Strain identifier
BacDive ID: 8581
Type strain:
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)
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
@ref | history |
---|---|
15915 | <- J. van Ingen, National Institute for Public Health and the Environment; NLA 000700772 <- K. Koesters |
67770 | CIP 109859 <-- J. van Ingen NLA000700772. |
123894 | CIP <- 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
@ref | cell shape | motility |
---|---|---|
29220 | rod-shaped | |
123894 | no |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
15915 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
37862 | MEDIUM 55 - for Mycobacterium | yes | ||
123894 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 | |
123894 | CIP Medium 750 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=750 |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
15915 | positive | growth | 37 |
29220 | positive | growth | 25-36 |
29220 | positive | optimum | 30.5 |
37862 | positive | growth | 37 |
67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 61691
- oxygen tolerance: microaerophile
spore formation
- @ref: 29220
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123894 | 17632 | nitrate | - | reduction |
123894 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 123894
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29220 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
123894 | oxidase | - | |
123894 | catalase | + | 1.11.1.6 |
123894 | urease | - | 3.5.1.5 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123894 | - | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
15915 | human, infected wound after dogbite | Limburg Province, Venlo | Netherlands | NLD | Europe | ||
61691 | Human wound,42-yr-old woman,dog bite,leg | Limburg | Netherlands | NLD | Europe | 2007 | |
67770 | Human, infected wound after dogbite, a left lower leg | Limburg | Netherlands | NLD | Europe | ||
123894 | Human, Infected wound after dogbite, left lower leg | Limburg | Netherlands | NLD | Europe | 2007 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
15915 | 2 | Risk group (German classification) |
123894 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
15915 | Mycobacterium vulneris partial 16S rRNA gene, strain DSM 45247 | LT718448 | 1508 | nuccore | 547163 |
67770 | Mycobacterium vulneris strain NLA000700772 16S ribosomal RNA gene, complete sequence | EU834055 | 1471 | nuccore | 547163 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium vulneris strain DSM 45247 | 547163.12 | wgs | patric | 547163 |
66792 | Mycobacterium vulneris strain DSM 45247 | 547163.3 | wgs | patric | 547163 |
66792 | Mycobacterium vulneris DSM 45247 | 2619619212 | draft | img | 547163 |
66792 | Mycolicibacterium vulneris DSM 45247 | 2867085808 | draft | img | 547163 |
67770 | Mycolicibacterium vulneris DSM 45247 | GCA_000612885 | contig | ncbi | 547163 |
67770 | Mycolicibacterium vulneris DSM 45247 | GCA_002104765 | contig | ncbi | 547163 |
GC content
- @ref: 67770
- GC-content: 66.8
- method: genome sequence analysis
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.218 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.505 | yes |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 63.235 | yes |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.084 | no |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.5 | no |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.5 | no |
External links
@ref: 15915
culture collection no.: DSM 45247, CIP 109859, CCUG 58459, JCM 18115
straininfo link
- @ref: 77965
- straininfo: 364160
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19620376 | Proposal 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 D | Int J Syst Evol Microbiol | 10.1099/ijs.0.008854-0 | 2009 | Antitubercular 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/metabolism | Metabolism |
Genetics | 24812218 | Draft Genome Sequence of Mycobacterium vulneris DSM 45247T. | Croce O, Robert C, Raoult D, Drancourt M | Genome Announc | 10.1128/genomeA.00370-14 | 2014 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15915 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45247) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45247 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
29220 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25641 | 28776041 | |
37862 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7651 | ||||
61691 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58459) | https://www.ccug.se/strain?id=58459 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
77965 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID364160.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123894 | Curators of the CIP | Collection of Institut Pasteur (CIP 109859) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109859 |