Strain identifier

BacDive ID: 22902

Type strain: Yes

Species: Arcanobacterium phocisimile

Strain Designation: 2698

Strain history: CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 2698

NCBI tax ID(s): 1302235 (species)

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General

@ref: 19334

BacDive-ID: 22902

DSM-Number: 26142

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped, animal pathogen

description: Arcanobacterium phocisimile 2698 is an anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from vaginal swab of a harbour seal.

NCBI tax id

  • NCBI tax id: 1302235
  • Matching level: species

strain history

@refhistory
376052012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 2698
19334<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; strain 2698
121804CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 2698

doi: 10.13145/bacdive22902.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Arcanobacterium
  • species: Arcanobacterium phocisimile
  • full scientific name: Arcanobacterium phocisimile Hijazin et al. 2013

@ref: 19334

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Arcanobacterium

species: Arcanobacterium phocisimile

full scientific name: Arcanobacterium phocisimile Hijazin et al. 2013

strain designation: 2698

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30836positive1.5 µm0.5 µmrod-shapedno
69480no92.071
69480positive100
121804positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37605MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
19334PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yesName: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled waterhttps://mediadive.dsmz.de/medium/104
19334COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
121804CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
19334positivegrowth37mesophilic
37605positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19334anaerobe
19334microaerophile
30836microaerophile
69480anaerobe98.601

spore formation

@refspore formationconfidence
30836no
69481no99
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3083628087glycogen+carbon source
3083617716lactose+carbon source
3083633942ribose+carbon source
3083617992sucrose+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30836alkaline phosphatase+3.1.3.1
30836catalase+1.11.1.6
30836pyrazinamidase+3.5.1.B15
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
19334---+-+----++-----+/-+--+/--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
19334vaginal swab of a harbour sealNorth SeaGermanyDEUEurope
121804Harbour sealsNorth SeaGermanyDEUEurope2004

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host#Mammals
#Host Body-Site#Urogenital tract#Vagina

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
19334yes, in single cases1Risk group (German classification)
1218041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19334
  • description: Arcanobacterium phocisimile partial 16S rRNA gene, type strain 2698T
  • accession: FN562996
  • length: 1337
  • database: ena
  • NCBI tax ID: 1302235

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcanobacterium phocisimile DSM 26142GCA_016904675completencbi1302235
66792Arcanobacterium phocisimile strain DSM 261421302235.3completepatric1302235

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedno97.115no
gram-positiveyes94.589yes
anaerobicno87.775no
aerobicno94.757yes
halophileno84.915no
spore-formingno95.941yes
thermophileno95.936yes
glucose-utilyes86.42no
motileno92.417yes
glucose-fermentyes80.31no

External links

@ref: 19334

culture collection no.: DSM 26142, CCM 8430, LMG 27073, CIP 110543

straininfo link

  • @ref: 87150
  • straininfo: 380918

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23041640Arcanobacterium phocisimile sp. nov., isolated from harbour seals.Hijazin M, Sammra O, Ulbegi-Mohyla H, Nagib S, Alber J, Lammler C, Kampfer P, Glaeser SP, Busse HJ, Kassmannhuber J, Prenger-Berninghoff E, Weiss R, Siebert U, Hassan AA, Abdulmawjood A, Zschock MInt J Syst Evol Microbiol10.1099/ijs.0.045591-02012Animals, Arcanobacterium/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phoca/*microbiology, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26373578Arcanobacterium pinnipediorum sp. nov., isolated from a harbour seal.Sammra O, Balbutskaya A, Ulbegi-Mohyla H, Nagib S, Lammler C, Kampfer P, Glaeser SP, Golke J, Busse HJ, Prenger-Berninghoff E, Siebert U, Abdulmawjood A, Klein GInt J Syst Evol Microbiol10.1099/ijsem.0.0006092015Animals, Arcanobacterium/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, North Sea, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phoca/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics34264110Complete Genome Sequence of Arcanobacterium phocisimile Strain DSM 26142, Isolated from a Harbor Seal.Borowiak M, Alssahen M, Malorny B, Lammler C, Siebert U, Plotz M, Abdulmawjood AMicrobiol Resour Announc10.1128/MRA.00215-212021Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19334Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26142)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26142
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
30836Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2716628776041
37605Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8414
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)
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87150Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID380918.1StrainInfo: A central database for resolving microbial strain identifiers
121804Curators of the CIPCollection of Institut Pasteur (CIP 110543)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110543