Strain identifier

BacDive ID: 24286

Type strain: Yes

Species: Paenibacillus vulneris

Strain history: CCUG 53270 <-- K. Öystese; Univ. Hosp. of Tromsö, Norway.

NCBI tax ID(s): 1133364 (species)

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

@ref: 20710

BacDive-ID: 24286

DSM-Number: 27954

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

description: Paenibacillus vulneris DSM 27954 is an aerobe, spore-forming, mesophilic 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
20710<- JCM <- CCUG 53270 <- K. Öystese, Univ. Hospital, Tromsø, Norway
67770CCUG 53270 <-- K. Öystese; Univ. Hosp. of Tromsö, Norway.

doi: 10.13145/bacdive24286.20230509.8.1

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 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

  • @ref: 30654
  • gram stain: positive
  • cell length: 2.5 µm
  • cell width: 0.9 µm
  • motility: no

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

@refgrowthtypetemperaturerange
20710positivegrowth30mesophilic
30654positivegrowth15-50
30654positiveoptimum30mesophilic
59853positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30654aerobe
59853aerobe

spore formation

  • @ref: 30654
  • spore formation: yes

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
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 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
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-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
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+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
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+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 typegeographic locationcountryorigin.countrycontinentsampling date
20710necrotic wound of a 35-year-old manTromsøNorwayNOREurope
59853Human necrotic wound,35-yr-old man,ankle fractureTromsöNorwayNOREurope2006-08-01
67770Necrotic wound of a 35-year-old man in TromsøNorwayNOREurope

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

Safety information

risk assessment

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

Sequence information

16S sequences

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

External links

@ref: 20710

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

straininfo link

  • @ref: 88224
  • 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
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

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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)
30654Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172698528776041
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/
88224Reimer, 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-ID303305.1