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)

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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/bacdive8581.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: 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

@refgrowthtypetemperaturerange
15915positivegrowth37mesophilic
29220positivegrowth25-36mesophilic
29220positiveoptimum30.5mesophilic
37862positivegrowth37mesophilic
67770positivegrowth37mesophilic

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

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 45247LT7184481508ena547163
67770Mycobacterium vulneris strain NLA000700772 16S ribosomal RNA gene, complete sequenceEU8340551471ena547163

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

traitpredictionconfidencetraining_data
gram-positiveyes87.072no
anaerobicno99.014no
halophileno93.84no
spore-formingno88.071yes
glucose-utilyes68.473no
thermophileno97.929yes
aerobicyes91.495no
motileno93.825no
flagellatedno98.901no
glucose-fermentno92.331no

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
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