Strain identifier

BacDive ID: 11552

Type strain: Yes

Species: Paenibacillus borealis

Strain Designation: KK19, KK19T

Strain history: CIP <- 2001, S. Elo, Helsinki Univ., Helsinki, Finland: strain KK19T

NCBI tax ID(s): 160799 (species)

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General

@ref: 4962

BacDive-ID: 11552

DSM-Number: 13188

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

description: Paenibacillus borealis KK19 is an aerobe, spore-forming, motile bacterium that was isolated from norway spruce forest humus.

NCBI tax id

  • NCBI tax id: 160799
  • Matching level: species

strain history

@refhistory
4962<- S. Elo, Univ. Helsinki
396462001, S. Elo, Univ. Helsinki, Finlande: strain KK19T
67771<- CCUG <- S Elo, Univ. Helsinki, Finland
116842CIP <- 2001, S. Elo, Helsinki Univ., Helsinki, Finland: strain KK19T

doi: 10.13145/bacdive11552.20240916.9.1

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 borealis
  • full scientific name: Paenibacillus borealis Elo et al. 2001

@ref: 4962

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus borealis

full scientific name: Paenibacillus borealis Elo et al. 2001

strain designation: KK19, KK19T

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedyes
67771negative
116842rod-shapedyespositive

colony morphology

  • @ref: 116842

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4962NUTRIENT 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
39646MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116842CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
4962positivegrowth30
39646positivegrowth30
55686positivegrowth28
67771positivegrowth28
116842positivegrowth22-45
116842nogrowth10

culture pH

  • @ref: 116842
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55686aerobe
67771facultative anaerobe
116842facultative anaerobe

spore formation

@refspore formationconfidence
69480yes92.706
69481yes100

halophily

@refsaltgrowthtested relationconcentration
116842NaClpositivegrowth0-4 %
116842NaClnogrowth6 %
116842NaClnogrowth8 %
116842NaClnogrowth10 %

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
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin+builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
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-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
116842citrate-carbon source16947
116842esculin+hydrolysis4853
116842hippurate+hydrolysis606565
116842nitrate+reduction17632
116842nitrite+reduction16301
116842nitrate+respiration17632

metabolite production

  • @ref: 116842
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11684215688acetoin+
11684217234glucose+

enzymes

@refvalueactivityec
116842oxidase+
116842beta-galactosidase+3.2.1.23
116842alcohol dehydrogenase-1.1.1.1
116842gelatinase+
116842amylase-
116842DNase+
116842caseinase+3.4.21.50
116842catalase+1.11.1.6
116842tween esterase-
116842gamma-glutamyltransferase-2.3.2.2
116842lecithinase+
116842lipase+
116842lysine decarboxylase-4.1.1.18
116842ornithine decarboxylase-4.1.1.17
116842urease-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
116842-+++-+-+-+++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116842+--+++/----++++/-----++--++++++++++++++++-++------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116842+++++-++++++++-+++++-++--------+++++-------------++--+-+---++-+--+---------+----+-------+++---+-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4962norway spruce forest humusKerimäkiFinlandFINEurope
55686Spruce humusFinlandFINEurope
67771From acid humus in norway spruce forestKerimakiFinlandFINEurope
116842Environment, Spruce forest humusFinlandFINEurope1992

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Host#Plants#Tree

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49621Risk group (German classification)
1168421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Paenibacillus borealis 16S rRNA gene, isolate KK19
  • accession: AJ011322
  • length: 1540
  • database: nuccore
  • NCBI tax ID: 160799

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus borealis DSM 13188GCA_000758665completencbi160799
66792Paenibacillus borealis DSM 13188160799.4completepatric160799
66792Paenibacillus borealis DSM 131882630968594completeimg160799

GC content

  • @ref: 67771
  • GC-content: 53.6

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes61.049yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.157no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no54.961no
69480spore-formingspore-formingAbility to form endo- or exosporesyes92.706no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.786yes
69480flagellatedmotile2+Ability to perform flagellated movementyes85.54no

External links

@ref: 4962

culture collection no.: DSM 13188, CCUG 43137, KCTC 3805, CIP 107056

straininfo link

  • @ref: 80780
  • straininfo: 49430

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321100Paenibacillus borealis sp. nov., a nitrogen-fixing species isolated from spruce forest humus in Finland.Elo S, Suominen I, Kampfer P, Juhanoja J, Salkinoja-Salonen M, Haahtela KInt J Syst Evol Microbiol10.1099/00207713-51-2-5352001Aniline Compounds, Bacterial Typing Techniques, Fatty Acids/analysis, Gram-Positive Endospore-Forming Bacteria/*classification/genetics/growth & development/ultrastructure, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Terminology as Topic, *TreesGenetics
Phylogeny20601486Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.Jin HJ, Zhou YG, Liu HC, Chen SFInt J Syst Evol Microbiol10.1099/ijs.0.025056-02010Amino Acids/analysis, Base Composition, Begoniaceae/*microbiology, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, Paenibacillus/*classification/*isolation & purification/physiology, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22791017Paenibacillus taohuashanense sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of the root of Caragana kansuensis Pojark.Xie JB, Zhang LH, Zhou YG, Liu HC, Chen SFAntonie Van Leeuwenhoek10.1007/s10482-012-9773-42012Bacterial Typing Techniques, Base Composition, Caragana/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, Paenibacillus/classification/genetics/*isolation & purification/*metabolism, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny28699855Paenibacillus tritici sp. nov., isolated from wheat roots.Menendez E, Flores-Felix JD, Mulas R, Andres FG, Fernandez-Pascual M, Peix A, Velazquez EInt J Syst Evol Microbiol10.1099/ijsem.0.0019492017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/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
Phylogeny28950930Paenibacillus albidus sp. nov., isolated from grassland soil.Zhuang J, Xin D, Zhang YQ, Guo J, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0023562017Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29971704Paenibacillus bryophyllum sp. nov., a nitrogen-fixing species isolated from Bryophyllum pinnatum.Liu L, Yuan T, Yang F, Liu Z, Yang M, Peng G, Tan ZAntonie Van Leeuwenhoek10.1007/s10482-018-1117-62018Base Composition, DNA Fingerprinting, Enzyme Assays, Fatty Acids/biosynthesis, Gene Expression, Kalanchoe/*microbiology, Kinetics, Nitrogen Fixation/*genetics, Nitrogenase/*genetics/metabolism, Paenibacillus/classification/*genetics/isolation & purification/metabolism, Phospholipids/biosynthesis, *Phylogeny, Plant Leaves/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Terpenes/metabolismEnzymology
Phylogeny34908521Paenibacillus tianjinensis sp. nov., isolated from corridor air.Liu H, Lu L, Wang S, Yu M, Cao X, Tang S, Bai H, Ma S, Liu R, Liu R, Jiang X, Yao S, Shao JInt J Syst Evol Microbiol10.1099/ijsem.0.0051582021*Air Microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Paenibacillus/classification/isolation & purification, Phospholipids/*chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34993761Paenibacillus piscarius sp. nov., a novel nitrogen-fixing species isolated from the gut of the armored catfish Parotocinclus maculicauda.da Silva MBF, Lemos EA, Vollu RE, Abreu F, Rosado AS, Seldin LAntonie Van Leeuwenhoek10.1007/s10482-021-01694-52022Animals, *Catfishes, DNA, Bacterial/genetics, Nitrogen, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics
Metabolism35947916Functional characterization of a novel GH94 glycoside phosphorylase, 3-O-beta-d-glucopyranosyl beta-d-glucuronide phosphorylase, and implication of the metabolic pathway of acidic carbohydrates in Paenibacillus borealis.Isono N, Mizutani E, Hayashida H, Katsuzaki H, Saburi WBiochem Biophys Res Commun10.1016/j.bbrc.2022.07.0982022Glucosyltransferases/metabolism, Glucuronic Acid, *Glucuronides, *Glycoside Hydrolases/chemistry, Glycosides/metabolism, Metabolic Networks and Pathways, Paenibacillus, Phosphorylases/chemistry/genetics/metabolism, Substrate Specificity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4962Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13188)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13188
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
39646Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19254
55686Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43137)https://www.ccug.se/strain?id=43137
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
80780Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49430.1StrainInfo: A central database for resolving microbial strain identifiers
116842Curators of the CIPCollection of Institut Pasteur (CIP 107056)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107056