Strain identifier

BacDive ID: 199

Type strain: Yes

Species: Arcanobacterium phocae

Strain Designation: M1590/94/3

Strain history: CIP <- 1998, CCUG <- 1998, DSM <- G. Foster: strain M1590/94/3

NCBI tax ID(s): 131112 (species)

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General

@ref: 3774

BacDive-ID: 199

DSM-Number: 10002

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, animal pathogen

description: Arcanobacterium phocae M1590/94/3 is an anaerobe, mesophilic animal pathogen that was isolated from lung of common seal.

NCBI tax id

  • NCBI tax id: 131112
  • Matching level: species

strain history

@refhistory
3774<- G. Foster, M1590/94/3
121800CIP <- 1998, CCUG <- 1998, DSM <- G. Foster: strain M1590/94/3

doi: 10.13145/bacdive199.20230509.8.1

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 phocae
  • full scientific name: Arcanobacterium phocae Pascual Ramos et al. 1997

@ref: 3774

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Arcanobacterium

species: Arcanobacterium phocae

full scientific name: Arcanobacterium phocae Pascual Ramos et al. 1997 emend. Nouioui et al. 2018

strain designation: M1590/94/3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.797
69480100positive
121800nopositiverod-shaped

colony morphology

  • @ref: 121800

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3774PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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 water
39346MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121800CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
121800CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137

culture temp

@refgrowthtypetemperaturerange
3774positivegrowth37mesophilic
39346positivegrowth37mesophilic
121800positivegrowth25-41
121800nogrowth10psychrophilic
121800nogrowth15psychrophilic
121800nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe96.445
121800facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
121800NaClpositivegrowth0-6 %
121800NaClnogrowth8 %
121800NaClnogrowth10 %

murein

  • @ref: 3774
  • murein short key: A11.01
  • type: A3alpha L-Lys-Gly

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2297617057cellobiose-builds acid from
2297617924D-sorbitol-builds acid from
2297665327D-xylose-builds acid from
2297628087glycogen-builds acid from
2297630849L-arabinose-builds acid from
2297662345L-rhamnose-builds acid from
2297637684mannose-builds acid from
2297616634raffinose-builds acid from
2297617814salicin-builds acid from
2297617992sucrose-builds acid from
2297627082trehalose-builds acid from
229765291gelatin-hydrolysis
22976606565hippurate-hydrolysis
2297617634D-glucose+builds acid from
2297616899D-mannitol+builds acid from
2297616988D-ribose+builds acid from
2297617754glycerol+builds acid from
2297617716lactose+builds acid from
2297617306maltose+builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
1218004853esculin-hydrolysis
121800606565hippurate+hydrolysis
12180017632nitrate+reduction
12180016301nitrite-reduction
12180017632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 121800
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
2297615688acetoinno
12180035581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
12180015688acetoin-
12180017234glucose+

enzymes

@refvalueactivityec
22976acid phosphatase+3.1.3.2
22976alkaline phosphatase+3.1.3.1
22976alpha-galactosidase+3.2.1.22
22976alpha-glucosidase+3.2.1.20
22976arginine dihydrolase-3.5.3.6
22976beta-galactosidase+3.2.1.23
22976beta-glucosidase-3.2.1.21
22976beta-glucuronidase-3.2.1.31
22976esterase lipase (C 8)+
22976leucine arylamidase+3.4.11.1
22976N-acetyl-beta-glucosaminidase+3.2.1.52
22976nitrate reductase-1.7.99.4
22976pyrazinamidase-3.5.1.B15
22976pyrrolidonyl arylamidase-3.4.19.3
22976urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
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
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
121800oxidase-
121800beta-galactosidase-3.2.1.23
121800alcohol dehydrogenase+1.1.1.1
121800gelatinase+/-
121800amylase-
121800DNase-
121800caseinase+3.4.21.50
121800catalase+1.11.1.6
121800tween esterase-
121800gamma-glutamyltransferase-2.3.2.2
121800lecithinase-
121800lipase-
121800lysine decarboxylase-4.1.1.18
121800ornithine decarboxylase-4.1.1.17
121800phenylalanine ammonia-lyase-4.3.1.24
121800protease-
121800tryptophan deaminase-
121800urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121800---+-+----++-+---+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121800+--------+/-+++--------+/----------+/--------+/----------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
3774--+/-+-+/-------------+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3774lung of common sealShetland IslesUnited KingdomGBREurope
54530Seal lung,common seal,Phoca vitulinaUnited KingdomGBREurope
121800Common seal, lung

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Canidae (Dog)
#Host Body-Site#Oral cavity and airways#Lung

taxonmaps

  • @ref: 69479
  • File name: preview.99_45345.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_28;96_49;97_25893;98_32877;99_45345&stattab=map
  • Last taxonomy: Arcanobacterium phocae
  • 16S sequence: FN562994
  • Sequence Identity:
  • Total samples: 71
  • soil counts: 1
  • aquatic counts: 13
  • animal counts: 56
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
3774yes2Risk group (German classification)
1218001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arcanobacterium phocae strain DSM 10002 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU194565528ena131112
20218Arcanobacterium phocae partial 16S rRNA gene, type strain DSM 10002TFN5629941256ena131112
20218Arcanobacterium phocae partial 16S rRNA gene, type strain DSM 10002T, clone 1FR7499601519ena131112
20218Arcanobacterium phocae partial 16S rRNA gene, type strain DSM 10002T, clone 2FR7499611519ena131112
20218Arcanobacterium phocae partial 16S rRNA gene, type strain DSM 10002T, clone 3FR7499621519ena131112

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcanobacterium phocae DSM 10002GCA_900105865chromosomencbi131112
66792Arcanobacterium phocae strain DSM 10002131112.3completepatric131112
66792Arcanobacterium phocae DSM 100022634166335draftimg131112

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.249no
gram-positiveyes93.128no
anaerobicno77.877no
halophileno84.455no
spore-formingno95.763no
glucose-utilyes86.244no
aerobicno96.372no
flagellatedno97.106no
glucose-fermentyes81.944no
thermophileno95.119yes

External links

@ref: 3774

culture collection no.: DSM 10002, CCUG 38888, LMG 18722, CIP 105740

straininfo link

  • @ref: 69882
  • straininfo: 12408

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny29519524Identification of Arcanobacterium phocae isolated from fur animals by phenotypic properties, by MALDI-TOF MS analysis and by detection of phocaelysin encoding gene phl as probable novel target.Alssahen M, Sammra O, Wickhorst JP, Hassan AA, Lammler C, Saarnisto MR, Prenger-Berninghoff E, Timke M, Becker A, Abdulmawjood AVet Microbiol10.1016/j.vetmic.2018.01.0172018Actinomycetales Infections/microbiology/*veterinary, Animals, Arcanobacterium/classification/*genetics/*isolation & purification, Bacterial Proteins/*genetics, Finland/epidemiology, Foxes/microbiology, Genotype, Mink/microbiology, *Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA/methods, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methodsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3774Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10002
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
22976A. F. Yassin,H. Hupfer,C. Siering,P. Schumann10.1099/ijs.0.020032-0Comparative chemotaxonomic and phylogenetic studies on the genus Arcanobacterium Collins et al. 1982 emend. Lehnen et al. 2006: proposal for Trueperella gen. nov. and emended description of the genus ArcanobacteriumIJSEM 61: 1265-1274 201120622055
39346Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17793
54530Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38888)https://www.ccug.se/strain?id=38888
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)
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
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
69882Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12408.1StrainInfo: A central database for resolving microbial strain identifiers
121800Curators of the CIPCollection of Institut Pasteur (CIP 105740)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105740