Name: Tumebacillus permanentifrigoris Eur1 9.5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1553

Type strain:

Species: Tumebacillus permanentifrigoris

Strain Designation: Eur1 9.5

Culture col. no.: DSM 18773, JCM 14557, CGMCC 1.10982

Strain history: L. Whyte Eur1 9.5.

NCBI tax ID(s): 378543 (species)

SI-ID 407982

DSM 18773

Special Collections

Section

Tumebacillus permanentifrigoris Eur1 9.5 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from 9-m-deep permafrost sample.

Gram-positive
rod-shaped
spore-forming
aerobe
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	*Alicyclobacillaceae*
	Genus	*Tumebacillus*
	Species	**Tumebacillus permanentifrigoris**
	Full Scientific Name (LPSN)	Tumebacillus permanentifrigoris Steven et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32193]	Gram stain	positive

[Ref.: #32193]	Cell length	3.25 µm

[Ref.: #32193]	Cell width	0.5 µm

[Ref.: #32193]	Cell shape	rod-shaped

[Ref.: #32193]	Motility	no

[Ref.: #32193]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7690]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7690]

Culture medium growth

[Ref.: #7690]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7690]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7690]	growth	25 °C
[Ref.: #32193]	growth	05-37 °C
[Ref.: #32193]	optimum	27.5 °C
[Ref.: #67770]	growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32193]

Oxygen tolerance

aerobe

[Ref.: #32193]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %92.131
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32193]	cellobiose ChEBI	+	carbon source
[Ref.: #32193]	galactose ChEBI	+	carbon source
[Ref.: #32193]	glucose ChEBI	+	carbon source
[Ref.: #32193]	lactose ChEBI	+	carbon source
[Ref.: #32193]	maltose ChEBI	+	carbon source
[Ref.: #32193]	mannitol ChEBI	+	carbon source
[Ref.: #32193]	trehalose ChEBI	+	carbon source

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

[Ref.: #7690]	Sample type/isolated from	9-m-deep permafrost sample
[Ref.: #7690]	Geographic location (country and/or sea, region)	High Arctic
[Ref.: #7690]	Country	Canada
[Ref.: #7690]	Country ISO 3 Code	CAN
[Ref.: #7690]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	9-m-deep permafrost sample from the Canadian high Arctic
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ444975 (>99% sequence identity) for Tumebacillus permanentifrigoris subclade from Microbeatlas

Aquatic Samples	1571
Soil Samples	9892
Animal Samples	651
Plant Samples	2181
Total Samples	14295

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

[Ref.: #7690]

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.: #7690]	Tumebacillus permanentifrigoris strain Eur1 9.5 16S ribosomal RNA gene, partial sequence	DQ444975	1407	GenBank ENA	378543 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Tumebacillus permanentifrigoris DSM 18773	GCA_003148565	scaffold	GenBank ENA	378543 tax ID
[Ref.: #66792]	Tumebacillus permanentifrigoris strain DSM 18773	378543.3	wgs	PATRIC	378543 tax ID	*
[Ref.: #66792]	Tumebacillus permanentifrigoris DSM 18773	2756170254	draft	JGI IMG/M	378543 tax ID	*

[Ref.: #7690]	GC-content	53.1 mol%
[Ref.: #67770]	GC-content	53.1 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Tumebacillus permanentifrigoris DSM 18773 NCBI: GCA_003148565.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tumebacillus permanentifrigoris strain DSM 18773 PATRIC: 378543.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	66.73	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	86.193	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	92.131	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	72.464	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	80.93	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	75.261	no

Availability in culture collections External links

[Ref.: #7690]

Culture collection no.

DSM 18773, JCM 14557, CGMCC 1.10982

[Ref.: #71198]

SI-ID 407982

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea.	Kang M, Chhetri G, Kim J, Kim I, So Y, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.005376	2022	*
Phylogeny	Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum.	Wu YF, Zhang B, Xing P, Wu QL, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.000240	2015	*
Phylogeny	Tumebacillus flagellatus sp. nov., an alpha-amylase/pullulanase-producing bacterium isolated from cassava wastewater.	Wang Q, Xie N, Qin Y, Shen N, Zhu J, Mi H, Huang R	Int J Syst Evol Microbiol	10.1099/ijs.0.045351-0	2013	*
Phylogeny	Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field.	Baek SH, Cui Y, Kim SC, Cui CH, Yin C, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.023358-0	2010	*
Phylogeny	Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost.	Steven B, Chen MQ, Greer CW, Whyte LG, Niederberger TD	Int J Syst Evol Microbiol	10.1099/ijs.0.65101-0	2008	*

References

#7690

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18773

#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 )

#32193

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28435 (see below)

#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 .

#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 )

#71198

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-ID407982.1 )

#28435

IJSEM 1497 2008 ( DOI 10.1099/ijs.0.65101-0 , PubMed 18523202 )

* These data were automatically processed and therefore are not curated

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Tumebacillus permanentifrigoris DSM 18773

Tumebacillus permanentifrigoris strain DSM 18773

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