Strain identifier

BacDive ID: 130474

Type strain: Yes

Species: Nocardia vulneris

Strain Designation: W9851

Strain history: CCUG 62683 <-- B. A. Lasker; CDC, USA; W9851.

NCBI tax ID(s): 1141657 (species)

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General

@ref: 21692

BacDive-ID: 130474

DSM-Number: 45737

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Nocardia vulneris W9851 is a microaerophile, mesophilic bacterium that was isolated from human leg wound.

NCBI tax id

  • NCBI tax id: 1141657
  • Matching level: species

strain history

@refhistory
21692<- B. A. Lasker, CDC; W9851<- Illinois Department of Public Health <- Vista Medical Center East Lab
67770CCUG 62683 <-- B. A. Lasker; CDC, USA; W9851.

doi: 10.13145/bacdive130474.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia vulneris
  • full scientific name: Nocardia vulneris Lasker et al. 2015

@ref: 21692

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia vulneris

full scientific name: Nocardia vulneris Lasker et al. 2015

strain designation: W9851

type strain: yes

Morphology

colony morphology

  • @ref: 62881
  • incubation period: 3-5 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21692GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
21692COLUMBIA 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
62881positivegrowth37mesophilic
21692positivegrowth28mesophilic
67770positivegrowth28mesophilic
21692positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 62881
  • oxygen tolerance: microaerophile

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl), MK-9, MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
21692+--+--+++-----------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21692human leg woundIllinois, WaukeganUSAUSANorth America
62881Human leg woundIllinois,WaukeganUSAUSANorth America2009-04-23
6777054-male patient with a leg woundILUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Limb#Leg
#Host Body-Site#Other#Wound
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_5593.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_3228;99_5593&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: JN705252
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 59
  • aquatic counts: 6
  • animal counts: 29
  • plant counts: 10

Sequence information

16S sequences

  • @ref: 21692
  • description: Nocardia vulneris strain W9851 16S ribosomal RNA gene, partial sequence
  • accession: JN705252
  • length: 1441
  • database: ena
  • NCBI tax ID: 1141657

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia vulneris W98511141657.3wgspatric1141657
66792Nocardia vulneris strain NBRC 1089361141657.5wgspatric1141657
66792Nocardia vulneris W98512645727695draftimg1141657
66792Nocardia vulneris NBRC 1089362772190757draftimg1141657
67770Nocardia vulneris NBRC 108936GCA_001613425contigncbi1141657
67770Nocardia vulneris W9851GCA_000811985contigncbi1141657

GC content

@refGC-contentmethod
2169268.4high performance liquid chromatography (HPLC)
6777068.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.874no
flagellatedno97.663no
gram-positiveyes87.582no
anaerobicno99.42yes
aerobicyes89.026yes
halophileno94.609no
spore-formingyes87.914no
thermophileno99.606yes
glucose-utilyes89.832no
glucose-fermentno91.238yes

External links

@ref: 21692

culture collection no.: DSM 45737, CCUG 62683, NBRC 108936, JCM 32220

straininfo link

  • @ref: 89003
  • straininfo: 406059

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25015412Nocardia vulneris sp. nov., isolated from wounds of human patients in North America.Lasker BA, Bell M, Klenk HP, Sproer C, Schumann C, Schumann P, Brown JMAntonie Van Leeuwenhoek10.1007/s10482-014-0226-02014Aged, Aged, 80 and over, Base Composition, Canada, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Humans, Male, Middle Aged, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, United States, Vitamin K 2/analysis, Wound Infection/*microbiologyPathogenicity
Phylogeny32375925Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis.Zhou T, Wang XY, Deng DQ, Xu LH, Li XL, Guo Y, Li WH, Xie H, Zhang PL, Zhou XHInt J Syst Evol Microbiol10.1099/ijsem.0.0038562020Adult, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Humans, Mycolic Acids/chemistry, Neck, Nocardia/*classification/isolation & purification, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorstitledoi/urlcatalogue
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
21692Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45737Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45737)
62881Curators of the CCUGhttps://www.ccug.se/strain?id=62683Culture Collection University of Gothenburg (CCUG) (CCUG 62683)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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/
89003Reimer, 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-ID406059.1