Name: Paenibacillus cellulosilyticus DSM 21372
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11619

Type strain:

Species: Paenibacillus cellulosilyticus

Culture col. no.: DSM 21372, CECT 5696, LMG 22232, PALXIL 08, CIP 109523

Strain history: CIP <- 2007, CECT <- 2004, R. Rivas, Univ. de Salamance, Spain: strain PALXIL08

NCBI tax ID(s): 375489 (species)

SI-ID 129432

LMG 22232, CECT 5696, CIP 109523, DSM 21372

Special Collections

DSMZ
CIP

Section

When using BacDive for research please cite our paper

Paenibacillus cellulosilyticus DSM 21372 is a mesophilic, Gram-negative, motile bacterium that was isolated from bract phyllosphere of Phoenix dactylifera.

Gram-negative
motile
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus cellulosilyticus**
	Full Scientific Name (LPSN)	Paenibacillus cellulosilyticus Rivas et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #117242]	Gram stain	negative

[Ref.: #117242]	Cell shape	rod-shaped

[Ref.: #117242]	Motility	yes
[Ref.: #125439]	Motility	yes Confidence in %92

Information on culture and growth conditions Culture and growth conditions

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Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #37753]

Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

CIP Medium 13

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

[Ref.: #117242]

Culture medium

CIP Medium 72

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Culture medium growth

[Ref.: #117242]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #15654]			growth	30 °C
[Ref.: #37753]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %94.5

[Ref.: #125438]

Ability of spore formation

yes Confidence in %91.053

	Enzymes	Enzyme	Enzyme activity
[Ref.: #117242]		oxidase	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
		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.: #15654]	Sample type/isolated from	bract phyllosphere of Phoenix dactylifera
[Ref.: #15654]	Host species	Phoenix dactylifera
[Ref.: #15654]	Country	Spain
[Ref.: #15654]	Country ISO 3 Code	ESP
[Ref.: #15654]	Continent	Europe

[Ref.: #117242]	Sample type/isolated from	Environment, Bract phyllosphere, Phoenix dactylifera
[Ref.: #117242]	Geographic location (country and/or sea, region)	Palma de Mallorca
[Ref.: #117242]	Country	Spain
[Ref.: #117242]	Country ISO 3 Code	ESP
[Ref.: #117242]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ407282 (>99% sequence identity) for Paenibacillus cellulosilyticus from Microbeatlas

Aquatic Samples	1
Soil Samples	20
Animal Samples	3
Plant Samples
Total Samples	24

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15654]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #117242]	Biosafety level	1	Risk group (French classification)

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.: #15654]	Paenibacillus cellulosilyticus strain PALXIL08 16S ribosomal RNA gene, partial sequence	DQ407282	1546	GenBank ENA	375489 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus cellulosilyticus CECT 5696	GCA_003182255	scaffold	GenBank ENA	375489 tax ID	*
[Ref.: #66792]	Paenibacillus cellulosilyticus strain CECT 5696	375489.3	wgs	PATRIC	375489 tax ID	*
[Ref.: #66792]	Paenibacillus cellulosilyticus CECT 5696	2770939575	draft	JGI IMG/M	375489 tax ID	*

[Ref.: #15654]

GC-content

51 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus cellulosilyticus CECT 5696 NCBI: GCA_003182255.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	62.582	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.546	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	68.655	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	91.053	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.687	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	83.423	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus cellulosilyticus CECT 5696 NCBI: GCA_003182255
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	89.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	92
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	84.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	94.5

Availability in culture collections External links

[Ref.: #15654]

Culture collection no.

DSM 21372, CECT 5696, LMG 22232, PALXIL 08, CIP 109523

[Ref.: #80845]

SI-ID 129432

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester.	Tachaapaikoon C, Tanasupawat S, Pason P, Sornyotha S, Waeonukul R, Kyu KL, Ratanakhanokchai K	J Microbiol	10.1007/s12275-012-1480-3	2012	*
Phylogeny	Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera.	Rivas R, Garcia-Fraile P, Mateos PF, Martinez-Molina E, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.64480-0	2006	*

References

#15654

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21372

#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 )

#37753 ; Curators of the CIP;

#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 .

#80845

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID129432.1 )

#117242 Collection of Institut Pasteur ; Curators of the CIP; CIP 109523

#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 .

* These data were automatically processed and therefore are not curated

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Paenibacillus cellulosilyticus CECT 5696

Paenibacillus cellulosilyticus CECT 5696

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