Strain identifier

BacDive ID: 140955

Type strain: Yes

Species: Flavivirga eckloniae

Strain Designation: ECD14

Strain history: <- Chi Nam Seong, Sunchon National Univ.

NCBI tax ID(s): 1803846 (species)

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General

@ref: 43856

BacDive-ID: 140955

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

description: Flavivirga eckloniae ECD14 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from seaweed Ecklonia cava obtained from the South Sea, Republic of Korea.

NCBI tax id

  • NCBI tax id: 1803846
  • Matching level: species

strain history

@refhistory
67770C. N. Seong; Sunchon Natl. Univ., South Korea; ECD14.
67771<- Chi Nam Seong, Sunchon National Univ.

doi: 10.13145/bacdive140955.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavivirga
  • species: Flavivirga eckloniae
  • full scientific name: Flavivirga eckloniae Lee et al. 2017

@ref: 43856

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavivirga

species: Flavivirga eckloniae

strain designation: ECD14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43856negative2.0-6.7 µm0.2-0.4 µmrod-shapedno
67771rod-shaped
67771negative
69480negative99.941

colony morphology

  • @ref: 43856
  • colony size: 2-3 mm
  • colony color: yellow
  • colony shape: irregular
  • incubation period: 3 days
  • medium used: Marine agar 2216

pigmentation

@refproductionname
43856yesFlexirubin-type pigment
43856yesCarotenoid

Culture and growth conditions

culture medium

@refnamegrowthcomposition
43856Marine agar (MA)yes
43856ZoBell's mediumnosea salt-free supplemented with NaCl only

culture temp

@refgrowthtypetemperaturerange
43856positivegrowth10-35
43856positiveoptimum25-30mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43856positivegrowth7.0-9.0alkaliphile
43856positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43856aerobe
67771aerobe

spore formation

@refspore formationconfidence
43856no
67771no
69481no100
69480no99.982

halophily

@refsaltgrowthtested relationconcentration
43856Marine saltspositivegrowth2-5 %(w/v)
43856Marine saltspositiveoptimum3 %(w/v)

observation

@refobservation
43856quinone MK-6
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4385617128adipate-assimilation
4385622599arabinose-assimilation
4385627689decanoate-assimilation
4385616947citrate-assimilation
4385624265gluconate-assimilation
4385617234glucose-assimilation
4385625115malate-assimilation
4385617306maltose-assimilation
4385629864mannitol-assimilation
4385637684mannose-assimilation
43856506227N-acetylglucosamine-assimilation
4385618401phenylacetate-assimilation
4385629864mannitol-builds acid from
4385626546rhamnose-builds acid from
4385617992sucrose-builds acid from
4385617029chitin-hydrolysis
4385616991dna-hydrolysis
43856egg yolk-hydrolysis
4385617368hypoxanthine-hydrolysis
4385653424tween 20-hydrolysis
4385616199urea-hydrolysis
4385615318xanthine-hydrolysis
4385617632nitrate-reduction
4385617306maltose+builds acid from
438562509agar+hydrolysis
4385658187alginate+hydrolysis
4385685146carboxymethylcellulose+hydrolysis
438564853esculin+hydrolysis
438565291gelatin+hydrolysis
4385617895L-tyrosine+hydrolysis
4385628017starch+hydrolysis
4385653426tween 80+hydrolysis
4385628757fructose+/-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4385628971ampicillinyesyes10 µg (disc)
43856100147nalidixic acidyesyes30 µg (disc)
438562637amikacinyesyes30 µg (disc)
4385617698chloramphenicolyesyes30 µg (disc)
4385648923erythromycinyesyes15 µg (disc)
4385617833gentamicinyesyes10 µg (disc)
438566104kanamycinyesyes30 µg (disc)
4385617334penicillinyesyes10 Unit (disc)
438568309polymyxin byesyes300 Unit (disc)
4385617076streptomycinyesyes10 µg (disc)
4385627902tetracyclineyesyes30 µg (disc)
4385628001vancomycinyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4385616136hydrogen sulfideno
4385635581indoleno
4385615688acetoinyes

enzymes

@refvalueactivityec
43856catalase-1.11.1.6
43856cytochrome oxidase+1.9.3.1
43856arginine dihydrolase-3.5.3.6
43856lysine decarboxylase-4.1.1.18
43856ornithine decarboxylase-4.1.1.17
43856tryptophan deaminase4.1.99.1
43856acid phosphatase+3.1.3.2
43856alkaline phosphatase+3.1.3.1
43856esterase (C 4)+
43856esterase Lipase (C 8)+
43856leucine arylamidase+3.4.11.1
43856naphthol-AS-BI-phosphohydrolase+
43856valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    43856C13:1 AT 12-131.3
    43856C15:03.4
    43856C15:1ω6c1.1
    43856C16:02
    43856C16:1ω7c / C16:1ω6c6.1
    43856C14:0 iso1.1
    43856C15:0 iso39.3
    43856C15:0 iso 3OH6.3
    43856C15:1 iso G13.5
    43856C16:0 iso1.5
    43856C16:1 iso H1.3
    43856C17:0 iso 3OH4.1
    43856iso-C17:1ω9c / C16:0 10-methyl2
    43856unknown 11.543411543
    43856unknown 13.56511.113565
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperaturehost species
43856seaweed Ecklonia cava obtained from the South Sea, Republic of KoreaSouth SeaRepublic of KoreaKORAsia34.0494127.333Marine agar 22167 days25
67770Seaweed EckloniacavaEckloniacava
67771From seaweed `Ecklonia cava`Geomun Island, the South SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Brown Algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_23616.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_11887;97_14401;98_17783;99_23616&stattab=map
  • Last taxonomy: Flavivirga eckloniae subclade
  • 16S sequence: KU725769
  • Sequence Identity:
  • Total samples: 13
  • aquatic counts: 12
  • animal counts: 1

Sequence information

16S sequences

  • @ref: 43856
  • description: 16S rRNA gene sequence
  • accession: KU725769
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavivirga eckloniae ECD14GCA_002886045completencbi1803846
66792Flavivirga eckloniae ECD142788500147completeimg1803846

GC content

@refGC-contentmethod
6777033high performance liquid chromatography (HPLC)
6777133.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.201yes
gram-positiveno98.603no
anaerobicno98.713no
aerobicyes76.723yes
halophileno90.164no
spore-formingno95.543yes
thermophileno98.412no
glucose-utilyes78.39yes
motileno91.718yes
glucose-fermentno86.636no

External links

@ref: 43856

culture collection no.: KCTC 52352, JCM 31797

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28820110Flavivirga eckloniae sp. nov. and Flavivirga aquimarina sp. nov., isolated from seaweed Ecklonia cava.Lee JH, Kang JW, Choe HN, Seong CNInt J Syst Evol Microbiol10.1099/ijsem.0.0020942017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Phaeophyta/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Seaweed/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34370661Palleronia sediminis sp. nov. and Flavivirga algicola sp. nov., two marine bacteria isolated from offshore areas near Weihai.Sun XK, Zhang YN, Jia YY, Zhong YL, Chen GJ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0049492021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Flavobacteriaceae/classification/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Rhodophyta/*microbiology, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryEnzymology

Reference

@idauthorstitledoi/urljournalpubmed
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
43856Ji Hee Lee, Joo Won Kang, Han Na Choe, Chi Nam SeongFlavivirga eckloniae sp. nov. and Flavivirga aquimarina sp. nov., isolated from seaweed Ecklonia cava10.1099/ijsem.0.002094IJSEM 67: 3089-3094 201728820110
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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