Name: Paenibacillus cavernae C4-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132384

Type strain:

Species: Paenibacillus cavernae

Strain Designation: C4-5

Culture col. no.: DSM 100100, KCTC 33652

Strain history: <- Soon Dong Lee, Jeju Univ.

NCBI tax ID(s): 1660197 (species)

SI-ID 399288

DSM 100100

Section

Paenibacillus cavernae C4-5 is an obligate aerobe, spore-forming, Gram-variable bacterium that forms circular colonies and was isolated from soil inside a natural cave.

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

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 cavernae**
	Full Scientific Name (LPSN)	Paenibacillus cavernae Lee 2016

Information on morphological and physiological properties Morphology

[Ref.: #43809]	Gram stain	variable
[Ref.: #67771]	Gram stain	variable

[Ref.: #43809]	Cell length	2.7-3.2 µm

[Ref.: #43809]	Cell width	0.9-1.1 µm

[Ref.: #43809]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #43809]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	monotrichous, polar

[Ref.: #43809]	Colony size	1-2 mm
[Ref.: #43809]	Colony color	White-cream
[Ref.: #43809]	Colony shape	circular
[Ref.: #43809]	Incubation period	3 days
[Ref.: #43809]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Trypticase soy agar

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Culture medium growth

[Ref.: #24173]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #24173]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24173]	growth	30 °C
[Ref.: #43809]	growth	20-42 °C
[Ref.: #43809]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #24173]	Temperature range	mesophilic
[Ref.: #43809]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43809]			optimum	7
[Ref.: #43809]			growth	6-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43809]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #43809]	Spore description	Ellipsoidal; formed in sporangia and at subterminal position of cells
[Ref.: #43809]	Type of spore	endospore
[Ref.: #43809]	Ability of spore formation	yes

[Ref.: #43809]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43809]		NaCl		growth	0-1	%(w/v)
[Ref.: #43809]		NaCl		optimum	0	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43809]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #43809]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43809]	adipate ChEBI	-	assimilation
[Ref.: #43809]	amygdalin ChEBI	-	builds acid from
[Ref.: #43809]	arbutin ChEBI	-	builds acid from
[Ref.: #43809]	casein	-	hydrolysis
[Ref.: #43809]	cellobiose ChEBI	-	builds acid from
[Ref.: #43809]	citrate ChEBI	-	assimilation
[Ref.: #43809]	D-arabinose ChEBI	-	assimilation
[Ref.: #43809]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43809]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43809]	D-fructose ChEBI	-	builds acid from
[Ref.: #43809]	D-fucose ChEBI	-	builds acid from
[Ref.: #43809]	D-galactose ChEBI	-	builds acid from
[Ref.: #43809]	D-glucose ChEBI	-	assimilation
[Ref.: #43809]	D-glucose ChEBI	-	builds acid from
[Ref.: #43809]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43809]	D-mannitol ChEBI	-	assimilation
[Ref.: #43809]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43809]	D-mannose ChEBI	-	assimilation
[Ref.: #43809]	D-mannose ChEBI	-	builds acid from
[Ref.: #43809]	D-ribose ChEBI	-	builds acid from
[Ref.: #43809]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43809]	D-xylose ChEBI	-	builds acid from
[Ref.: #43809]	decanoate ChEBI	-	assimilation
[Ref.: #43809]	dna ChEBI	+	hydrolysis
[Ref.: #43809]	erythritol ChEBI	-	builds acid from
[Ref.: #43809]	esculin ChEBI	-	builds acid from
[Ref.: #43809]	esculin ChEBI	+/-	degradation
[Ref.: #43809]	galactitol ChEBI	-	builds acid from
[Ref.: #43809]	gelatin ChEBI	-	hydrolysis
[Ref.: #43809]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43809]	gluconate ChEBI	-	assimilation
[Ref.: #43809]	gluconate ChEBI	-	builds acid from
[Ref.: #43809]	glucose ChEBI	-	fermentation
[Ref.: #43809]	glycerol ChEBI	-	builds acid from
[Ref.: #43809]	glycogen ChEBI	-	builds acid from
[Ref.: #43809]	inulin ChEBI	-	builds acid from
[Ref.: #43809]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43809]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43809]	L-fucose ChEBI	-	builds acid from
[Ref.: #43809]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43809]	L-xylose ChEBI	-	builds acid from
[Ref.: #43809]	lactose ChEBI	-	builds acid from
[Ref.: #43809]	malate ChEBI	-	assimilation
[Ref.: #43809]	maltose ChEBI	-	assimilation
[Ref.: #43809]	maltose ChEBI	+	builds acid from
[Ref.: #43809]	melezitose ChEBI	-	builds acid from
[Ref.: #43809]	melibiose ChEBI	+	builds acid from
[Ref.: #43809]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43809]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43809]	methyl D-glucoside ChEBI	-	builds acid from
[Ref.: #43809]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43809]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43809]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43809]	nitrate ChEBI	-	reduction
[Ref.: #43809]	phenylacetate ChEBI	-	assimilation
[Ref.: #43809]	raffinose ChEBI	-	builds acid from
[Ref.: #43809]	rhamnose ChEBI	-	builds acid from
[Ref.: #43809]	ribitol ChEBI	-	builds acid from
[Ref.: #43809]	salicin ChEBI	-	builds acid from
[Ref.: #43809]	sorbitol ChEBI	-	builds acid from
[Ref.: #43809]	starch ChEBI	-	builds acid from
[Ref.: #43809]	starch ChEBI	-	hydrolysis
[Ref.: #43809]	sucrose ChEBI	+	builds acid from
[Ref.: #43809]	trehalose ChEBI	+	builds acid from
[Ref.: #43809]	turanose ChEBI	+	builds acid from
[Ref.: #43809]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43809]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43809]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43809]	beta-galactosidase	+	3.2.1.23
[Ref.: #43809]	catalase	+	1.11.1.6
[Ref.: #43809]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43809]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43809]

Fatty acid	Percentage
C15:0 anteiso	44.7
C16:0 iso	15.83
C16:0	14.16
C18:0	6.39
C15:0 iso	5.48
C17:0 anteiso	5.4
C14:0 iso	1.69
C17:0 iso	1.4
C14:0	1.08

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

[Ref.: #24173]	Sample type/isolated from	soil inside a natural cave
[Ref.: #24173]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #24173]	Country	Republic of Korea
[Ref.: #24173]	Country ISO 3 Code	KOR
[Ref.: #24173]	Continent	Asia

[Ref.: #43809]	Sample type/isolated from	A soil sample of a natural cave in Jeju; collected at a distance of 3 mm from the entrance of the cave
[Ref.: #43809]	Geographic location (country and/or sea, region)	Jeju Island
[Ref.: #43809]	Country	Republic of Korea
[Ref.: #43809]	Country ISO 3 Code	KOR
[Ref.: #43809]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil inside a natural cave in Jeju
[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	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

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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.: #24173]	Paenibacillus sp. C4-5 partial 16S rRNA gene, strain C4-5	LN852381	1431	ENA	1660197 tax ID

[Ref.: #24173]	GC-content	54.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	54.8 mol%

Availability in culture collections External links

[Ref.: #24173]

Culture collection no.

DSM 100100, KCTC 33652

[Ref.: #90727]

SI-ID 399288

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 cavernae sp. nov., isolated from soil of a natural cave.	Dong Lee S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000762	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 )

#24173

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100100

#43809

Soon Dong Lee: Paenibacillus cavernae sp. nov., isolated from soil of a natural cave. IJSEM 66: 598 - 603 2016 ( DOI 10.1099/ijsem.0.000762 , PubMed 26558840 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#90727

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-ID399288.1 )

* These data were automatically processed and therefore are not curated

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