Strain identifier
BacDive ID: 24286
Type strain:
Species: Paenibacillus vulneris
Strain history: CCUG 53270 <-- K. Öystese; Univ. Hosp. of Tromsö, Norway.
NCBI tax ID(s): 1133364 (species)
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
@ref | history |
---|---|
20710 | <- JCM <- CCUG 53270 <- K. Öystese, Univ. Hospital, Tromsø, Norway |
67770 | CCUG 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
@ref | name | growth | link | composition |
---|---|---|---|---|
20710 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
20710 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20710 | positive | growth | 30 | mesophilic |
30654 | positive | growth | 15-50 | |
30654 | positive | optimum | 30 | mesophilic |
59853 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30654 | positive | growth | 5.5-11.5 | alkaliphile |
30654 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30654 | aerobe |
59853 | aerobe |
spore formation
- @ref: 30654
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30654 | NaCl | positive | growth | 0-2 % |
30654 | NaCl | positive | optimum | 1 % |
observation
- @ref: 67770
- observation: quinones: MK-7, MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30654 | 22599 | arabinose | + | carbon source |
30654 | 17057 | cellobiose | + | carbon source |
30654 | 28757 | fructose | + | carbon source |
30654 | 28260 | galactose | + | carbon source |
30654 | 24265 | gluconate | + | carbon source |
30654 | 17234 | glucose | + | carbon source |
30654 | 25115 | malate | + | carbon source |
30654 | 17306 | maltose | + | carbon source |
30654 | 29864 | mannitol | + | carbon source |
30654 | 37684 | mannose | + | carbon source |
30654 | 506227 | N-acetylglucosamine | + | carbon source |
30654 | 15361 | pyruvate | + | carbon source |
30654 | 26546 | rhamnose | + | carbon source |
30654 | 17814 | salicin | + | carbon source |
30654 | 30911 | sorbitol | + | carbon source |
30654 | 17992 | sucrose | + | carbon source |
30654 | 27082 | trehalose | + | carbon source |
30654 | 18222 | xylose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | + | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | + | builds acid from |
68371 | 32528 | turanose | + | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 17268 | myo-inositol | + | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30654 | catalase | + | 1.11.1.6 |
30654 | cytochrome oxidase | + | 1.9.3.1 |
30654 | urease | + | 3.5.1.5 |
68368 | cytochrome oxidase | + | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
59853 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
59853 | - | + | - | - | + | + | + | - | - | + | + | + | + | - | - | - | - | + | + | - | - | + | + | + | + | + | + | + | + | + | + | + | + | - | - | + | - | - | - | + | + | + | - | - | + | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
20710 | necrotic wound of a 35-year-old man | Tromsø | Norway | NOR | Europe | |
59853 | Human necrotic wound,35-yr-old man,ankle fracture | Tromsö | Norway | NOR | Europe | 2006-08-01 |
67770 | Necrotic wound of a 35-year-old man in Tromsø | Norway | NOR | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22581904 | Paenibacillus vulneris sp. nov., isolated from a necrotic wound. | Glaeser SP, Falsen E, Busse HJ, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.041210-0 | 2012 | Adult, 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/*microbiology | Pathogenicity |
Phylogeny | 26843192 | Paenibacillus 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 M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000953 | 2016 | Bacterial 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/chemistry | Genetics |
Phylogeny | 28875915 | Paenibacillus 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 M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000496 | 2015 | ||
Phylogeny | 29235981 | Paenibacillus limicola sp. nov., isolated from tidal flat sediment. | Nahar S, Cha CJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002522 | 2017 | Bacterial 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/chemistry | Transcriptome |
Phylogeny | 29701575 | Paenibacillus esterisolvens sp. nov., isolated from soil. | Zhao ZL, Ming H, Ji WL, Khieu TN, Chu-Ky S, Cheng LJ, Meng XL, Li WJ, Nie GX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002754 | 2018 | Bacterial 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, Vietnam | Transcriptome |
Phylogeny | 31661046 | Paenibacillus piri sp. nov., isolated from urban soil. | Trinh NH, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003811 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
20710 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27954 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27954) | |||
30654 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26985 | 28776041 | |
59853 | Curators of the CCUG | https://www.ccug.se/strain?id=53270 | Culture Collection University of Gothenburg (CCUG) (CCUG 53270) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68371 | Automatically annotated from API 50CH acid | |||||
69479 | João 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 beta | https://microbeatlas.org/ | |||
88224 | Reimer, 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 identifiers | 10.60712/SI-ID303305.1 |