Strain identifier

BacDive ID: 3204

Type strain: Yes

Species: Corynebacterium phocae

Strain Designation: Collins 31, M408/89/1, 31

Strain history: CIP <- 1998, CCUG <- M.D. Collins, IFR, Reading, UK: strain 31

NCBI tax ID(s): 161895 (species)

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General

@ref: 11925

BacDive-ID: 3204

DSM-Number: 44612

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Corynebacterium phocae Collins 31 is a facultative anaerobe, mesophilic bacterium that was isolated from common seal Phoca vitulina.

NCBI tax id

  • NCBI tax id: 161895
  • Matching level: species

strain history

@refhistory
11925<- CCUG <- M. D. Collins, IFR Reading <- G. Foster, SAC, Inverness
67770CCUG 38205 <-- M. D. Collins 31 <-- G. Foster M408/89/1.
121801CIP <- 1998, CCUG <- M.D. Collins, IFR, Reading, UK: strain 31

doi: 10.13145/bacdive3204.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium phocae
  • full scientific name: Corynebacterium phocae Pascual et al. 1998

@ref: 11925

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium phocae

full scientific name: Corynebacterium phocae Pascual et al. 1998

strain designation: Collins 31, M408/89/1, 31

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.041
69480100positive
121801nopositiverod-shaped

colony morphology

  • @ref: 121801

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11925TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11925COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
40248MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121801CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
11925positivegrowth37mesophilic
40248positivegrowth37mesophilic
67770positivegrowth37mesophilic
121801positivegrowth15-45
121801nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121801
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
121801NaClpositivegrowth0-6 %
121801NaClnogrowth8 %
121801NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121801citrate-carbon source16947
121801esculin-hydrolysis4853
121801hippurate-hydrolysis606565
121801nitrate-reduction17632
121801nitrite-reduction16301
121801nitrate+respiration17632

metabolite production

  • @ref: 121801
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12180115688acetoin+
12180117234glucose+

enzymes

@refvalueactivityec
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
121801oxidase-
121801beta-galactosidase-3.2.1.23
121801alcohol dehydrogenase-1.1.1.1
121801gelatinase-
121801amylase+
121801DNase-
121801caseinase-3.4.21.50
121801catalase+1.11.1.6
121801tween esterase-
121801gamma-glutamyltransferase-2.3.2.2
121801lecithinase-
121801lipase-
121801lysine decarboxylase+4.1.1.18
121801ornithine decarboxylase+4.1.1.17
121801phenylalanine ammonia-lyase-4.3.1.24
121801tryptophan deaminase-
121801urease+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
121801-+++-+----++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121801----------+++--------------+-------++--+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
11925common seal Phoca vitulinaPhoca vitulinaNorth Sea, InvernessUnited KingdomGBREurope
54131Seal,common seal,Phoca vitulina,nasal cavityNorth Sea1989
67770Nasal cavity of a common seal (Phoca vitulina)Phoca vitulina
121801Common seal, nasal cavities

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_5427.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2631;97_3223;98_4050;99_5427&stattab=map
  • Last taxonomy: Corynebacterium phocae subclade
  • 16S sequence: Y10076
  • Sequence Identity:
  • Total samples: 1952
  • soil counts: 55
  • aquatic counts: 49
  • animal counts: 1832
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119251Risk group (German classification)
1218012Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11925
  • description: Corynebacterium phocae 16S rRNA gene, strain M408/89/1; CCUG 38205
  • accession: Y10076
  • length: 1387
  • database: ena
  • NCBI tax ID: 161895

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium phocae M408/89/1GCA_001941565completencbi161895
66792Corynebacterium phocae strain M408/89/1161895.4completepatric161895
66792Corynebacterium phocae strain M408/89/1161895.5plasmidpatric161895
66792Corynebacterium phocae DSM 446122623620533completeimg161895
67770Corynebacterium phocae CCUG 38205TGCA_008693075contigncbi161895

GC content

  • @ref: 11925
  • GC-content: 58

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.654no
gram-positiveyes93.737no
anaerobicno99.509no
halophileyes72.031no
spore-formingno93.543no
glucose-utilyes87.898no
aerobicno63.495no
thermophileno94.406no
motileno94.056no
glucose-fermentyes58.832no

External links

@ref: 11925

culture collection no.: DSM 44612, CCUG 38205, CIP 105741, LMG 19052, NCIMB 13757, JCM 12105

straininfo link

  • @ref: 72719
  • straininfo: 12975

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731303Corynebacterium phocae sp. nov., isolated from the common seal (Phoca vitulina).Pascual C, Foster G, Alvarez N, Collins MDInt J Syst Bacteriol10.1099/00207713-48-2-6011998Animals, Base Sequence, Corynebacterium/*classification/genetics, Corynebacterium Infections/microbiology/*veterinary, DNA, Bacterial, Molecular Sequence Data, Phylogeny, Seals, Earless/*microbiologyGenetics
Phylogeny33974533Corynebacterium lizhenjunii sp. nov., isolated from the respiratory tract of Marmota himalayana, and Corynebacterium qintianiae sp. nov., isolated from the lung tissue of Pseudois nayaur.Zhou J, Xu M, Guo W, Yang J, Pu J, Lai XH, Jin D, Lu S, Zhang S, Huang Y, Zhu W, Huang Y, Zheng H, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0048032021Animals, Bacterial Typing Techniques, Base Composition, China, Corynebacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lung/*microbiology, Marmota/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Respiratory System/*microbiology, Sequence Analysis, DNA, Sheep/*microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11925Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44612)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44612
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
40248Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17794
54131Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38205)https://www.ccug.se/strain?id=38205
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
72719Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12975.1StrainInfo: A central database for resolving microbial strain identifiers
121801Curators of the CIPCollection of Institut Pasteur (CIP 105741)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105741