Paenibacillus cisolokensis (DSM 101873, NRRL B-65368, UICC B-42)

Name: Paenibacillus cisolokensis (DSM 101873, NRRL B-65368, UICC B-42)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132589

Type strain

Strain Designation LC2-13A

Culture col. no. DSM 101873 NRRL B-65368 UICC B-42 LC2-13A

NCBI tax ID(s) 1658519

Special Collections DSMZ Literature strains

History <- W. Sjamsuridzal, Universitas Indonesia, Kampus UI Depok, LC2-13A

Links

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

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

Name and taxonomic classification

SI-ID 397607

DSM 101873

@ref 20215

Last LPSN update 2026-02-09 11:31:45

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus cisolokensis

Full scientific name Paenibacillus cisolokensis Yokota et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement	Confidence
43088	positive	0.8-09 µm	2.0-2.4 µm	rod-shaped		peritrichous
125439							92.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43088	2-3 mm	white	circular	3 days	ISP1 medium

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43088	ISP1 medium
43088	ISP2 medium
43088	Trypticase Soy Agar (TSA)
43088	TSB		with 0-2.0 % (w/v) NaCl
24378	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24378	positive	growth	45
43088	positive	optimum	45-50
43088	positive	growth	37-55

Culture pH

@ref	Ability	Type	PH	PH range
43088	positive	optimum	6.0-7.0
43088	positive	growth	5.7-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43088	aerobe
125439	aerobe	96

Spore formation

@ref	Type of spore	Confidence
43088	endospore
125438		94.152
125439		94.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43088	NaCl	positive	growth	0-2.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43088	17019 ChEBI	(R)-amygdalin	+	assimilation
43088		2-oxogluconate	-	builds acid from
43088	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
43088	17128 ChEBI	adipate	-	assimilation
43088	27613 ChEBI	amygdalin	+	builds acid from
43088	18305 ChEBI	arbutin	-	builds acid from
43088	17057 ChEBI	cellobiose	+	builds acid from
43088	62968 ChEBI	cellulose	+	hydrolysis
43088	17029 ChEBI	chitin	+	hydrolysis
43088	16947 ChEBI	citrate	-	assimilation
43088	17108 ChEBI	D-arabinose	+	builds acid from
43088	18333 ChEBI	D-arabitol	-	builds acid from
43088	15824 ChEBI	D-fructose	+	builds acid from
43088	28847 ChEBI	D-fucose	-	builds acid from
43088	12936 ChEBI	D-galactose	-	builds acid from
43088	17634 ChEBI	D-glucose	+	builds acid from
43088	17634 ChEBI	D-glucose	-	assimilation
43088	62318 ChEBI	D-lyxose	-	builds acid from
43088	16899 ChEBI	D-mannitol	-	assimilation
43088	16899 ChEBI	D-mannitol	+	builds acid from
43088	16024 ChEBI	D-mannose	-	assimilation
43088	16024 ChEBI	D-mannose	-	builds acid from
43088	17924 ChEBI	D-sorbitol	+	assimilation
43088	17924 ChEBI	D-sorbitol	+	builds acid from
43088	16443 ChEBI	D-tagatose	-	builds acid from
43088	65327 ChEBI	D-xylose	+	builds acid from
43088	27689 ChEBI	decanoate	-	assimilation
43088	17113 ChEBI	erythritol	-	builds acid from
43088	4853 ChEBI	esculin	+	hydrolysis
43088		esculin ferric citrate	+	builds acid from
43088	16813 ChEBI	galactitol	-	builds acid from
43088	5291 ChEBI	gelatin	+	hydrolysis
43088	28066 ChEBI	gentiobiose	+	builds acid from
43088	24265 ChEBI	gluconate	-	builds acid from
43088	17234 ChEBI	glucose	+	builds acid from
43088	17754 ChEBI	glycerol	-	builds acid from
43088	28087 ChEBI	glycogen	-	builds acid from
43088	15443 ChEBI	inulin	-	builds acid from
43088	30849 ChEBI	L-arabinose	+	assimilation
43088	30849 ChEBI	L-arabinose	+	builds acid from
43088	18403 ChEBI	L-arabitol	-	builds acid from
43088	18287 ChEBI	L-fucose	+	builds acid from
43088	62345 ChEBI	L-rhamnose	+	builds acid from
43088	17266 ChEBI	L-sorbose	-	builds acid from
43088	65328 ChEBI	L-xylose	-	builds acid from
43088	17716 ChEBI	lactose	+	builds acid from
43088	25115 ChEBI	malate	-	assimilation
43088	17306 ChEBI	maltose	+	assimilation
43088	17306 ChEBI	maltose	+	builds acid from
43088	6731 ChEBI	melezitose	-	builds acid from
43088	28053 ChEBI	melibiose	+	assimilation
43088	28053 ChEBI	melibiose	-	builds acid from
43088	320055 ChEBI	methyl beta-D-glucopyranoside	+	builds acid from
43088	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from
43088	17268 ChEBI	myo-inositol	+	builds acid from
43088	506227 ChEBI	N-acetylglucosamine	-	assimilation
43088	506227 ChEBI	N-acetylglucosamine	-	builds acid from
43088	17632 ChEBI	nitrate	+	reduction
43088	18401 ChEBI	phenylacetate	-	assimilation
43088	32032 ChEBI	potassium gluconate	-	assimilation
43088	16634 ChEBI	raffinose	-	builds acid from
43088	15963 ChEBI	ribitol	+	builds acid from
43088	33942 ChEBI	ribose	-	builds acid from
43088	17814 ChEBI	salicin	+	builds acid from
43088	53258 ChEBI	sodium citrate	-	assimilation
43088	63675 ChEBI	sodium succinate	-	assimilation
43088	28017 ChEBI	starch	+	hydrolysis
43088	28017 ChEBI	starch	-	builds acid from
43088	17992 ChEBI	sucrose	+	builds acid from
43088	17992 ChEBI	sucrose	-	assimilation
43088	27082 ChEBI	trehalose	+	builds acid from
43088	32528 ChEBI	turanose	+	builds acid from
43088	37166 ChEBI	xylan	+	hydrolysis
43088	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
43088	15688 ChEBI	acetoin
43088	16136 ChEBI	hydrogen sulfide
43088	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43088	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
43088	acid phosphatase	+	3.1.3.2
43088	alkaline phosphatase	+	3.1.3.1
43088	alpha-chymotrypsin	+	3.4.21.1
43088	alpha-fucosidase	-	3.2.1.51
43088	alpha-galactosidase	+	3.2.1.22
43088	alpha-glucosidase	+	3.2.1.20
43088	alpha-mannosidase	-	3.2.1.24
43088	arginine dihydrolase	+	3.5.3.6
43088	beta-D-galactosidase	+	3.2.1.23
43088	beta-galactosidase	+	3.2.1.23
43088	beta-glucosidase	-	3.2.1.21
43088	beta-glucuronidase	+	3.2.1.31
43088	catalase	+	1.11.1.6
43088	cystine arylamidase	-	3.4.11.3
43088	cytochrome oxidase	+	1.9.3.1
43088	esterase (C 4)	+
43088	esterase Lipase (C 8)	+
43088	leucine arylamidase	+	3.4.11.1
43088	lipase (C 14)	-
43088	lysine decarboxylase	+	4.1.1.18
43088	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43088	naphthol-AS-BI-phosphohydrolase	+
43088	ornithine decarboxylase	+	4.1.1.17
43088	trypsin	+	3.4.21.4
43088	tryptophan deaminase	+	4.1.99.1
43088	urease	+	3.5.1.5
43088	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic
#Condition	#Thermophilic (>45°C)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24378	litter of geyser	West Java, Cisolok geyser	Indonesia	IDN	Asia	-6.9333	106.45 -6.9333/106.45
43088	fallen leaf of Cisolok geyser	West Java, Indonesia	Indonesia	IDN	Asia	-6	106 -6/106

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24378	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1840366v1 assembly for Paenibacillus cisolokensis LC2-13A	contig	GCA_018403665	1658519.3	1658519	2.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24378	Paenibacillus cisolokensis gene for 16S ribosomal RNA, partial sequence	LC055784	1423		1658519

GC content

@ref	GC-content (mol%)	Method
24378	56.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus cisolokensis LC2-13A
NCBI: GCA_018403665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.70	no
125439	motility	BacteriaNetⓘ	yes	92.50	no
125439	gram_stain	BacteriaNetⓘ	variable	88.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus cisolokensis strain LC2-13A
PATRIC: 1658519.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.51	yes
125438	anaerobic	anaerobicⓘ	no	97.39	yes
125438	spore-forming	spore-formingⓘ	yes	94.15	yes
125438	aerobic	aerobicⓘ	yes	69.97	yes
125438	thermophilic	thermophileⓘ	no	91.33	no
125438	flagellated	motile2+ⓘ	yes	79.34	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars.	Duhamel S, Hamilton CW, Palsson S, Bjornsdottir SH.	Astrobiology	10.1089/ast.2021.0124	2022
	Characterization of a thermophilic facultatively anaerobic bacterium Paenibacillus sp. strain DA-C8 that exhibits xylan degradation under anaerobic conditions.	Chhe C, Uke A, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A.	J Biotechnol	10.1016/j.jbiotec.2021.10.008	2021
Genetics	Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8.	Chhe C, Uke A, Baramee S, Ungkulpasvich U, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A.	Data Brief	10.1016/j.dib.2021.106784	2021
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
	Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost.	Chhe C, Uke A, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005724	2023
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 .
#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 cisolokensis (DSM 101873, NRRL B-65368, UICC B-42)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_018403665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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