimazuella alba sp. nov. isolated from desert soil and emended description of the genus Shimazuella Park et al. 2007.	Saygin H, Ay H, Sahin N	Arch Microbiol	10.1007/s00203-020-01894-z	2020	*
Phylogeny	Shimazuella kribbensis gen. nov., sp. nov., a mesophilic representative of the family Thermoactinomycetaceae.	Park DJ, Dastager SG, Lee JC, Yeo SH, Yoon JH, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65194-0	2007	*

References

#12332

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45090

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#85801

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-ID107666.1 )

* These data were automatically processed and therefore are not curated

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