Strain identifier

BacDive ID: 11511

Type strain: Yes

Species: Paenibacillus kobensis

Strain Designation: YK205

Strain history: CIP <- 1995, IFO <- 1955, T. Harada, Kobe Women's Univ., Japan: strain YK205

NCBI tax ID(s): 1220566 (strain), 59841 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3869

BacDive-ID: 11511

DSM-Number: 10249

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, motile

description: Paenibacillus kobensis YK205 is a spore-forming, mesophilic, motile bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
59841species
1220566strain

strain history

@refhistory
3869<- IFO
67770NBRC 15729 <-- IFO 15729 <-- T. Harada YK205.
120455CIP <- 1995, IFO <- 1955, T. Harada, Kobe Women's Univ., Japan: strain YK205

doi: 10.13145/bacdive11511.20230509.8.1

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 kobensis
  • full scientific name: Paenibacillus kobensis (Kanzawa et al. 1995) Shida et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Bacillus kobensis

@ref: 3869

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus kobensis

full scientific name: Paenibacillus kobensis (Kanzawa et al. 1995) Shida et al. 1997

strain designation: YK205

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.851
69480100positive
120455yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3869TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92; with strain-specific modifications) Composition: Trypticase soy broth 30.0 g/l Yeast extract 3.0 g/l Distilled water
41228MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120455CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3869positivegrowth30mesophilic
41228positivegrowth30mesophilic
67770positivegrowth30mesophilic
120455positivegrowth30-37mesophilic
120455nogrowth10psychrophilic
120455nogrowth45thermophilic
120455nogrowth55thermophilic

culture pH

  • @ref: 120455
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100
120455yes

compound production

  • @ref: 3869
  • compound: exo-(1-3)-ß-D glucanase

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120455citrate-carbon source16947
120455nitrate+reduction17632
120455nitrite-reduction16301
120455nitrate-respiration17632

metabolite production

  • @ref: 120455
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120455
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
120455oxidase-
120455alcohol dehydrogenase-1.1.1.1
120455gelatinase-
120455catalase+1.11.1.6
120455lysine decarboxylase-4.1.1.18
120455ornithine decarboxylase-4.1.1.17
120455urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120455--++------++----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120455---------+/-+-+---------+-+-++-+/------+/-+-+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120455---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3869soilKobe CityJapanJPNAsia
67770SoilKobe CityJapanJPNAsia
120455Environment, SoilKobeJapanJPNAsia1990

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_133374.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2361;97_18918;98_33932;99_133374&stattab=map
  • Last taxonomy: Paenibacillus kobensis subclade
  • 16S sequence: AB073363
  • Sequence Identity:
  • Total samples: 3
  • soil counts: 1
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
38691Risk group (German classification)
1204551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus kobensis gene for 16S rRNA, partial sequenceAB0733631503ena59841
20218Paenibacillus kobensis DNA for 16S rRNAD784711436ena59841
20218Paenibacillus kobensis gene for 16S rRNA, partial sequence, strain: NBRC 15729AB6809521478ena59841

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus kobensis NBRC 157291220566.3wgspatric1220566
67770Paenibacillus kobensis NBRC 15729GCA_004000825contigncbi1220566

GC content

  • @ref: 3869
  • GC-content: 51
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.407no
gram-positiveyes85.352no
anaerobicno99.274no
aerobicyes89.897no
halophileno97.352no
spore-formingyes95.671no
glucose-utilyes92.118no
flagellatedyes78.2no
thermophileno99.006no
glucose-fermentno88.363no

External links

@ref: 3869

culture collection no.: DSM 10249, IFO 15729, NBRC 15729, JCM 12164, ATCC 51900, CCM 4537, CIP 104576, HSCC 488, LMG 18049, NRRL B-23246

straininfo link

  • @ref: 80743
  • straininfo: 10547

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8590679Bacillus curdlanolyticus sp. nov. and Bacillus kobensis sp. nov., which hydrolyze resistant curdlan.Kanzawa Y, Harada A, Takeuchi M, Yokota A, Harada TInt J Syst Bacteriol10.1099/00207713-45-3-5151995Aerobiosis, Bacillus/*classification/genetics/metabolism, Bacterial Proteins/chemistry, Base Composition, Carbohydrate Metabolism, Culture Media, DNA, Bacterial/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/chemistry, Glucans/*metabolism, Nucleic Acid Hybridization, Polysaccharides, Bacterial/*metabolism, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, *beta-GlucansMetabolism
Phylogeny12361272Paenibacillus glycanilyticus sp. nov., a novel species that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune.Dasman, Kajiyama S, Kawasaki H, Yagi M, Seki T, Fukusaki E, Kobayashi AInt J Syst Evol Microbiol10.1099/00207713-52-5-16692002Bacillus/*classification/genetics/isolation & purification/metabolism, Base Composition, Base Sequence, Biodegradation, Environmental, Cyanobacteria/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Polysaccharides, Bacterial/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3869Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10249)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10249
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41228Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16499
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80743Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10547.1StrainInfo: A central database for resolving microbial strain identifiers
120455Curators of the CIPCollection of Institut Pasteur (CIP 104576)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104576