"Paenibacillus beijingensis" (DSM 24997, ACCC 03082, 7188)

BacDive ID 11662

Type strain

Strain Designation 7188

Culture col. no. DSM 24997 ACCC 03082 7188

NCBI tax ID(s) 1126833

Special Collections DSMZ

History <- M. Gao, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; strain 7188

Links

"Paenibacillus beijingensis" 7188 is a mesophilic prokaryote that was isolated from rhizospere soil of jujube.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402339

DSM 24997

@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 beijingensis"

Full scientific name Paenibacillus beijingensis Gao et al. 2012

Morphology

Cell morphology

@ref	Motility	Confidence
125439		91

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17816	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
17816	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	90

Spore formation

@ref	Spore formation	Confidence
125439		95.7
125438		92.204

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	cardiolipin biosynthesis	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	taurine degradation	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ribulose monophosphate pathway	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	Entner Doudoroff pathway	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	serine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	degradation of sugar alcohols	87.5	14 of 16
66794	isoleucine metabolism	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	methionine metabolism	84.62	22 of 26
66794	NAD metabolism	83.33	15 of 18
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	d-xylose degradation	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	oxidative phosphorylation	70.33	64 of 91
66794	coenzyme M biosynthesis	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	formaldehyde oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	tryptophan metabolism	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of pentoses	60.71	17 of 28
66794	3-chlorocatechol degradation	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	ascorbate metabolism	59.09	13 of 22
66794	propanol degradation	57.14	4 of 7
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	degradation of hexoses	55.56	10 of 18
66794	phenol degradation	55	11 of 20
66794	metabolism of disaccharids	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	chlorophyll metabolism	50	9 of 18
66794	propionate fermentation	50	5 of 10
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	degradation of sugar acids	36	9 of 25
66794	tyrosine metabolism	35.71	5 of 14
66794	methane metabolism	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

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	Geographic location	Country	Country ISO 3 Code	Continent
17816	rhizospere soil of jujube	Wangsiying, Beijing	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JN408292 (>99% sequence identity) for Paenibacillus beijingensis subclade from Microbeatlas

Aquatic Samples	246
Soil Samples	2103
Animal Samples	787
Plant Samples	280
Total Samples	3416

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM96109v1 assembly for Paenibacillus beijingensis DSM 24997	complete	GCA_000961095	1126833.4	2627854173	1126833	98.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17816	Paenibacillus beijingensis strain 7188 16S ribosomal RNA gene, partial sequence	JN408292	1515		1126833

GC content

17816

GC-content (mol%)60.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus beijingensis DSM 24997
NCBI: GCA_000961095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.00	no
125439	gram_stain	BacteriaNetⓘ	variable	83.80	no
125439	motility	BacteriaNetⓘ	yes	91.00	no
125439	spore_formation	BacteriaNetⓘ	yes	95.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus beijingensis DSM 24997
NCBI: GCA_000961095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.70	no
125438	anaerobic	anaerobicⓘ	no	91.34	no
125438	aerobic	aerobicⓘ	yes	63.79	no
125438	spore-forming	spore-formingⓘ	yes	92.20	no
125438	thermophilic	thermophileⓘ	no	95.46	yes
125438	flagellated	motile2+ⓘ	yes	80.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Unprecedented Diversity of the Glycoside Hydrolase Family 70: A Comprehensive Analysis of Sequence, Structure, and Function.	Pijning T, Dijkhuizen L.	J Agric Food Chem	10.1021/acs.jafc.4c04807	2024
Metabolism	Mining novel starch-converting Glycoside Hydrolase 70 enzymes from the Nestlé Culture Collection genome database: The Lactobacillus reuteri NCC 2613 GtfB.	Gangoiti J, van Leeuwen SS, Meng X, Duboux S, Vafiadi C, Pijning T, Dijkhuizen L.	Sci Rep	10.1038/s41598-017-07190-z	2017
Enzymology	Characterization of the Paenibacillus beijingensis DSM 24997 GtfD and its glucan polymer products representing a new glycoside hydrolase 70 subfamily of 4,6-alpha-glucanotransferase enzymes.	Gangoiti J, Lamothe L, van Leeuwen SS, Vafiadi C, Dijkhuizen L	PLoS One	10.1371/journal.pone.0172622	2017
Genetics	Complete genome sequence of Paenibacillus beijingensis 7188(T) (=DSM 24997(T)), a novel rhizobacterium from jujube garden soil.	Kwak Y, Shin JH	J Biotechnol	10.1016/j.jbiotec.2015.04.015	2015
Phylogeny	Paenibacillus beijingensis sp. nov., a novel nitrogen-fixing species isolated from jujube garden soil.	Gao M, Xie LQ, Wang YX, Chen J, Xu J, Zhang XX, Sui XH, Gao JL, Sun JG	Antonie Van Leeuwenhoek	10.1007/s10482-012-9767-2	2012

References

#17816	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24997
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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 beijingensis" (DSM 24997, ACCC 03082, 7188)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000961095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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