Strain identifier

BacDive ID: 24012

Type strain: Yes

Species: Flammeovirga pacifica

Strain Designation: WPAGA1

Strain history: <- H. Xu, Third Inst. Oceanography, State Oceanic Admin., China; WPAGA1 <- Z. Ding

NCBI tax ID(s): 915059 (species)

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General

@ref: 20564

BacDive-ID: 24012

DSM-Number: 24597

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

description: Flammeovirga pacifica WPAGA1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from deep sea sediment.

NCBI tax id

  • NCBI tax id: 915059
  • Matching level: species

strain history

  • @ref: 20564
  • history: <- H. Xu, Third Inst. Oceanography, State Oceanic Admin., China; WPAGA1 <- Z. Ding

doi: 10.13145/bacdive24012.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flammeovirgaceae
  • genus: Flammeovirga
  • species: Flammeovirga pacifica
  • full scientific name: Flammeovirga pacifica Xu et al. 2012

@ref: 20564

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flammeovirgaceae

genus: Flammeovirga

species: Flammeovirga pacifica

full scientific name: Flammeovirga pacifica Xu et al. 2012

strain designation: WPAGA1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
30204negative03-08 µm0.5-0.8 µmrod-shaped
69480negative99.978

pigmentation

  • @ref: 30204
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20564
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
20564positivegrowth28mesophilic
30204positivegrowth04-42
30204positiveoptimum32mesophilic

culture pH

@refabilitytypepHPH range
30204positivegrowth06-10alkaliphile
30204positiveoptimum07-09

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.937

halophily

@refsaltgrowthtested relationconcentration
30204NaClpositivegrowth0-5 %
30204NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3020417128adipate+carbon source
3020425115malate+carbon source
3020417306maltose+carbon source
30204506227N-acetylglucosamine+carbon source
302044853esculin+hydrolysis
3020417632nitrate+reduction

enzymes

@refvalueactivityec
30204acid phosphatase+3.1.3.2
30204alkaline phosphatase+3.1.3.1
30204alpha-galactosidase+3.2.1.22
30204cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 20564
  • sample type: deep sea sediment
  • geographic location: West Pacific Ocean, site CM3MC04-1 (157° 24' 31''E 19°30' 30'' N)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 19.5083
  • longitude: 157.409

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7921.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16066;96_1341;97_1592;98_5782;99_7921&stattab=map
  • Last taxonomy: Flammeovirga pacifica subclade
  • 16S sequence: HQ412594
  • Sequence Identity:
  • Total samples: 2593
  • soil counts: 305
  • aquatic counts: 1812
  • animal counts: 382
  • plant counts: 94

Safety information

risk assessment

  • @ref: 20564
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20564
  • description: Flammeovirga pacifica strain WPAGA1 16S ribosomal RNA gene, partial sequence
  • accession: HQ412594
  • length: 1489
  • database: ena
  • NCBI tax ID: 915059

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flammeovirga pacifica WPAGA1GCA_000807855scaffoldncbi915059
66792Flammeovirga pacifica WPAGA1915059.3wgspatric915059
66792Flammeovirga pacifica WPAGA12648501771draftimg915059

GC content

@refGC-contentmethod
2056432.9high performance liquid chromatography (HPLC)
3020432.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno86.486no
motileno86.486no
flagellatedno92.773no
flagellatedno92.773no
gram-positiveno98.517yes
gram-positiveno98.517yes
anaerobicno97.154no
anaerobicno97.154no
aerobicyes71.37no
aerobicyes71.37no
halophileno79.985no
halophileno79.985no
spore-formingno91.668no
spore-formingno91.668no
glucose-utilyes90.138no
glucose-utilyes90.138no
thermophileno96.951yes
thermophileno96.951yes
glucose-fermentno79.796no
glucose-fermentno79.796no

External links

@ref: 20564

culture collection no.: DSM 24597, CCTCC AB 2010364, LMG 26175, MCCC 1A06425

straininfo link

  • @ref: 87986
  • straininfo: 405555

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21669915Flammeovirga pacifica sp. nov., isolated from deep-sea sediment.Xu H, Fu Y, Yang N, Ding Z, Lai Q, Zeng RInt J Syst Evol Microbiol10.1099/ijs.0.030676-02011Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Cadaverine/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Genetics25526668Draft genome sequence of an agar-degrading marine bacterium Flammeovirga pacifica WPAGA1.Chan Z, Wang R, Liu S, Zhao C, Yang S, Zeng RMar Genomics10.1016/j.margen.2014.12.0012014Agar/*metabolism, Bacteroidetes/*genetics/*metabolism, *Genome, Bacterial, Molecular Sequence Data, Seawater/microbiology, Water MicrobiologyMetabolism
28443080Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1.Gao B, Jin M, Li L, Qu W, Zeng RFront Microbiol10.3389/fmicb.2017.006002017
Enzymology30021136Characterization of a novel psychrophilic and halophilic beta-1, 3-xylanase from deep-sea bacterium, Flammeovirga pacifica strain WPAGA1.Cai ZW, Ge HH, Yi ZW, Zeng RY, Zhang GYInt J Biol Macromol10.1016/j.ijbiomac.2018.07.0902018Bacteroidetes/*enzymology, Endo-1,4-beta Xylanases/chemistry/isolation & purification/*metabolism, Enzyme Stability/drug effects, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Models, Molecular, *Oceans and Seas, Recombinant Proteins/isolation & purification, Sequence Analysis, Protein, Sodium Chloride/pharmacology, Static Electricity, TemperaturePhylogeny
Biotechnology31244790A Novel Strategy for Efficient Agaro-Oligosaccharide Production Based on the Enzymatic Degradation of Crude Agarose in Flammeovirga pacifica WPAGA1.Gao B, Li L, Wu H, Zhu D, Jin M, Qu W, Zeng RFront Microbiol10.3389/fmicb.2019.012312019Metabolism
Enzymology32906756Identification and Characterization of a Novel Thermostable and Salt-Tolerant beta-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1.Yi Z, Cai Z, Zeng B, Zeng R, Zhang GBiomolecules10.3390/biom100912872020Bacteroidetes/*enzymology/genetics, Cations/metabolism, Enzyme Stability, Hydrogen-Ion Concentration, Kinetics, Models, Molecular, Receptors, Cell Surface/metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Salt Tolerance, Sequence Alignment, Sodium Chloride, Temperature, Xylan Endo-1,3-beta-Xylosidase/*chemistry/genetics/isolation & purification/*metabolism, Xylans/metabolismMetabolism
Metabolism33133041Amelioration of Androgenetic Alopecia by Algal Oligosaccharides Prepared by Deep-Sea Bacterium Biodegradation.Jin M, Chen YL, He X, Hou Y, Chan Z, Zeng RFront Microbiol10.3389/fmicb.2020.5670602020

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20564Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24597Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24597)
30204Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172654928776041
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
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
87986Reimer, 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-ID405555.1