Strain identifier

BacDive ID: 22929

Type strain: Yes

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)

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

@refhistory
19185<- JCM <- J.-W. Bae; TW25
67770J.-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

@refgrowthtypetemperaturerange
19185positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19185dead ark clamGang-jin BayRepublic of KoreaKORAsia
67770Dead ark clam collected at Gang-jin Bay in the Southern coastal region of the Korean peninsula

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinibacillus scapharcae TW25981383.3wgspatric981383
66792Ornithinibacillus scapharcae TW252513237297draftimg981383
67770Ornithinibacillus scapharcae TW25GCA_000190475contigncbi981383

GC content

@refGC-contentmethod
1918536.7
6777036.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.68no
flagellatedyes73.359no
gram-positiveyes89.627no
anaerobicno99.048no
halophileyes80.302no
spore-formingyes94.293no
thermophileno98.005yes
glucose-utilyes87.522no
aerobicyes92.368no
glucose-fermentno90.349no

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

@idauthorscataloguedoi/urltitle
19185Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26677)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26677
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
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/
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
87177Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406027.1StrainInfo: A central database for resolving microbial strain identifiers