Strain identifier

BacDive ID: 5626

Type strain: Yes

Species: Polaribacter filamentus

Strain Designation: 215

Strain history: CIP <- 2000, J.T. Staley, Univ. Washington, Seattle, USA: strain 215

NCBI tax ID(s): 53483 (species)

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General

@ref: 5199

BacDive-ID: 5626

DSM-Number: 13964

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative

description: Polaribacter filamentus 215 is a psychrophilic, Gram-negative bacterium that was isolated from surface sea water.

NCBI tax id

  • NCBI tax id: 53483
  • Matching level: species

strain history

@refhistory
5199<- J. Dodsworth, Dept. of Microbiol., Univ. of Washington <- J. J. Gosink
329742000, J.T. Staley, Univ. Washington, Seattle, USA: strain 215
119346CIP <- 2000, J.T. Staley, Univ. Washington, Seattle, USA: strain 215

doi: 10.13145/bacdive5626.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Polaribacter
  • species: Polaribacter filamentus
  • full scientific name: Polaribacter filamentus Gosink et al. 1998

@ref: 5199

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Polaribacter

species: Polaribacter filamentus

full scientific name: Polaribacter filamentus Gosink et al. 1998

strain designation: 215

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.851
119346negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5199BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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
32974MEDIUM 345 - for PolaribacteryesYeast extract (0.400 g);Ammonium chloride (0.200 g);Succinic acid (0.200g);Tryptone (0.500 g);Beef extract (0.400 g);Di Potassium monohydrogenophosphate (0.010g);Solution SL-6 - M00545 (1.000 ml);Vitamins solution - M00646 (Balch,1979) (10.000 ml);Synthet
119346CIP Medium 345yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=345

culture temp

@refgrowthtypetemperaturerange
5199positivegrowth4psychrophilic
32974positivegrowth4psychrophilic
119346positivegrowth5-15psychrophilic
119346nogrowth22psychrophilic
119346nogrowth30mesophilic
119346nogrowth37mesophilic
119346nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.982

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
119346esculin-hydrolysis4853
119346nitrate-reduction17632
119346nitrite-reduction16301

metabolite production

  • @ref: 119346
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
119346oxidase-
119346alcohol dehydrogenase-1.1.1.1
119346gelatinase-
119346caseinase-3.4.21.50
119346catalase+1.11.1.6
119346tween esterase+
119346gamma-glutamyltransferase+2.3.2.2
119346lecithinase-
119346lipase-
119346lysine decarboxylase-4.1.1.18
119346ornithine decarboxylase-4.1.1.17
119346phenylalanine ammonia-lyase-4.3.1.24
119346protease-
119346tryptophan deaminase-
119346urease-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
119346-+++-++++-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119346--+------++-+-+---------+------------------+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5199surface sea water350 km offshore from Deadhorse
119346Environment, Surface sea waterAlaskaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_61077.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_760;97_18652;98_43354;99_61077&stattab=map
  • Last taxonomy: Polaribacter
  • 16S sequence: U73726
  • Sequence Identity:
  • Total samples: 1409
  • soil counts: 54
  • aquatic counts: 1327
  • animal counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51991Risk group (German classification)
1193461Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Polaribacter filamentus 16S ribosomal RNA gene, partial sequence
  • accession: U73726
  • length: 1440
  • database: ena
  • NCBI tax ID: 53483

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polaribacter filamentus ATCC 700397GCA_002943715contigncbi53483
66792Polaribacter filamentus strain ATCC 70039753483.7wgspatric53483
66792Polaribacter filamentus ATCC 7003972839188362draftimg53483

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.194no
anaerobicno99.616no
halophileno68.052no
spore-formingno95.93no
glucose-utilyes82.213no
thermophileno99.053no
aerobicyes89.753no
motileno93.521no
glucose-fermentno88.968no
flagellatedno96.461no

External links

@ref: 5199

culture collection no.: DSM 13964, ATCC 700397, CIP 106479

straininfo link

  • @ref: 75109
  • straininfo: 43913

literature

  • topic: Phylogeny
  • Pubmed-ID: 9542092
  • title: Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov.
  • authors: Gosink JJ, Woese CR, Staley JT
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-1-223
  • year: 1998
  • mesh: Antarctic Regions, Arctic Regions, Bacteriological Techniques, Bacteroides/*classification/genetics/ultrastructure, Cytophaga/*classification/genetics/ultrastructure, DNA, Bacterial/analysis, Flavobacterium/*classification/genetics/ultrastructure, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Seawater/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5199Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13964)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13964
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
32974Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18614
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
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
75109Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43913.1StrainInfo: A central database for resolving microbial strain identifiers
119346Curators of the CIPCollection of Institut Pasteur (CIP 106479)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106479