Name: Paenibacillus cisolokensis LC2-13A
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132589

Type strain:

Species: Paenibacillus cisolokensis

Strain Designation: LC2-13A

Culture col. no.: DSM 101873, NRRL B-65368, UICC B-42

Strain history: <- W. Sjamsuridzal, Universitas Indonesia, Kampus UI Depok, LC2-13A

NCBI tax ID(s): 1658519 (species)

SI-ID 397607

DSM 101873

Section

Paenibacillus cisolokensis LC2-13A is an aerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from litter of geyser.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
aerobe
thermophilic
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 cisolokensis**
	Full Scientific Name (LPSN)	Paenibacillus cisolokensis Yokota et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43088]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43088]	Cell length	0.8-09 µm

[Ref.: #43088]	Cell width	2.0-2.4 µm

[Ref.: #43088]	Cell shape	rod-shaped

[Ref.: #43088]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.409

[Ref.: #43088]	Flagellum arrangement	peritrichous

[Ref.: #43088]	Colony size	2-3 mm
[Ref.: #43088]	Colony color	white
[Ref.: #43088]	Colony shape	circular
[Ref.: #43088]	Incubation period	3 days
[Ref.: #43088]	Cultivation medium used	ISP1 medium

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP1 medium

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Culture medium growth

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Culture medium

ISP2 medium

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

TSB

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #24378]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #24378]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24378]	growth	45 °C
[Ref.: #43088]	optimum	45-50 °C
[Ref.: #43088]	growth	37-55 °C

[Ref.: #24378]	Temperature range	thermophilic
[Ref.: #43088]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #43088]			optimum	6.0-7.0
[Ref.: #43088]			growth	5.7-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43088]

Oxygen tolerance

aerobe

[Ref.: #43088]	Type of spore	endospore
[Ref.: #43088]	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.: #43088]		NaCl		growth	0-2.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43088]	(R)-amygdalin ChEBI	+	assimilation
[Ref.: #43088]	2-oxogluconate	-	builds acid from
[Ref.: #43088]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #43088]	adipate ChEBI	-	assimilation
[Ref.: #43088]	amygdalin ChEBI	+	builds acid from
[Ref.: #43088]	arbutin ChEBI	-	builds acid from
[Ref.: #43088]	cellobiose ChEBI	+	builds acid from
[Ref.: #43088]	cellulose ChEBI	+	hydrolysis
[Ref.: #43088]	chitin ChEBI	+	hydrolysis
[Ref.: #43088]	citrate ChEBI	-	assimilation
[Ref.: #43088]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43088]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43088]	D-fructose ChEBI	+	builds acid from
[Ref.: #43088]	D-fucose ChEBI	-	builds acid from
[Ref.: #43088]	D-galactose ChEBI	-	builds acid from
[Ref.: #43088]	D-glucose ChEBI	+	builds acid from
[Ref.: #43088]	D-glucose ChEBI	-	assimilation
[Ref.: #43088]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43088]	D-mannitol ChEBI	-	assimilation
[Ref.: #43088]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43088]	D-mannose ChEBI	-	assimilation
[Ref.: #43088]	D-mannose ChEBI	-	builds acid from
[Ref.: #43088]	D-sorbitol ChEBI	+	assimilation
[Ref.: #43088]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43088]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43088]	D-xylose ChEBI	+	builds acid from
[Ref.: #43088]	decanoate ChEBI	-	assimilation
[Ref.: #43088]	erythritol ChEBI	-	builds acid from
[Ref.: #43088]	esculin ChEBI	+	hydrolysis
[Ref.: #43088]	esculin ferric citrate	+	builds acid from
[Ref.: #43088]	galactitol ChEBI	-	builds acid from
[Ref.: #43088]	gelatin ChEBI	+	hydrolysis
[Ref.: #43088]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43088]	gluconate ChEBI	-	builds acid from
[Ref.: #43088]	glucose ChEBI	+	builds acid from
[Ref.: #43088]	glycerol ChEBI	-	builds acid from
[Ref.: #43088]	glycogen ChEBI	-	builds acid from
[Ref.: #43088]	inulin ChEBI	-	builds acid from
[Ref.: #43088]	L-arabinose ChEBI	+	assimilation
[Ref.: #43088]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43088]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43088]	L-fucose ChEBI	+	builds acid from
[Ref.: #43088]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43088]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43088]	L-xylose ChEBI	-	builds acid from
[Ref.: #43088]	lactose ChEBI	+	builds acid from
[Ref.: #43088]	malate ChEBI	-	assimilation
[Ref.: #43088]	maltose ChEBI	+	assimilation
[Ref.: #43088]	maltose ChEBI	+	builds acid from
[Ref.: #43088]	melezitose ChEBI	-	builds acid from
[Ref.: #43088]	melibiose ChEBI	+	assimilation
[Ref.: #43088]	melibiose ChEBI	-	builds acid from
[Ref.: #43088]	methyl beta-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #43088]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #43088]	myo-inositol ChEBI	+	builds acid from
[Ref.: #43088]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43088]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43088]	nitrate ChEBI	+	reduction
[Ref.: #43088]	phenylacetate ChEBI	-	assimilation
[Ref.: #43088]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43088]	raffinose ChEBI	-	builds acid from
[Ref.: #43088]	ribitol ChEBI	+	builds acid from
[Ref.: #43088]	ribose ChEBI	-	builds acid from
[Ref.: #43088]	salicin ChEBI	+	builds acid from
[Ref.: #43088]	sodium citrate ChEBI	-	assimilation
[Ref.: #43088]	sodium succinate ChEBI	-	assimilation
[Ref.: #43088]	starch ChEBI	+	hydrolysis
[Ref.: #43088]	starch ChEBI	-	builds acid from
[Ref.: #43088]	sucrose ChEBI	+	builds acid from
[Ref.: #43088]	sucrose ChEBI	-	assimilation
[Ref.: #43088]	trehalose ChEBI	+	builds acid from
[Ref.: #43088]	turanose ChEBI	+	builds acid from
[Ref.: #43088]	xylan ChEBI	+	hydrolysis
[Ref.: #43088]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43088]	acetoin ChEBI	no
[Ref.: #43088]	hydrogen sulfide ChEBI	no
[Ref.: #43088]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43088]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43088]	acid phosphatase	+	3.1.3.2
[Ref.: #43088]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43088]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43088]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43088]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43088]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43088]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43088]	arginine dihydrolase	+	3.5.3.6
[Ref.: #43088]	beta-D-galactosidase	+	3.2.1.23
[Ref.: #43088]	beta-galactosidase	+	3.2.1.23
[Ref.: #43088]	beta-glucosidase	-	3.2.1.21
[Ref.: #43088]	beta-glucuronidase	+	3.2.1.31
[Ref.: #43088]	catalase	+	1.11.1.6
[Ref.: #43088]	cystine arylamidase	-	3.4.11.3
[Ref.: #43088]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43088]	esterase (C 4)	+
[Ref.: #43088]	esterase Lipase (C 8)	+
[Ref.: #43088]	leucine arylamidase	+	3.4.11.1
[Ref.: #43088]	lipase (C 14)	-
[Ref.: #43088]	lysine decarboxylase	+	4.1.1.18
[Ref.: #43088]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43088]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43088]	ornithine decarboxylase	+	4.1.1.17
[Ref.: #43088]	trypsin	+	3.4.21.4
[Ref.: #43088]	tryptophan deaminase	+	4.1.99.1
[Ref.: #43088]	urease	+	3.5.1.5
[Ref.: #43088]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43088]

Fatty acid	Percentage
C16:0 iso	23.4
C16:0	23.2
C15:0 anteiso	21.5
C15:0 iso	11.4
C14:0 iso	4.5
C17:0 iso	4.2
C14:0	3.5
C17:0	2.7
C15:0	2.5
C12:0	1.3
C18:0	1

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

[Ref.: #24378]	Sample type/isolated from	litter of geyser
[Ref.: #24378]	Geographic location (country and/or sea, region)	West Java, Cisolok geyser
[Ref.: #24378]	Country	Indonesia
[Ref.: #24378]	Country ISO 3 Code	IDN
[Ref.: #24378]	Continent	Asia
[Ref.: #24378]	Geographic location	-6.9333°/106.4500°

[Ref.: #43088]	Sample type/isolated from	fallen leaf of Cisolok geyser
[Ref.: #43088]	Geographic location (country and/or sea, region)	West Java, Indonesia
[Ref.: #43088]	Country	Indonesia
[Ref.: #43088]	Country ISO 3 Code	IDN
[Ref.: #43088]	Continent	Asia
[Ref.: #43088]	Geographic location	-6.0000°/106.0000°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC055784 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	444
Soil Samples	1539
Animal Samples	993
Plant Samples	363
Total Samples	3339

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

[Ref.: #24378]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24378]	Paenibacillus cisolokensis gene for 16S ribosomal RNA, partial sequence	LC055784	1423	ENA	1658519 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus cisolokensis LC2-13A	GCA_018403665	contig	GenBank	1658519 tax ID	*
[Ref.: #66792]	Paenibacillus cisolokensis strain LC2-13A	1658519.3	wgs	PATRIC	1658519 tax ID	*

[Ref.: #24378]

GC-content

56.6 mol%

high performance liquid chromatography (HPLC)

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 cisolokensis strain LC2-13A PATRIC: 1658519.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus cisolokensis strain LC2-13A PATRIC: 1658519.3
[Ref.: #69480]	motile	yes	85.313	yes
[Ref.: #69480]	gram-positive	yes	87.688	no
[Ref.: #69480]	anaerobic	no	98.7	no
[Ref.: #69480]	aerobic	yes	89.196	yes
[Ref.: #69480]	halophile	no	91.283	no
[Ref.: #69480]	spore-forming	yes	96.119	no
[Ref.: #69480]	thermophile	no	90.699	no
[Ref.: #69480]	glucose-util	yes	85.976	yes
[Ref.: #69480]	flagellated	yes	80.772	yes
[Ref.: #69480]	glucose-ferment	no	90.344	no

Availability in culture collections External links

[Ref.: #24378]

Culture collection no.

DSM 101873, NRRL B-65368, UICC B-42

[Ref.: #90906]

SI-ID 397607

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13.	Uke A, Chhe C, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A	Data Brief	10.1016/j.dib.2021.107361	2021	*
Phylogeny	Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser.	Yokota A, Ningsih F, Nurlaili DG, Sakai Y, Yabe S, Oetari A, Santoso I, Sjamsuridzal W	Int J Syst Evol Microbiol	10.1099/ijsem.0.001151	2016	*

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 )

#24378

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101873

#43088

Akira Yokota, Fitria Ningsih, Dafina Ghossani Nurlaili, Yasuteru Sakai, Shuhei Yabe, Ariyanti Oetari, Iman Santoso and Wellyzar Sjamsuridzal: Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser. IJSEM 66: 3088 - 3094 2016 ( DOI 10.1099/ijsem.0.001151 , PubMed 27188601 )

#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) .

#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 )

#90906

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-ID397607.1 )

* These data were automatically processed and therefore are not curated

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Paenibacillus cisolokensis strain LC2-13A

Paenibacillus cisolokensis strain LC2-13A

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