Paenibacillus rigui (KCTC 13282, JCM 16352, WPCB173)

Name: Paenibacillus rigui (KCTC 13282, JCM 16352, WPCB173)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133620

Type strain

Strain Designation WPCB173

Culture col. no. KCTC 13282 JCM 16352 WPCB173 LMG 31321 DSM 25278

NCBI tax ID(s) 554312

Special Collections DSMZ JCM KCTC Literature strains

History C. N. Seong WPCB173. <- CN Seong, Sunchon Natl. Univ.

Links

Paenibacillus rigui WPCB173 is an aerobe, spore-forming, Gram-variable bacterium that was isolated from freshwater .

spore-forming Gram-variable motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 273129

LMG 31321,KCTC 13282,JCM 16352

@ref 20215

Last LPSN update 2026-02-09 11:31:59

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus rigui

Full scientific name Paenibacillus rigui Baik et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29804	variable	3.5 µm	0.5 µm	rod-shaped
67771				rod-shaped
67771	variable
125439					92

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29804	positive	growth	15-37
29804	positive	optimum	30
67770	positive	growth	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
29804	positive	optimum	06-07
29804	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29804	aerobe
67771	aerobe

Spore formation

@ref	Type of spore	Confidence
29804
67771	endospore
125438		92.755
125439		95.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29804	NaCl	positive	growth	<1 %

Observation

@ref	Observation
29804	aggregates in chains
67770	quinones: MK-7
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29804	30089 ChEBI	acetate	+	carbon source
29804	22599 ChEBI	arabinose	+	carbon source
29804	4853 ChEBI	esculin	+	hydrolysis
29804	17234 ChEBI	glucose	+	carbon source
29804	28087 ChEBI	glycogen	+	carbon source
29804	17306 ChEBI	maltose	+	carbon source
29804	29864 ChEBI	mannitol	+	carbon source
29804	28053 ChEBI	melibiose	+	carbon source
29804	51850 ChEBI	methyl pyruvate	+	carbon source
29804	17632 ChEBI	nitrate	+	reduction
29804	15361 ChEBI	pyruvate	+	carbon source
29804	16634 ChEBI	raffinose	+	carbon source
29804	33942 ChEBI	ribose	+	carbon source
29804	30031 ChEBI	succinate	+	carbon source
29804	17992 ChEBI	sucrose	+	carbon source
29804	27082 ChEBI	trehalose	+	carbon source
29804	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29804	catalase	+	1.11.1.6
29804	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	vitamin B1 metabolism	100	13 of 13
66794	ribulose monophosphate pathway	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	pentose phosphate pathway	100	11 of 11
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	NAD metabolism	100	18 of 18
66794	adipate degradation	100	2 of 2
66794	photosynthesis	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	methionine metabolism	84.62	22 of 26
66794	pyrimidine metabolism	84.44	38 of 45
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	vitamin B12 metabolism	82.35	28 of 34
66794	degradation of sugar alcohols	81.25	13 of 16
66794	factor 420 biosynthesis	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	degradation of sugar acids	80	20 of 25
66794	alanine metabolism	79.31	23 of 29
66794	degradation of pentoses	78.57	22 of 28
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	allantoin degradation	77.78	7 of 9
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	arginine metabolism	66.67	16 of 24
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	phenol degradation	65	13 of 20
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	tryptophan metabolism	60.53	23 of 38
66794	myo-inositol biosynthesis	60	6 of 10
66794	coenzyme M biosynthesis	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	citric acid cycle	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	lipid A biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	lipid metabolism	54.84	17 of 31
66794	vitamin B6 metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	lysine metabolism	47.62	20 of 42
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	chlorophyll metabolism	38.89	7 of 18
66794	carotenoid biosynthesis	36.36	8 of 22
66794	tyrosine metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
29804	freshwater (river, lake, pond)
67770	Freshwater collected from the Woopo wetland		Republic of Korea	KOR	Asia
67771	From freshwater	Woopo wetland	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU939688 (>99% sequence identity) for Paenibacillus rigui subclade from Microbeatlas

Aquatic Samples
Soil Samples	3
Animal Samples
Plant Samples	25
Total Samples	28

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM223461v1 assembly for Paenibacillus rigui JCM 16352	contig	GCA_002234615	554312.4	2916390109	554312	57.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29804	Paenibacillus rigui strain WPCB173 16S ribosomal RNA gene, partial sequence	EU939688	1453		554312

GC content

@ref	GC-content (mol%)	Method
29804	48.3
67770	48.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus rigui JCM 16352
NCBI: GCA_002234615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.40	no
125439	motility	BacteriaNetⓘ	yes	92.00	no
125439	gram_stain	BacteriaNetⓘ	variable	87.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus rigui strain JCM 16352
PATRIC: 554312.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	53.53	yes
125438	anaerobic	anaerobicⓘ	no	89.42	yes
125438	spore-forming	spore-formingⓘ	yes	92.76	yes
125438	thermophilic	thermophileⓘ	no	90.60	no
125438	aerobic	aerobicⓘ	yes	63.07	no
125438	flagellated	motile2+ⓘ	yes	79.91	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic and Metabolic Characterization of a Potentially Novel Paenibacillus Species Isolated as a Laboratory Contaminant Growing on Medium Supporting Cotton Tissue Culture.	Topcu I, Parunandi SS, Gregory TA, Campbell LM, Rathore K, Antony-Babu S.	Microbiologyopen	10.1002/mbo3.70107	2025
	Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils.	Kim J, Chhetri G, Kim I, So Y, Seo T.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005640	2022
Phylogeny	Paenibacillus xerothermodurans sp. nov., an extremely dry heat resistant spore forming bacterium isolated from the soil of Cape Canaveral, Florida.	Kaur N, Seuylemezian A, Patil PP, Patil P, Krishnamurti S, Varelas J, Smith DJ, Mayilraj S, Vaishampayan P	Int J Syst Evol Microbiol	10.1099/ijsem.0.002967	2018
Phylogeny	Paenibacillus rigui sp. nov., isolated from a freshwater wetland.	Baik KS, Lim CH, Choe HN, Kim EM, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.021485-0	2010
Phylogeny	Paenibacillus piri sp. nov., isolated from urban soil.	Trinh NH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003811	2020
Phylogeny	Paenibacillus yunnanensis sp. nov., isolated from Pu'er tea.	Niu L, Tang T, Ma Z, Song L, Zhang K, Chen Y, Hua Z, Hu X, Zhao M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000496	2015

References

#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 )
#26181	IJSEM 529 2011 ( DOI 10.1099/ijs.0.021485-0 , PubMed 20382792 )
#29804	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 #26181
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 rigui (KCTC 13282, JCM 16352, WPCB173)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002234615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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