Strain identifier

BacDive ID: 132589

Type strain: Yes

Species: Paenibacillus cisolokensis

Strain Designation: LC2-13A

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

NCBI tax ID(s): 1658519 (species)

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General

@ref: 24378

BacDive-ID: 132589

DSM-Number: 101873

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped, colony-forming

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

NCBI tax id

  • NCBI tax id: 1658519
  • Matching level: species

strain history

  • @ref: 24378
  • history: <- W. Sjamsuridzal, Universitas Indonesia, Kampus UI Depok, LC2-13A

doi: 10.13145/bacdive132589.20230509.8.1

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 cisolokensis
  • full scientific name: Paenibacillus cisolokensis Yokota et al. 2016

@ref: 24378

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus cisolokensis

full scientific name: Paenibacillus cisolokensis Yokota et al. 2016

strain designation: LC2-13A

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43088positive0.8-09 µm2.0-2.4 µmrod-shapedyesperitrichous
69480yes94.409
69480positive100

colony morphology

  • @ref: 43088
  • colony size: 2-3 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: ISP1 medium

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43088ISP1 mediumyes
43088ISP2 mediumyes
43088Trypticase Soy Agar (TSA)yes
43088TSByeswith 0-2.0 % (w/v) NaCl
24378CASO AGAR (MERCK 105458) (DSMZ Medium 220)yesName: 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 waterhttps://mediadive.dsmz.de/medium/220

culture temp

@refgrowthtypetemperaturerange
43088positiveoptimum45-50thermophilic
43088positivegrowth37-55
24378positivegrowth45thermophilic

culture pH

@refabilitytypepHPH range
43088positivegrowth5.7-9.0alkaliphile
43088positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43088
  • oxygen tolerance: aerobe

spore formation

@reftype of sporespore formationconfidence
43088endosporeyes
69481yes100
69480yes100

halophily

  • @ref: 43088
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4308828017starch+hydrolysis
4308862968cellulose+hydrolysis
4308837166xylan+hydrolysis
430884853esculin+hydrolysis
430885291gelatin+hydrolysis
4308817029chitin+hydrolysis
4308817632nitrate+reduction
4308817234glucose+builds acid from
4308816947citrate-assimilation
4308830849L-arabinose+assimilation
4308817306maltose+assimilation
4308817924D-sorbitol+assimilation
4308828053melibiose+assimilation
4308817019(R)-amygdalin+assimilation
4308816024D-mannose-assimilation
4308816899D-mannitol-assimilation
43088506227N-acetylglucosamine-assimilation
4308827689decanoate-assimilation
4308817128adipate-assimilation
4308825115malate-assimilation
4308863675sodium succinate-assimilation
4308818401phenylacetate-assimilation
4308817108D-arabinose+builds acid from
4308830849L-arabinose+builds acid from
4308865327D-xylose+builds acid from
4308815963ribitol+builds acid from
4308874863methyl beta-D-xylopyranoside+builds acid from
4308817634D-glucose+builds acid from
4308815824D-fructose+builds acid from
4308862345L-rhamnose+builds acid from
4308817268myo-inositol+builds acid from
4308816899D-mannitol+builds acid from
4308817924D-sorbitol+builds acid from
43088320055methyl beta-D-glucopyranoside+builds acid from
4308827613amygdalin+builds acid from
43088esculin ferric citrate+builds acid from
4308817814salicin+builds acid from
4308817057cellobiose+builds acid from
4308817306maltose+builds acid from
4308817716lactose+builds acid from
4308817992sucrose+builds acid from
4308827082trehalose+builds acid from
4308828066gentiobiose+builds acid from
4308832528turanose+builds acid from
4308818287L-fucose+builds acid from
4308817754glycerol-builds acid from
4308817113erythritol-builds acid from
4308833942ribose-builds acid from
4308865328L-xylose-builds acid from
4308812936D-galactose-builds acid from
4308816024D-mannose-builds acid from
4308817266L-sorbose-builds acid from
4308816813galactitol-builds acid from
43088506227N-acetylglucosamine-builds acid from
4308818305arbutin-builds acid from
4308828053melibiose-builds acid from
4308815443inulin-builds acid from
430886731melezitose-builds acid from
4308816634raffinose-builds acid from
4308828017starch-builds acid from
4308828087glycogen-builds acid from
4308817151xylitol-builds acid from
4308862318D-lyxose-builds acid from
4308816443D-tagatose-builds acid from
4308828847D-fucose-builds acid from
4308818333D-arabitol-builds acid from
4308818403L-arabitol-builds acid from
4308824265gluconate-builds acid from
430882-oxogluconate-builds acid from
43088581435-dehydro-D-gluconate-builds acid from
4308817634D-glucose-assimilation
4308832032potassium gluconate-assimilation
4308853258sodium citrate-assimilation
4308817992sucrose-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4308835581indoleno
4308816136hydrogen sulfideno
4308815688acetoinno

metabolite tests

  • @ref: 43088
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43088C12:01.3
    43088C14:03.5
    43088C15:02.5
    43088C16:023.2
    43088C17:02.7
    43088C18:01
    43088C14:0 iso4.5
    43088C15:0 iso11.4
    43088C15:0 anteiso21.5
    43088C16:0 iso23.4
    43088C17:0 iso4.2
  • type of FA analysis: whole cell analysis
  • incubation medium: tripricase soy broth (TSB)
  • agar/liquid: liquid
  • incubation temperature: 50
  • incubation time: 3
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24378litter of geyserWest Java, Cisolok geyserIndonesiaIDNAsia-6.9333106.45
43088fallen leaf of Cisolok geyserWest Java, IndonesiaIndonesiaIDNAsia-6106

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6930.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_3256;97_3995;98_5098;99_6930&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: LC055784
  • Sequence Identity:
  • Total samples: 3339
  • soil counts: 1539
  • aquatic counts: 444
  • animal counts: 993
  • plant counts: 363

Safety information

risk assessment

  • @ref: 24378
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24378
  • description: Paenibacillus cisolokensis gene for 16S ribosomal RNA, partial sequence
  • accession: LC055784
  • length: 1423
  • database: ena
  • NCBI tax ID: 1658519

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus cisolokensis LC2-13AGCA_018403665contigncbi1658519
66792Paenibacillus cisolokensis strain LC2-13A1658519.3wgspatric1658519

GC content

  • @ref: 24378
  • GC-content: 56.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.313yes
gram-positiveyes87.688no
anaerobicno98.7no
aerobicyes89.196yes
halophileno91.283no
spore-formingyes96.119no
thermophileno90.699no
glucose-utilyes85.976yes
flagellatedyes80.772yes
glucose-fermentno90.344no

External links

@ref: 24378

culture collection no.: DSM 101873, NRRL B-65368, UICC B-42

straininfo link

  • @ref: 90906
  • straininfo: 397607

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27188601Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser.Yokota A, Ningsih F, Nurlaili DG, Sakai Y, Yabe S, Oetari A, Santoso I, Sjamsuridzal WInt J Syst Evol Microbiol10.1099/ijsem.0.0011512016Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indonesia, Nucleic Acid Hybridization, Paenibacillus/classification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics34557574Draft 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 AData Brief10.1016/j.dib.2021.1073612021

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
24378Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101873Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101873)
43088Akira Yokota, Fitria Ningsih, Dafina Ghossani Nurlaili, Yasuteru Sakai, Shuhei Yabe, Ariyanti Oetari, Iman Santoso and Wellyzar SjamsuridzalPaenibacillus cisolokensis sp. nov., isolated from litter of a geyser10.1099/ijsem.0.001151IJSEM 66: 3088-3094 201627188601
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90906Reimer, 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-ID397607.1