Paenibacillus contaminans (BCRC 17728, LMG 24216, CKOBP-6)

Name: Paenibacillus contaminans (BCRC 17728, LMG 24216, CKOBP-6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133429

Type strain

Strain Designation CKOBP-6

Culture col. no. BCRC 17728 LMG 24216 CKOBP-6

NCBI tax ID(s) 450362

Special Collections Literature strains

Links

Paenibacillus contaminans CKOBP-6 is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from contaminated lab plate.

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

Name and taxonomic classification

SI-ID 309045

LMG 24216,BCRC 17728,KCTC 13623

@ref 20215

Last LPSN update 2026-02-09 11:31:57

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus contaminans

Full scientific name Paenibacillus contaminans Chou et al. 2009

BacDive ID	Other strains from **Paenibacillus contaminans** (1)	Type strain
156809	P. contaminans CCUG 65521

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
28915	variable	2.5 µm	0.9 µm	rod-shaped
125439						93.3

Pigmentation

28915

Productionno

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
28915	positive	growth	10-37
28915	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
28915	positive	optimum	7
28915	positive	growth	6.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28915	facultative anaerobe
125439	aerobe	91.7

Spore formation

@ref	Spore formation	Confidence
28915
125439		95.4
125438		92.436

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28915	NaCl	positive	growth	0-2 %
28915	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28915	22599 ChEBI	arabinose	+	carbon source
28915	17057 ChEBI	cellobiose	+	carbon source
28915	16947 ChEBI	citrate	+	carbon source
28915	4853 ChEBI	esculin	+	hydrolysis
28915	17234 ChEBI	glucose	+	carbon source
28915	17754 ChEBI	glycerol	+	carbon source
28915	17306 ChEBI	maltose	+	carbon source
28915	28053 ChEBI	melibiose	+	carbon source
28915	506227 ChEBI	N-acetylglucosamine	+	carbon source
28915	26546 ChEBI	rhamnose	+	carbon source
28915	17992 ChEBI	sucrose	+	carbon source
28915	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28915	catalase	+	1.11.1.6
28915	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	ketogluconate metabolism	100	8 of 8
66794	lipoate biosynthesis	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	propanol degradation	100	7 of 7
66794	cellulose degradation	100	5 of 5
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	methionine metabolism	84.62	22 of 26
66794	vitamin B1 metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	pyrimidine metabolism	82.22	37 of 45
66794	proline metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	propionate fermentation	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	degradation of pentoses	75	21 of 28
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	citric acid cycle	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	coenzyme M biosynthesis	70	7 of 10
66794	polyamine pathway	69.57	16 of 23
66794	oxidative phosphorylation	68.13	62 of 91
66794	degradation of sugar acids	68	17 of 25
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	lysine metabolism	61.9	26 of 42
66794	cysteine metabolism	61.11	11 of 18
66794	glycine betaine biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	histidine metabolism	55.17	16 of 29
66794	vitamin B6 metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	leucine metabolism	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ribulose monophosphate pathway	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	phenol degradation	50	10 of 20
66794	butanoate fermentation	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	cholesterol biosynthesis	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	vitamin B12 metabolism	41.18	14 of 34
66794	glycogen metabolism	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Laboratory	#Lab enrichment

Isolation

28915

Sample typecontaminated lab plate

Taxonmaps

69479

Global distribution of 16S sequence EF626690 (>99% sequence identity) for Paenibacillus contaminans subclade from Microbeatlas

Aquatic Samples	816
Soil Samples	6458
Animal Samples	723
Plant Samples	765
Total Samples	8762

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM328501v1 assembly for Paenibacillus contaminans CKOBP-6	scaffold	GCA_003285015	450362.3	2961978095	450362	54.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
28915	Paenibacillus contaminans strain CKOBP-6 16S ribosomal RNA gene, partial sequence	EF626690	1472		450362

GC content

28915

GC-content (mol%)51.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus contaminans CKOBP-6
NCBI: GCA_003285015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.40	no
125439	motility	BacteriaNetⓘ	yes	93.30	no
125439	gram_stain	BacteriaNetⓘ	variable	89.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus contaminans CKOBP-6
NCBI: GCA_003285015.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	53.14	yes
125438	anaerobic	anaerobicⓘ	no	94.19	yes
125438	aerobic	aerobicⓘ	yes	66.87	yes
125438	spore-forming	spore-formingⓘ	yes	92.44	no
125438	thermophilic	thermophileⓘ	no	92.99	yes
125438	flagellated	motile2+ⓘ	yes	81.22	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus doosanensis sp. nov., isolated from soil.	Kim JH, Kang H, Kim W	Int J Syst Evol Microbiol	10.1099/ijs.0.050716-0	2014
Phylogeny	Paenibacillus contaminans sp. nov., isolated from a contaminated laboratory plate.	Chou JH, Lee JH, Lin MC, Chang PS, Arun AB, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.001495-0	2009
Phylogeny	Paenibacillus cymbidii sp. nov., isolated from Cymbidium goeringii roots.	Sun L, Wang P, Zhao D, Wang J, Wu Q, Liu L, Lyu Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004731	2021
Phylogeny	Paenibacillus arcticus sp. nov., isolated from Arctic soil.	Cha IT, Cho ES, Yoo Y, Seok YJ, Park I, Lim HS, Park JM, Roh SW, Nam YD, Choi HJ, Lee YK, Seo MJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002299	2017
Phylogeny	Paenibacillus cavernae sp. nov., isolated from soil of a natural cave.	Dong Lee S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000762	2015
Phylogeny	Paenibacillus cucumis sp. nov. isolated from greenhouse soil.	Ahn JH, Kim BC, Kim BY, Kim SJ, Song J, Kwon SW, Weon HY	J Microbiol	10.1007/s12275-014-4071-7	2014

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 )
#25354	IJSEM 125 2009 ( DOI 10.1099/ijs.0.001495-0 , PubMed 19126735 )
#28915	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 #25354
#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 contaminans (BCRC 17728, LMG 24216, CKOBP-6)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

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_003285015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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