Strain identifier
BacDive ID: 130474
Type strain:
Species: Nocardia vulneris
Strain Designation: W9851
Strain history: CCUG 62683 <-- B. A. Lasker; CDC, USA; W9851.
NCBI tax ID(s): 1141657 (species)
General
@ref: 21692
BacDive-ID: 130474
DSM-Number: 45737
keywords: genome sequence, 16S sequence, Bacteria, microaerophile
description: Nocardia vulneris W9851 is a microaerophile bacterium that was isolated from human leg wound.
NCBI tax id
- NCBI tax id: 1141657
- Matching level: species
strain history
@ref | history |
---|---|
21692 | <- B. A. Lasker, CDC; W9851<- Illinois Department of Public Health <- Vista Medical Center East Lab |
67770 | CCUG 62683 <-- B. A. Lasker; CDC, USA; W9851. |
doi: 10.13145/bacdive130474.20240916.9.1
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
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 91.382
colony morphology
- @ref: 62881
- incubation period: 3-5 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
21692 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
21692 | 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 |
---|---|---|---|
62881 | positive | growth | 37 |
21692 | positive | growth | 28 |
67770 | positive | growth | 28 |
21692 | positive | growth | 30 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | catalase | + | 1.11.1.6 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | Control | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21692 | + | - | - | + | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
21692 | human leg wound | Illinois, Waukegan | USA | USA | North America | |
62881 | Human leg wound | Illinois,Waukegan | USA | USA | North America | 2009-04-23 |
67770 | 54-male patient with a leg wound | IL | USA | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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: nuccore
- NCBI tax ID: 1141657
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardia vulneris W9851 | 1141657.3 | wgs | patric | 1141657 |
66792 | Nocardia vulneris strain NBRC 108936 | 1141657.5 | wgs | patric | 1141657 |
66792 | Nocardia vulneris W9851 | 2645727695 | draft | img | 1141657 |
66792 | Nocardia vulneris NBRC 108936 | 2772190757 | draft | img | 1141657 |
67770 | Nocardia vulneris NBRC 108936 | GCA_001613425 | contig | ncbi | 1141657 |
67770 | Nocardia vulneris W9851 | GCA_000811985 | contig | ncbi | 1141657 |
GC content
@ref | GC-content | method |
---|---|---|
21692 | 68.4 | high performance liquid chromatography (HPLC) |
67770 | 68.1 | 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 | 91.382 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.918 | no |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 72.23 | no |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.791 | no |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.4 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 85.5 | no |
External links
@ref: 21692
culture collection no.: DSM 45737, CCUG 62683, NBRC 108936, JCM 32220
straininfo link
- @ref: 89003
- straininfo: 406059
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25015412 | Nocardia 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 JM | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0226-0 | 2014 | Aged, 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/*microbiology | Pathogenicity |
Phylogeny | 32375925 | Nocardia 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 XH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003856 | 2020 | Adult, 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/chemistry | Pathogenicity |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
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 | |
21692 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45737 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45737) | |
62881 | Curators of the CCUG | https://www.ccug.se/strain?id=62683 | Culture Collection University of Gothenburg (CCUG) (CCUG 62683) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68379 | Automatically annotated from API Coryne | |||
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/ | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
89003 | 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-ID406059.1 |