Paenibacillus xylanexedens (DSM 21292, CIP 110619, NRRL B-51090)

Name: Paenibacillus xylanexedens (DSM 21292, CIP 110619, NRRL B-51090)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11641

Type strain

Strain Designation B22a

Culture col. no. DSM 21292 CIP 110619 NRRL B-51090 B22a

NCBI tax ID(s) 528191

Special Collections DSMZ CIP Literature strains

History DSMZ <- D.M. Nelson, Institute for Genomic Biology, University of Illinois, Urbana; B22a CIP <- 2013, DSMZ <- D.M Nelson, Illinois Univ., Urbana, USA: strain B22a

Links

Paenibacillus xylanexedens B22a is a spore-forming, motile, rod-shaped bacterium that was isolated from soil from moist non-acidic tundra.

spore-forming motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396909

DSM 21292,CIP 110619

@ref 20215

Last LPSN update 2026-05-29 08:27:36

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus xylanexedens

Full scientific name Paenibacillus xylanexedens Nelson et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
29038		rod-shaped
123992	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15606	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
123992	CIP Medium 372		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15606	positive	growth	30
29038	positive	growth	13-32
29038	positive	optimum	23

Culture pH

@ref	Ability	Type	PH	PH range
29038	positive	optimum	6
29038	positive	growth	5.7-8.8	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	95.305

Spore formation

@ref	Spore formation	Confidence
29038
125438		91.551
125439		95.125

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29038	23652 ChEBI	dextrin	+	carbon source
29038	28757 ChEBI	fructose	+	carbon source
29038	28260 ChEBI	galactose	+	carbon source
29038	17234 ChEBI	glucose	+	carbon source
29038	28087 ChEBI	glycogen	+	carbon source
29038	17596 ChEBI	inosine	+	carbon source
29038	17716 ChEBI	lactose	+	carbon source
29038	17306 ChEBI	maltose	+	carbon source
29038	29864 ChEBI	mannitol	+	carbon source
29038	37684 ChEBI	mannose	+	carbon source
29038	28053 ChEBI	melibiose	+	carbon source
29038	37657 ChEBI	methyl D-glucoside	+	carbon source
29038	51850 ChEBI	methyl pyruvate	+	carbon source
29038	17632 ChEBI	nitrate	+	reduction
29038	15361 ChEBI	pyruvate	+	carbon source
29038	16634 ChEBI	raffinose	+	carbon source
29038	17814 ChEBI	salicin	+	carbon source
29038	17992 ChEBI	sucrose	+	carbon source
29038	27082 ChEBI	trehalose	+	carbon source
29038	16704 ChEBI	uridine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29038	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Climate	#Cold	#Tundra

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
15606	soil from moist non-acidic tundra	northern Alaska, Arctic Foothills (69°15'58'' N; 148°22'40'' W)	USA	USA	North America	69.2661	-148.378 69.2661/-148.378
123992	Environment, Soil from moist non-acidic tundra	Northern Alaska, Artic Foothills	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence EU558281 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	297
Soil Samples	2237
Animal Samples	665
Plant Samples	1871
Total Samples	5070

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15606	1	Risk group (German classification) According to TRBA 466
123992	1	Risk group (French 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	ASM1787461v1 assembly for Paenibacillus xylanexedens DSM 21292	contig	GCA_017874615	528191.20	2913387726	528191	68.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15606	Paenibacillus xylanexedens strain B22a 16S ribosomal RNA gene, partial sequence	EU558281	1514		528191

GC content

@ref	GC-content (mol%)	Method
15606	46.4	thermal denaturation, midpoint method (Tm)
29038	46.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1787461v1 assembly for Paenibacillus xylanexedens DSM 21292
NCBI: GCA_017874615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.31	no
125439	motility	BacteriaNetⓘ	yes	89.79	no
125439	gram_stain	BacteriaNetⓘ	variable	70.06	no
125439	spore_formation	BacteriaNetⓘ	yes	95.13	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus xylanexedens strain DSM 21292
PATRIC: 528191.20

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.43	no
125438	anaerobic	anaerobicⓘ	no	92.47	no
125438	spore-forming	spore-formingⓘ	yes	91.55	yes
125438	aerobic	aerobicⓘ	no	52.83	no
125438	thermophilic	thermophileⓘ	no	92.95	yes
125438	flagellated	motile2+ⓘ	yes	86.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus seodonensis sp. nov., isolated from a plant of the genus Campanula.	Kang MS, Lee KE, Lee EY, Park SJ	J Microbiol	10.1007/s12275-018-8455-y	2018
Phylogeny	Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra.	Nelson DM, Glawe AJ, Labeda DP, Cann IK, Mackie RI	Int J Syst Evol Microbiol	10.1099/ijs.0.004572-0	2009

References

#15606	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21292
#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 )
#25468	IJSEM 1708 2009 ( DOI 10.1099/ijs.0.004572-0 , PubMed 19542122 )
#29038	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 #25468
#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) .
#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 .
#123992	Collection of Institut Pasteur ; Curators of the CIP; CIP 110619
#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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Paenibacillus xylanexedens (DSM 21292, CIP 110619, NRRL B-51090)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017874615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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