Strain identifier

BacDive ID: 130762

Type strain: Yes

Species: Vibrio cyclitrophicus

Strain Designation: P-2P44

Strain history: CIP <- 2000, B.P. Hedlund, Univ. Washington, Seattle, USA: strain P-2P44 <- A.D. Geiselbrecht

NCBI tax ID(s): 47951 (species)

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General

@ref: 21976

BacDive-ID: 130762

DSM-Number: 14264

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Vibrio cyclitrophicus P-2P44 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from creosote-contaminated marine sediment.

NCBI tax id

  • NCBI tax id: 47951
  • Matching level: species

strain history

@refhistory
21976<- B. P. Hedlund, Univers. Washington; P-2P44
118828CIP <- 2000, B.P. Hedlund, Univ. Washington, Seattle, USA: strain P-2P44 <- A.D. Geiselbrecht

doi: 10.13145/bacdive130762.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio cyclitrophicus
  • full scientific name: Vibrio cyclitrophicus corrig. Hedlund and Staley 2001

  • synonyms

    • @ref: 20215
    • synonym: Vibrio cyclotrophicus

@ref: 21976

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio cyclitrophicus

full scientific name: Vibrio cyclitrophicus Hedlund and Staley 2001

strain designation: P-2P44

type strain: yes

Morphology

cell morphology

  • @ref: 118828
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21976REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)yeshttps://mediadive.dsmz.de/medium/514cName: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
41187Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118828CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
21976positivegrowth28mesophilic
41187positivegrowth30mesophilic
61144positivegrowth30mesophilic
118828positivegrowth15-25psychrophilic
118828nogrowth5psychrophilic
118828nogrowth37mesophilic
118828nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61144aerobe
118828facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
118828NaClpositivegrowth2-10 %
118828NaClnogrowth0 %

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
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
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
118828citrate-carbon source16947
118828esculin-hydrolysis4853
118828glucose-fermentation17234
118828lactose-fermentation17716
118828nitrate+reduction17632
118828nitrite-reduction16301
118828sodium thiosulfate-builds gas from132112

metabolite production

  • @ref: 118828
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11882815688acetoin-
11882817234glucose-

enzymes

@refvalueactivityec
118828oxidase+
118828beta-galactosidase+3.2.1.23
118828alcohol dehydrogenase-1.1.1.1
118828gelatinase-
118828amylase-
118828caseinase+3.4.21.50
118828catalase+1.11.1.6
118828tween esterase+
118828gamma-glutamyltransferase-2.3.2.2
118828lecithinase-
118828lipase+
118828lysine decarboxylase-4.1.1.18
118828ornithine decarboxylase-4.1.1.17
118828phenylalanine ammonia-lyase-4.3.1.24
118828protease-
118828tryptophan deaminase-
118828urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118828-+++-++-+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118828+---++---++++----+---+-+/-+/-+/-+++/-+/-++---++---------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118828+++++-++-+++-+++--++-+--------+-+----------------++--------++--------------+--+++-+---+--++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
21976creosote-contaminated marine sedimentEagle Harbor, Puget Sand, WashingtonUSAUSANorth America
61144Creosote-contaminated marine sedimentEagle HarborUSAUSANorth America1993
118828Environment, Creosote-contaminated marine sedimentEagle Harbor, MichiganUnited States of AmericaUSANorth America1993

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_498.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_409;99_498&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: AM162656
  • Sequence Identity:
  • Total samples: 8493
  • soil counts: 235
  • aquatic counts: 6823
  • animal counts: 1389
  • plant counts: 46

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
219761Risk group (German classification)
1188282Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio cyclitrophicus strain LMG21359 16S ribosomal RNA gene, partial sequenceDQ4816101435ena47951
20218Vibrio 2P44 16S rRNA gene sequenceU579191461ena47951
21976Vibrio cyclitrophicus partial 16S rRNA gene, type strain LMG 21359TAM1626561365ena47951

Genome sequences

  • @ref: 66792
  • description: Vibrio cyclitrophicus LMG 21359
  • accession: GCA_024347435
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 47951

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes91.213no
gram-positiveno98.702no
anaerobicno97.035yes
aerobicyes89.982yes
halophileyes63.48no
spore-formingno95.388no
motileyes89.923no
glucose-fermentyes86.082no
thermophileno99.374no
glucose-utilyes91.78no

External links

@ref: 21976

culture collection no.: DSM 14264, ATCC 700982, CIP 106644, CCUG 56965, LMG 21359, KCTC 12925, NCIMB 13790

straininfo link

@refstraininfo
8925944240
89260408968

literature

  • topic: Phylogeny
  • Pubmed-ID: 11211274
  • title: Vibrio cyclotrophicus sp. nov., a polycyclic aromatic hydrocarbon (PAH)-degrading marine bacterium.
  • authors: Hedlund BP, Staley JT
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-1-61
  • year: 2001
  • mesh: Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Vibrio/*classification/genetics/metabolism/ultrastructure, *Water Pollution, Chemical
  • topic2: Phenotype

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
21976Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-14264Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14264)
41187Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18797
61144Curators of the CCUGhttps://www.ccug.se/strain?id=56965Culture Collection University of Gothenburg (CCUG) (CCUG 56965)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89259Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID44240.1
89260Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408968.1
118828Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106644Collection of Institut Pasteur (CIP 106644)