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BacDive ID 132384
Type strain
Strain Designation C4-5
Culture col. no. DSM 100100 KCTC 33652 C4-5
NCBI tax ID(s) 1660197
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9 (current version):
version 9 (current version)

General

@ref: 24173

BacDive-ID: 132384

DSM-Number: 100100

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

description: 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.

NCBI tax id

  • NCBI tax id: 1660197
  • Matching level: species

strain history

@refhistory
24173<- S. D. Lee, Jeju National Univ., Rep. of Korea; C4-5
67771<- Soon Dong Lee, Jeju Univ.

doi: 10.13145/bacdive132384.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus cavernae
  • full scientific name: Paenibacillus cavernae Lee 2016

@ref: 24173

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus cavernae

full scientific name: Paenibacillus cavernae Lee 2016

strain designation: C4-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
43809variable2.7-3.2 µm0.9-1.1 µmrod-shapedyes
67771rod-shapedyesmonotrichous, polar
67771variable

colony morphology

  • @ref: 43809
  • colony size: 1-2 mm
  • colony color: White-cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43809Nutrient agar (NA)yes
43809Reasoner's 2A agar (R2A)yes
43809Trypticase soy agaryes
24173NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
43809positivegrowth20-42
43809positiveoptimum30
24173positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepHPH range
43809positivegrowth6-10alkaliphile
43809positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43809obligate aerobe
67771aerobe

spore formation

  • @ref: 43809
  • spore description: Ellipsoidal; formed in sporangia and at subterminal position of cells
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43809NaClpositivegrowth0-1 %(w/v)
43809NaClpositiveoptimum0 %(w/v)non-halophilic

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4380917128adipate-assimilation
4380927689decanoate-assimilation
4380916947citrate-assimilation
4380917108D-arabinose-assimilation
4380917634D-glucose-assimilation
4380916899D-mannitol-assimilation
4380916024D-mannose-assimilation
4380925115malate-assimilation
4380924265gluconate-assimilation
4380917306maltose-assimilation
43809506227N-acetylglucosamine-assimilation
4380918401phenylacetate-assimilation
43809168082-dehydro-D-gluconate-builds acid from
4380915963ribitol-builds acid from
4380927613amygdalin-builds acid from
4380918305arbutin-builds acid from
4380917108D-arabinose-builds acid from
4380918333D-arabitol-builds acid from
4380917057cellobiose-builds acid from
4380915824D-fructose-builds acid from
4380928847D-fucose-builds acid from
4380912936D-galactose-builds acid from
4380917634D-glucose-builds acid from
4380962318D-lyxose-builds acid from
4380916899D-mannitol-builds acid from
4380916024D-mannose-builds acid from
4380916988D-ribose-builds acid from
4380916443D-tagatose-builds acid from
4380965327D-xylose-builds acid from
4380916813galactitol-builds acid from
4380917113erythritol-builds acid from
438094853esculin-builds acid from
4380924265gluconate-builds acid from
4380917754glycerol-builds acid from
4380928087glycogen-builds acid from
4380917268myo-inositol-builds acid from
4380915443inulin-builds acid from
4380930849L-arabinose-builds acid from
4380918403L-arabitol-builds acid from
4380918287L-fucose-builds acid from
4380917266L-sorbose-builds acid from
4380965328L-xylose-builds acid from
4380917716lactose-builds acid from
438096731melezitose-builds acid from
4380943943methyl alpha-D-mannoside-builds acid from
4380974863methyl beta-D-xylopyranoside-builds acid from
4380937657methyl D-glucoside-builds acid from
43809506227N-acetylglucosamine-builds acid from
4380916634raffinose-builds acid from
4380926546rhamnose-builds acid from
4380917814salicin-builds acid from
4380930911sorbitol-builds acid from
4380928017starch-builds acid from
4380917151xylitol-builds acid from
4380917234glucose-fermentation
43809casein-hydrolysis
438095291gelatin-hydrolysis
4380928017starch-hydrolysis
4380917632nitrate-reduction
43809581435-dehydro-D-gluconate+builds acid from
4380928066gentiobiose+builds acid from
4380917306maltose+builds acid from
4380928053melibiose+builds acid from
4380917992sucrose+builds acid from
4380927082trehalose+builds acid from
4380932528turanose+builds acid from
4380916991dna+hydrolysis
438094853esculin+/-degradation

metabolite production

  • @ref: 43809
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43809cytochrome oxidase+1.9.3.1
43809catalase+1.11.1.6
43809beta-galactosidase+3.2.1.23
43809arginine dihydrolase-3.5.3.6
43809urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43809C15:0 anteiso44.7
    43809C17:0 anteiso5.4
    43809C14:01.08
    43809C16:014.16
    43809C18:06.39
    43809C14:0 iso1.69
    43809C15:0 iso5.48
    43809C16:0 iso15.83
    43809C17:0 iso1.4
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24173soil inside a natural caveJejuRepublic of KoreaKORAsia
43809A soil sample of a natural cave in Jeju; collected at a distance of 3 mm from the entrance of the caveJeju IslandRepublic of KoreaKORAsia
67771From soil inside a natural cave in JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 24173
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24173
  • description: Paenibacillus sp. C4-5 partial 16S rRNA gene, strain C4-5
  • accession: LN852381
  • length: 1431
  • database: nuccore
  • NCBI tax ID: 1660197

GC content

@refGC-contentmethod
2417354.8high performance liquid chromatography (HPLC)
6777154.8

External links

@ref: 24173

culture collection no.: DSM 100100, KCTC 33652

straininfo link

  • @ref: 90727
  • straininfo: 399288

literature

topicPubmed-IDtitleauthorsjournalDOIyear
Phylogeny26558840Paenibacillus cavernae sp. nov., isolated from soil of a natural cave.Dong Lee SInt J Syst Evol Microbiol10.1099/ijsem.0.0007622015
Phylogeny33666545Paenibacillus cymbidii sp. nov., isolated from Cymbidium goeringii roots.Sun L, Wang P, Zhao D, Wang J, Wu Q, Liu L, Lyu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0047312021

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24173Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100100Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100100)
43809Soon Dong LeePaenibacillus cavernae sp. nov., isolated from soil of a natural cave10.1099/ijsem.0.000762IJSEM 66: 598-603 201626558840
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
90727Reimer, 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 identifiers10.60712/SI-ID399288.1

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