Strain identifier

BacDive ID: 133846

Type strain: Yes

Species: Polaribacter porphyrae

Strain Designation: LNM-20

NCBI tax ID(s): 1137780 (species)

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General

@ref: 30663

BacDive-ID: 133846

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

description: Polaribacter porphyrae LNM-20 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from thalli of a marine red alga.

NCBI tax id

  • NCBI tax id: 1137780
  • Matching level: species

doi: 10.13145/bacdive133846.20230509.8.1

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 porphyrae
  • full scientific name: Polaribacter porphyrae Fukui et al. 2013

@ref: 30663

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Polaribacter

species: Polaribacter porphyrae

strain designation: LNM-20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30663negative1.39 µm0.37 µmrod-shapedno
69480negative99.814

pigmentation

  • @ref: 30663
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30663positivegrowth10-30
30663positiveoptimum25mesophilic

culture pH

@refabilitytypepH
30663positivegrowth06-08
30663positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30663
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30663NaClpositivegrowth02-05 %
30663NaClpositiveoptimum3 %

observation

  • @ref: 30663
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3066330089acetate+carbon source
3066321217L-alaninamide+carbon source
3066316449alanine+carbon source
3066340585alpha-cyclodextrin+carbon source
30663286442-oxopentanoate+carbon source
3066335391aspartate+carbon source
3066323652dextrin+carbon source
3066328260galactose+carbon source
3066317234glucose+carbon source
3066329987glutamate+carbon source
3066315428glycine+carbon source
3066328087glycogen+carbon source
3066324996lactate+carbon source
3066317716lactose+carbon source
3066317306maltose+carbon source
3066337684mannose+carbon source
3066318257ornithine+carbon source
3066326271proline+carbon source
3066351850methyl pyruvate+carbon source
3066317822serine+carbon source
3066330031succinate+carbon source
3066326986threonine+carbon source
3066353423tween 40+carbon source
3066316704uridine+carbon source
306634853esculin+hydrolysis

enzymes

@refvalueactivityec
30663acid phosphatase+3.1.3.2
30663alkaline phosphatase+3.1.3.1
30663catalase+1.11.1.6
30663gelatinase+
30663cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 30663
  • sample type: thalli of a marine red alga

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Algae#Red algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_35978.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_760;97_21166;98_26528;99_35978&stattab=map
  • Last taxonomy: Polaribacter porphyrae subclade
  • 16S sequence: AB695286
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 2
  • aquatic counts: 35
  • animal counts: 6

Sequence information

16S sequences

  • @ref: 30663
  • description: Polaribacter porphyrae gene for 16S ribosomal RNA, partial sequence, strain: LNM-20
  • accession: AB695286
  • length: 1389
  • database: nuccore
  • NCBI tax ID: 1137780

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polaribacter porphyrae NBRC 108759GCA_002954685scaffoldncbi1137780
66792Polaribacter porphyrae LMG 26671GCA_020532745contigncbi1137780
66792Polaribacter porphyrae strain NBRC 1087591137780.3wgspatric1137780
66792Polaribacter porphyrae NBRC 1087592895253024draftimg1137780

GC content

  • @ref: 30663
  • GC-content: 28.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.931yes
gram-positiveno98.102yes
anaerobicno99.57yes
aerobicyes89.915yes
halophileno83.337no
spore-formingno96.318no
thermophileno98.895no
glucose-utilyes87.707yes
motileno89.84yes
glucose-fermentno92.395no

External links

@ref: 30663

culture collection no.: LMG 26671, NBRC 108759

straininfo link

  • @ref: 91618
  • straininfo: 378088

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904227Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species.Fukui Y, Abe M, Kobayashi M, Saito H, Oikawa H, Yano Y, Satomi MInt J Syst Evol Microbiol10.1099/ijs.0.041434-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Polyenes/analysis, Porphyra/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25224356Polaribacter marinivivus sp. nov., a member of the family Flavobacteriaceae isolated from seawater.Park S, Park JM, Jung YT, Lee KC, Lee JS, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-014-0283-42014Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Phylogeny32579104Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea.Choo S, Borchert E, Wiese J, Saha M, Kunzel S, Weinberger F, Hentschel UInt J Syst Evol Microbiol10.1099/ijsem.0.0042902020Bacterial Typing Techniques, Base Composition, *Biofilms, Carotenoids/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, North Sea, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
30663Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172699428776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91618Reimer, 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-ID378088.1