Strain identifier

BacDive ID: 11561

Type strain: Yes

Species: Paenibacillus daejeonensis

Strain Designation: AP-20

Strain history: CIP <- 2003, JCM <- 2001, Lee, strain AP-20

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5955

BacDive-ID: 11561

DSM-Number: 15491

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

description: Paenibacillus daejeonensis AP-20 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1122917strain
135193species

strain history

@refhistory
5955<- K. S. Bae, Korea Research Inst. Bioscence and Biotechnol.; AP-20
67770J.-S. Lee AP-20.
67771<- JS Lee, KRIBB
118844CIP <- 2003, JCM <- 2001, Lee, strain AP-20

doi: 10.13145/bacdive11561.20230509.8.1

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 daejeonensis
  • full scientific name: Paenibacillus daejeonensis Lee et al. 2002

@ref: 5955

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus daejeonensis

full scientific name: Paenibacillus daejeonensis Lee et al. 2002

strain designation: AP-20

type strain: yes

Morphology

cell morphology

@refcell shapemotilityflagellum arrangementgram stainconfidence
67771rod-shapedyesperitrichous
67771variable
69480yes98.26
69480positive100
118844rod-shapedyespositive

colony morphology

  • @ref: 118844

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5955TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
38232MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118844CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5955positivegrowth30mesophilic
38232positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
118844positivegrowth25-37mesophilic
118844nogrowth10psychrophilic
118844nogrowth22psychrophilic
118844nogrowth45thermophilic

culture pH

  • @ref: 118844
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
118844obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
118844NaClpositivegrowth2 %
118844NaClnogrowth0 %
118844NaClnogrowth4 %
118844NaClnogrowth6 %
118844NaClnogrowth8 %
118844NaClnogrowth10 %

observation

@refobservation
67770quinones: MK-7
67771quinones: 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
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118844citrate-carbon source16947
118844esculin+hydrolysis4853
118844hippurate+hydrolysis606565
118844nitrate-reduction17632
118844nitrite-reduction16301

metabolite production

  • @ref: 118844
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11884415688acetoin-
11884417234glucose-

enzymes

@refvalueactivityec
118844oxidase+
118844beta-galactosidase+3.2.1.23
118844alcohol dehydrogenase-1.1.1.1
118844gelatinase-
118844amylase+
118844DNase-
118844caseinase-3.4.21.50
118844catalase+1.11.1.6
118844tween esterase-
118844gamma-glutamyltransferase-2.3.2.2
118844lecithinase-
118844lipase-
118844lysine decarboxylase-4.1.1.18
118844ornithine decarboxylase-4.1.1.17
118844tryptophan deaminase-
118844urease-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
118844--++-+-----+-+--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118844---+/-----+/-+/-----+/---+/----+/---+/-+/-+/-+/-+/-+/-+/-+/---+/-+/-+/--+/-+/----+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118844--++--+++++++++++++---+++------+--++------------------++---+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5955soilKorea, Daejeon CityRepublic of KoreaKORAsia
67770SoilDaejeonRepublic of KoreaKORAsia
67771From soilDaejeonRepublic of KoreaKORAsia
118844Environment, SoilDaejeonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_122705.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_7719;97_9270;98_82527;99_122705&stattab=map
  • Last taxonomy: Paenibacillus daejeonensis subclade
  • 16S sequence: AF290916
  • Sequence Identity:
  • Total samples: 14
  • soil counts: 5
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59551Risk group (German classification)
1188441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Paenibacillus daejeonensis strain AP-20 16S ribosomal RNA gene, partial sequence
  • accession: AF290916
  • length: 1465
  • database: ena
  • NCBI tax ID: 135193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus daejeonensis DSM 154911122917.3wgspatric1122917
66792Paenibacillus daejeonensis DSM 154912519103188draftimg1122917
67770Paenibacillus daejeonensis DSM 15491GCA_000378385scaffoldncbi1122917

GC content

@refGC-contentmethod
6777053high performance liquid chromatography (HPLC)
6777153.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.129yes
flagellatedyes87.123yes
gram-positiveyes78.153yes
anaerobicno98.965no
aerobicyes91.629yes
halophileno81.034no
spore-formingyes92.686no
glucose-utilyes92.144no
glucose-fermentno88.718no
thermophileno99.904yes

External links

@ref: 5955

culture collection no.: DSM 15491, JCM 11236, KCTC 3745, BCRC 17345, CIP 107805

straininfo link

  • @ref: 80789
  • straininfo: 97892

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508876Paenibacillus daejeonensis sp. nov., a novel alkaliphilic bacterium from soil.Lee JS, Lee KC, Chang YH, Hong SG, Oh HW, Pyun YR, Bae KSInt J Syst Evol Microbiol10.1099/00207713-52-6-21072002Bacillus/*classification/genetics/isolation & purification, Bacteria, Aerobic/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as TopicEnzymology
Phylogeny18768608Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China.Wang M, Yang M, Zhou G, Luo X, Zhang L, Tang Y, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.65445-02008Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Silicon Dioxide, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny27503428Paenibacillus hispanicus sp. nov. isolated from Triticum aestivum roots.Menendez E, Carro L, Tejedor C, Fernandez-Pascual M, Martinez-Molina E, Peix A, Velazquez EInt J Syst Evol Microbiol10.1099/ijsem.0.0014012016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Triticum/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5955Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15491)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15491
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
38232Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5280
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
80789Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97892.1StrainInfo: A central database for resolving microbial strain identifiers
118844Curators of the CIPCollection of Institut Pasteur (CIP 107805)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107805