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BacDive ID 24286
Type strain
Culture col. no. DSM 27954 CCUG 53270 JCM 18268
NCBI tax ID(s) 1133364
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 11 (current version):
version 11 (current version)

General

@ref: 20710

BacDive-ID: 24286

DSM-Number: 27954

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Paenibacillus vulneris DSM 27954 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from necrotic wound of a 35-year-old man.

NCBI tax id

  • NCBI tax id: 1133364
  • Matching level: species

strain history

@refhistory
20710DSMZ <- JCM <- CCUG 53270 <- K. Öystese, Univ. Hospital, Tromsø, Norway
67770JCM <-- CCUG 53270 <-- K. Öystese; Univ. Hosp. of Tromsö, Norway.

doi: 10.13145/bacdive24286.20260601.11

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 vulneris
  • full scientific name: Paenibacillus vulneris Glaeser et al. 2013

@ref: 20710

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus vulneris

full scientific name: Paenibacillus vulneris Glaeser et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
30654positive2.5 µm0.9 µmno
125439yes91.725

pigmentation

  • @ref: 30654
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20710TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
20710COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperature
20710positivegrowth30
30654positivegrowth15-50
30654positiveoptimum30
59853positivegrowth37
67770positivegrowth37

culture pH

@refabilitytypepHPH range
30654positivegrowth5.5-11.5alkaliphile
30654positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30654aerobe
59853aerobe
125439aerobe94.243

spore formation

@refspore formationconfidence
30654yes
125439yes96.525

halophily

@refsaltgrowthtested relationconcentration
30654NaClpositivegrowth0-2 %
30654NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3065422599arabinose+carbon source
3065417057cellobiose+carbon source
3065428757fructose+carbon source
3065428260galactose+carbon source
3065424265gluconate+carbon source
3065417234glucose+carbon source
3065425115malate+carbon source
3065417306maltose+carbon source
3065429864mannitol+carbon source
3065437684mannose+carbon source
30654506227N-acetylglucosamine+carbon source
3065415361pyruvate+carbon source
3065426546rhamnose+carbon source
3065417814salicin+carbon source
3065430911sorbitol+carbon source
3065417992sucrose+carbon source
3065427082trehalose+carbon source
3065418222xylose+carbon source
683710Potassium 5-ketogluconate-builds acid from
6837132528turanose+builds acid from
6837128087glycogen-builds acid from
6837117151xylitol-builds acid from
6837128066gentiobiose+builds acid from
6837128017starch-builds acid from
683714853esculin+builds acid from
6837127613amygdalin+builds acid from
6837118305arbutin+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837162345L-rhamnose-builds acid from
6837116813galactitol-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
683710Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
30654catalase+1.11.1.6
30654cytochrome oxidase+1.9.3.1
30654urease+3.5.1.5
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
59853+-------------------+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
59853-+--+++--++++----++--++++++++++++--+---+++--+-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
20710necrotic wound of a 35-year-old manHomo sapiensTromsøNorwayNOREurope
59853Human necrotic wound,35-yr-old man,ankle fractureHomo sapiensTromsöNorwayNOREurope2006-08-01
67770Necrotic wound of a 35-year-old man in TromsøHomo sapiensNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body-Site#Other#Wound
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_8088.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_3732;97_4589;98_5891;99_8088&stattab=map
  • Last taxonomy: Paenibacillus vulneris
  • 16S sequence: HE649498
  • Sequence Identity:
  • Total samples: 107
  • soil counts: 82
  • aquatic counts: 12
  • animal counts: 8
  • plant counts: 5

Interaction and safety

risk assessment

  • @ref: 20710
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionassembly levelINSDC accessionNCBI tax IDscore
124043ASM4267914v1 assembly for Paenibacillus vulneris CCUG 53270scaffoldGCA_042679145113336463.68
124043ASM3954318v1 assembly for Paenibacillus vulneris JCM 18268scaffoldGCA_039543185113336464.08
124043ASM4266072v1 assembly for Paenibacillus vulneris JCM 18268contigGCA_042660725113336463.91

16S sequences

  • @ref: 20710
  • description: Paenibacillus vulneris partial 16S rRNA gene, type strain CCUG 53270T
  • accession: HE649498
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 1133364

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetgram_stainReaction to gram-stainingvariable77.299
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe94.243
125439BacteriaNetmotilityAbility to perform movementyes91.725
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.525

Literature

@ref: 20710

culture collection no.: DSM 27954, CCUG 53270, JCM 18268

straininfo link

  • @ref: 126262
  • straininfo: 303305

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22581904Paenibacillus vulneris sp. nov., isolated from a necrotic wound.Glaeser SP, Falsen E, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.041210-02012Adult, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Humans, Male, Molecular Sequence Data, Necrosis/microbiology, Norway, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analysis, Vitamin K 2/analogs & derivatives/analysis, Wounds and Injuries/*microbiologyPathogenicity
Phylogeny26843192Paenibacillus periandrae sp. nov., isolated from nodules of Periandra mediterranea.Menendez E, Ramirez-Bahena MH, Carro L, Fernandez-Pascual M, Peter Klenk H, Velazquez E, Mateos PF, Peix A, Rita Scotti MInt J Syst Evol Microbiol10.1099/ijsem.0.0009532016Bacterial Typing Techniques, Base Composition, Brazil, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fabaceae/*microbiology, Fatty Acids/chemistry, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28875915Paenibacillus yunnanensis sp. nov., isolated from Pu'er tea.Niu L, Tang T, Ma Z, Song L, Zhang K, Chen Y, Hua Z, Hu X, Zhao MInt J Syst Evol Microbiol10.1099/ijsem.0.0004962015
Phylogeny29235981Paenibacillus limicola sp. nov., isolated from tidal flat sediment.Nahar S, Cha CJInt J Syst Evol Microbiol10.1099/ijsem.0.0025222017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Paenibacillus/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29701575Paenibacillus esterisolvens sp. nov., isolated from soil.Zhao ZL, Ming H, Ji WL, Khieu TN, Chu-Ky S, Cheng LJ, Meng XL, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0027542018Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Glycolipids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, VietnamTranscriptome
30042576Microbial occurrence and antibiotic resistance in ready-to-go food items.Cole ML, Singh OV.J Food Sci Technol10.1007/s13197-018-3180-42018Microorganisms, Antibiotic Resistance, Foodborne pathogens, Multiple Antibiotic Resistance, Ready-to-go Food
Phylogeny31661046Paenibacillus piri sp. nov., isolated from urban soil.Trinh NH, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0038112020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics41195570Genomic and Metabolic Characterization of a Potentially Novel Paenibacillus Species Isolated as a Laboratory Contaminant Growing on Medium Supporting Cotton Tissue Culture.Topcu I, Parunandi SS, Gregory TA, Campbell LM, Rathore K, Antony-Babu S.Microbiologyopen10.1002/mbo3.701072025Taxonomy, Metabolites, New species, Plant tissue culture, Genome sequence, Paenibacillus Sp, Gossypium, Genome, Bacterial, Paenibacillus

Reference

@idauthorstitledoi/urlcataloguepubmedID_cross_reference
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
20710Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27954Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27954)
2698510.1099/ijs.0.041210-022581904
30654Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604126985
59853Curators of the CCUGhttps://www.ccug.se/strain?id=53270Culture Collection University of Gothenburg (CCUG) (CCUG 53270)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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/
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. ReimerStrainInfo—the central database for linked microbial strain identifiers10.1093/database/baaf059

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