Paenibacillus sophorae (DSM 23020, CGMCC 1.10238, CIP 110614)

Name: Paenibacillus sophorae (DSM 23020, CGMCC 1.10238, CIP 110614)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11656

Type strain

Strain Designation S27

Culture col. no. DSM 23020 CGMCC 1.10238 CIP 110614 S27

NCBI tax ID(s) 1333845

Special Collections DSMZ CIP Literature strains

History <- H. Jin, Center Life Sci. Res., China Agricultural Univ., Beijing, China; S27 CIP <- 2013, DSMZ, H. Jin, China Agricultural Univ., Beijing, China: strain S27

Links

Paenibacillus sophorae S27 is a facultative anaerobe, spore-forming, mesophilic prokaryote that was isolated from rhizosphere soil of Sophora japonica.

spore-forming Gram-positive motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400868

DSM 23020,CIP 110614

@ref 20215

Last LPSN update 2026-02-09 11:20:37

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus sophorae

Full scientific name Paenibacillus sophorae Jin et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29814	positive	2.25 µm	0.45 µm	rod-shaped
122680	positive			rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16652	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
122680	CIP Medium 372		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16652	positive	growth	30	mesophilic
29814	positive	growth	15-50
29814	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29814	positive	optimum	6
29814	positive	growth	4.0-8.0	acidophile

Physiology and metabolism

Oxygen tolerance

29814

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
29814
125438		91.468
125439		92.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29814	NaCl	positive	growth	0.0-3.0 %
29814	NaCl	positive	optimum	1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29814	17057 ChEBI	cellobiose	+	carbon source
29814	16947 ChEBI	citrate	+	carbon source
29814	28260 ChEBI	galactose	+	carbon source
29814	17234 ChEBI	glucose	+	carbon source
29814	28087 ChEBI	glycogen	+	carbon source
29814	17716 ChEBI	lactose	+	carbon source
29814	17306 ChEBI	maltose	+	carbon source
29814	29864 ChEBI	mannitol	+	carbon source
29814	37684 ChEBI	mannose	+	carbon source
29814	506227 ChEBI	N-acetylglucosamine	+	carbon source
29814	17632 ChEBI	nitrate	+	reduction
29814	30911 ChEBI	sorbitol	+	carbon source
29814	27082 ChEBI	trehalose	+	carbon source
29814	18222 ChEBI	xylose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16652	rhizosphere soil of Sophora japonica	Sophora japonica	Beijing	China	CHN	Asia
122680	Environment, Rhizosphere soil of Sophora japonica		Beijing	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16652	1	Risk group (German classification) According to TRBA 466
122680	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	ASM1896652v1 assembly for Paenibacillus sophorae DSM 23020	complete	GCA_018966525	1333845.6	8110823445	1333845	96.45
66792	IMG-taxon 2617270876 annotated assembly for Paenibacillus sophorae CGMCC 1.10238	contig	GCA_900110315	1333845.3	2617270876	1333845	69.5
66792	s4 assembly for Paenibacillus sophorae S27	contig	GCA_000520675	682957.3	2579778832	682957

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16652	Paenibacillus sophorae strain S27 16S ribosomal RNA gene, partial sequence	GQ985395	1463		682957

GC content

@ref	GC-content (mol%)	Method
16652	46.0	thermal denaturation, midpoint method (Tm)
29814	46

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus sophorae DSM 23020
NCBI: GCA_018966525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	92.70	no
125439	motility	BacteriaNetⓘ	yes	88.50	no
125439	gram_stain	BacteriaNetⓘ	variable	83.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	79.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus sophorae DSM 23020
NCBI: GCA_018966525.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	68.38	no
125438	anaerobic	anaerobicⓘ	no	83.69	no
125438	aerobic	aerobicⓘ	no	67.22	yes
125438	spore-forming	spore-formingⓘ	yes	91.47	yes
125438	thermophilic	thermophileⓘ	no	93.77	no
125438	flagellated	motile2+ⓘ	yes	82.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus taohuashanense sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of the root of Caragana kansuensis Pojark.	Xie JB, Zhang LH, Zhou YG, Liu HC, Chen SF	Antonie Van Leeuwenhoek	10.1007/s10482-012-9773-4	2012
Phylogeny	Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica.	Jin HJ, Lv J, Chen SF	Int J Syst Evol Microbiol	10.1099/ijs.0.021709-0	2010

References

#16652	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23020
#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 )
#26191	IJSEM 767 2011 ( DOI 10.1099/ijs.0.021709-0 , PubMed 20435753 )
#29814	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 #26191
#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) .
#122680	Collection of Institut Pasteur ; Curators of the CIP; CIP 110614
#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 sophorae (DSM 23020, CGMCC 1.10238, CIP 110614)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_018966525

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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