Strain identifier
BacDive ID: 22929
Type strain:
Species: Ornithinibacillus scapharcae
Strain Designation: TW25
Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW25.
NCBI tax ID(s): 1147159 (species)
General
@ref: 19185
BacDive-ID: 22929
DSM-Number: 26677
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, human pathogen
description: Ornithinibacillus scapharcae TW25 is a mesophilic human pathogen that was isolated from dead ark clam.
NCBI tax id
- NCBI tax id: 1147159
- Matching level: species
strain history
@ref | history |
---|---|
19185 | <- JCM <- J.-W. Bae; TW25 |
67770 | J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; TW25. |
doi: 10.13145/bacdive22929.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Ornithinibacillus
- species: Ornithinibacillus scapharcae
- full scientific name: Ornithinibacillus scapharcae Shin et al. 2012
@ref: 19185
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Ornithinibacillus
species: Ornithinibacillus scapharcae
full scientific name: Ornithinibacillus scapharcae Shin et al. 2012
strain designation: TW25
type strain: yes
Culture and growth conditions
culture medium
- @ref: 19185
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19185 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19185 | dead ark clam | Gang-jin Bay | Republic of Korea | KOR | Asia |
67770 | Dead ark clam collected at Gang-jin Bay in the Southern coastal region of the Korean peninsula |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Other | #Decomposing animal |
#Host | #Invertebrates (Other) | #Mollusca |
taxonmaps
- @ref: 69479
- File name: preview.99_7919.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_867;97_3435;98_5781;99_7919&stattab=map
- Last taxonomy: Ornithinibacillus scapharcae
- 16S sequence: HQ171440
- Sequence Identity:
- Total samples: 139
- soil counts: 61
- aquatic counts: 20
- animal counts: 46
- plant counts: 12
Safety information
risk assessment
- @ref: 19185
- pathogenicity human: yes, in single cases
- pathogenicity animal: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19185
- description: Ornithinibacillus scapharcae TW25 16S ribosomal RNA gene, partial sequence
- accession: HQ171440
- length: 1444
- database: ena
- NCBI tax ID: 981383
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ornithinibacillus scapharcae TW25 | 981383.3 | wgs | patric | 981383 |
66792 | Ornithinibacillus scapharcae TW25 | 2513237297 | draft | img | 981383 |
67770 | Ornithinibacillus scapharcae TW25 | GCA_000190475 | contig | ncbi | 981383 |
GC content
@ref | GC-content | method |
---|---|---|
19185 | 36.7 | |
67770 | 36.7 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 86.68 | no |
flagellated | yes | 73.359 | no |
gram-positive | yes | 89.627 | no |
anaerobic | no | 99.048 | no |
halophile | yes | 80.302 | no |
spore-forming | yes | 94.293 | no |
thermophile | no | 98.005 | yes |
glucose-util | yes | 87.522 | no |
aerobic | yes | 92.368 | no |
glucose-ferment | no | 90.349 | no |
External links
@ref: 19185
culture collection no.: DSM 26677, JCM 17314, KACC 15116
straininfo link
- @ref: 87177
- straininfo: 406027
literature
- topic: Phylogeny
- Pubmed-ID: 21952732
- title: Ornithinibacillus scapharcae sp. nov., isolated from a dead ark clam.
- authors: Shin NR, Whon TW, Kim MS, Roh SW, Jung MJ, Kim YO, Bae JW
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-011-9645-3
- year: 2011
- mesh: Aerobiosis, Amino Acids/analysis, Animals, Bacillaceae/*classification/genetics/*isolation & purification/physiology, Base Composition, Bivalvia/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hemolysin Proteins/metabolism, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
19185 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26677) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26677 | |
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 | |
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/ | ||
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 | |
87177 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406027.1 | StrainInfo: A central database for resolving microbial strain identifiers |