Name: Paenibacillus rigui WPCB173
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133620

Type strain:

Species: Paenibacillus rigui

Strain Designation: WPCB173

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

Strain history: <- CN Seong, Sunchon Natl. Univ.

NCBI tax ID(s): 554312 (species)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus rigui**
	Full Scientific Name (LPSN)	Paenibacillus rigui Baik et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29804]	Gram stain	variable
[Ref.: #67771]	Gram stain	variable
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29804]	Cell length	3.5 µm

[Ref.: #29804]	Cell width	0.5 µm

[Ref.: #29804]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29804]	Motility	yes
[Ref.: #67771]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.355

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #29804]	growth	15-37 °C
[Ref.: #29804]	optimum	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #29804]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29804]			optimum	06-07
[Ref.: #29804]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29804]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #67771]	Type of spore	endospore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #29804]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29804]		NaCl		growth	<1	%

[Ref.: #29804]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29804]	acetate ChEBI	+	carbon source
[Ref.: #29804]	arabinose ChEBI	+	carbon source
[Ref.: #29804]	esculin ChEBI	+	hydrolysis
[Ref.: #29804]	glucose ChEBI	+	carbon source
[Ref.: #29804]	glycogen ChEBI	+	carbon source
[Ref.: #29804]	maltose ChEBI	+	carbon source
[Ref.: #29804]	mannitol ChEBI	+	carbon source
[Ref.: #29804]	melibiose ChEBI	+	carbon source
[Ref.: #29804]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #29804]	nitrate ChEBI	+	reduction
[Ref.: #29804]	pyruvate ChEBI	+	carbon source
[Ref.: #29804]	raffinose ChEBI	+	carbon source
[Ref.: #29804]	ribose ChEBI	+	carbon source
[Ref.: #29804]	succinate ChEBI	+	carbon source
[Ref.: #29804]	sucrose ChEBI	+	carbon source
[Ref.: #29804]	trehalose ChEBI	+	carbon source
[Ref.: #29804]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29804]		catalase	+	1.11.1.6
[Ref.: #29804]		cytochrome oxidase	+	1.9.3.1

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #29804]	Sample type/isolated from	freshwater (river, lake, pond)

[Ref.: #67770]	Sample type/isolated from	Freshwater collected from the Woopo wetland
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From freshwater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Woopo wetland
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29804]	Paenibacillus rigui strain WPCB173 16S ribosomal RNA gene, partial sequence	EU939688	1453	GenBank	554312 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paenibacillus rigui JCM 16352	GCA_002234615	contig	GenBank	554312 tax ID
[Ref.: #66792]	Paenibacillus rigui strain JCM 16352	554312.4	wgs	PATRIC	554312 tax ID	*
[Ref.: #66792]	Paenibacillus rigui JCM 16352	2916390109	draft	JGI IMG/M	554312 tax ID	*

[Ref.: #29804]	GC-content	48.3 mol%
[Ref.: #67770]	GC-content	48.3 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paenibacillus rigui strain JCM 16352 PATRIC: 554312.4
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus rigui strain JCM 16352 PATRIC: 554312.4
[Ref.: #69480]	gram-positive	yes	58.392	yes
[Ref.: #69480]	anaerobic	no	98.433	yes
[Ref.: #69480]	halophile	no	96.889	yes
[Ref.: #69480]	spore-forming	yes	92.77	yes
[Ref.: #69480]	glucose-util	yes	91.394	no
[Ref.: #69480]	thermophile	no	99.552	no
[Ref.: #69480]	aerobic	yes	85.807	yes
[Ref.: #69480]	motile	yes	90.194	yes
[Ref.: #69480]	flagellated	yes	83.707	no
[Ref.: #69480]	glucose-ferment	no	90.464	no

Availability in culture collections External links

[Ref.: #29804]

Culture collection no.

KCTC 13282, JCM 16352, LMG 31321, DSM 25278

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#26181

IJSEM 529 2011 ( DOI 10.1099/ijs.0.021485-0 , PubMed 20382792 )

* These data were automatically processed and therefore are not curated

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Paenibacillus rigui strain JCM 16352

Paenibacillus rigui strain JCM 16352

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