Cite this strain

Tumebacillus permanentifrigoris (DSM 18773, JCM 14557, Eur1 9.5)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1553

Type strain

Strain Designation Eur1 9.5

Culture col. no. DSM 18773 JCM 14557 Eur1 9.5 CGMCC 1.10982

NCBI tax ID(s) 378543

Special Collections DSMZ JCM Literature strains

Links

Name and taxonomic classification

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

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 407982

DSM 18773

Last LPSN update 2024-12-09 10:43:19

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Alicyclobacillaceae

Genus Tumebacillus

Species Tumebacillus permanentifrigoris

Full scientific name Tumebacillus permanentifrigoris Steven et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
32193	positive	3.25 µm	0.5 µm	rod-shaped

Pigmentation

32193

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7690	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7690	positive	growth	25	mesophilic
32193	positive	growth	05-37
32193	positive	optimum	27.5	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Observation

67770

Observationquinones: MK-7

Spore formation

@ref	Spore formation
32193
125438

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32193	17057 ChEBI	cellobiose	+	carbon source
32193	28260 ChEBI	galactose	+	carbon source
32193	17234 ChEBI	glucose	+	carbon source
32193	17716 ChEBI	lactose	+	carbon source
32193	17306 ChEBI	maltose	+	carbon source
32193	29864 ChEBI	mannitol	+	carbon source
32193	27082 ChEBI	trehalose	+	carbon source

Oxygen tolerance

32193

Oxygen toleranceaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7690	9-m-deep permafrost sample	High Arctic	Canada	CAN	North America
67770	9-m-deep permafrost sample from the Canadian high Arctic

Taxonmaps

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

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
7690	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)
7690	53.1
67770	53.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7690	Tumebacillus permanentifrigoris strain Eur1 9.5 16S ribosomal RNA gene, partial sequence	DQ444975	1407		378543

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Tumebacillus permanentifrigoris strain DSM 18773	378543.3	wgs	PATRIC	378543
66792	Tumebacillus permanentifrigoris DSM 18773	2756170254	draft	JGI IMG/M	378543
67770	Tumebacillus permanentifrigoris DSM 18773	GCA_003148565	scaffold		378543

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Tumebacillus permanentifrigoris DSM 18773
NCBI: GCA_003148565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	87.90	no
125439	motility	BacteriaNetⓘ	no	76.30	no
125439	gram_stain	BacteriaNetⓘ	positive	78.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	83.40	no

Predictions from Diaspora project based on:
Tumebacillus permanentifrigoris strain DSM 18773
PATRIC: 378543.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	66.73	yes
125438	anaerobic	anaerobicⓘ	no	86.19	yes
125438	spore-forming	spore-formingⓘ	yes	92.13	yes
125438	aerobic	aerobicⓘ	yes	72.46	yes
125438	thermophilic	thermophileⓘ	no	80.93	yes
125438	flagellated	motile2+ⓘ	yes	75.26	no

External links

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

Straininfo Link

@ref	Straininfo	Culture collections
71198	407982	DSM 18773

Culture collection no.

Culture collection no.
DSM 18773
JCM 14557
Eur1 9.5
CGMCC 1.10982

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 .
#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 )
#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 .

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