Strain identifier

BacDive ID: 8581

Type strain: Yes

Species: Mycobacterium vulneris

Strain Designation: NLA 000700772, NLA000700772

Strain history: CIP <- 2008, RIVM <- J. Van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000700772

NCBI tax ID(s): 547163 (species)

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

@ref: 15915

BacDive-ID: 8581

DSM-Number: 45247

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped

description: Mycobacterium vulneris NLA 000700772 is a microaerophile, mesophilic, rod-shaped bacterium that was isolated from human, infected wound after dogbite.

NCBI tax id

  • NCBI tax id: 547163
  • Matching level: species

strain history

@refhistory
15915<- J. van Ingen, National Institute for Public Health and the Environment; NLA 000700772 <- K. Koesters
67770CIP 109859 <-- J. van Ingen NLA000700772.
123894CIP <- 2008, RIVM <- J. Van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000700772

doi: 10.13145/bacdive8581.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium vulneris
  • full scientific name: Mycobacterium vulneris van Ingen et al. 2009
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium vulneris

@ref: 15915

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium vulneris

full scientific name: Mycobacterium vulneris van Ingen et al. 2009 emend. Nouioui et al. 2018

strain designation: NLA 000700772, NLA000700772

type strain: yes

Morphology

cell morphology

@refcell shapemotility
29220rod-shaped
123894no

colony morphology

  • @ref: 61691
  • incubation period: 3-5 days

pigmentation

  • @ref: 29220
  • production: yes

multimedia

  • @ref: 15915
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45247.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15915MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
37862MEDIUM 55 - for Mycobacteriumyes
123894CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55
123894CIP Medium 750yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=750

culture temp

@refgrowthtypetemperature
15915positivegrowth37
29220positivegrowth25-36
29220positiveoptimum30.5
37862positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 61691
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 29220
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12389417632nitrate-reduction
12389416301nitrite-reduction

metabolite production

  • @ref: 123894
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29220catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
123894oxidase-
123894catalase+1.11.1.6
123894urease-3.5.1.5
68382alpha-chymotrypsin-3.4.21.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123894--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
15915human, infected wound after dogbiteLimburg Province, VenloNetherlandsNLDEurope
61691Human wound,42-yr-old woman,dog bite,legLimburgNetherlandsNLDEurope2007
67770Human, infected wound after dogbite, a left lower legLimburgNetherlandsNLDEurope
123894Human, Infected wound after dogbite, left lower legLimburgNetherlandsNLDEurope2007

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host#Mammals#Canidae (Dog)
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_402&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: LT718448
  • Sequence Identity:
  • Total samples: 24078
  • soil counts: 12779
  • aquatic counts: 4789
  • animal counts: 3677
  • plant counts: 2833

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159152Risk group (German classification)
1238941Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15915Mycobacterium vulneris partial 16S rRNA gene, strain DSM 45247LT7184481508nuccore547163
67770Mycobacterium vulneris strain NLA000700772 16S ribosomal RNA gene, complete sequenceEU8340551471nuccore547163

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium vulneris strain DSM 45247547163.12wgspatric547163
66792Mycobacterium vulneris strain DSM 45247547163.3wgspatric547163
66792Mycobacterium vulneris DSM 452472619619212draftimg547163
66792Mycolicibacterium vulneris DSM 452472867085808draftimg547163
67770Mycolicibacterium vulneris DSM 45247GCA_000612885contigncbi547163
67770Mycolicibacterium vulneris DSM 45247GCA_002104765contigncbi547163

GC content

  • @ref: 67770
  • GC-content: 66.8
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes88.218no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.505yes
69480spore-formingspore-formingAbility to form endo- or exosporesno63.235yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.084no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5no
69480flagellatedmotile2+Ability to perform flagellated movementno86.5no

External links

@ref: 15915

culture collection no.: DSM 45247, CIP 109859, CCUG 58459, JCM 18115

straininfo link

  • @ref: 77965
  • straininfo: 364160

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19620376Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov.van Ingen J, Boeree MJ, Kosters K, Wieland A, Tortoli E, Dekhuijzen PN, van Soolingen DInt J Syst Evol Microbiol10.1099/ijs.0.008854-02009Antitubercular Agents/pharmacology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Catalase/metabolism, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Humans, Hydroxylamine/pharmacology, Lymph Nodes/*microbiology, Molecular Sequence Data, Mycobacterium Infections/*microbiology, Mycobacterium avium Complex/*classification/*genetics/isolation & purification/physiology, Mycolic Acids/analysis, Oleic Acid/pharmacology, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Urease/metabolismMetabolism
Genetics24812218Draft Genome Sequence of Mycobacterium vulneris DSM 45247T.Croce O, Robert C, Raoult D, Drancourt MGenome Announc10.1128/genomeA.00370-142014

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15915Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45247)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45247
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
29220Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2564128776041
37862Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7651
61691Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58459)https://www.ccug.se/strain?id=58459
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
77965Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364160.1StrainInfo: A central database for resolving microbial strain identifiers
123894Curators of the CIPCollection of Institut Pasteur (CIP 109859)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109859