Strain identifier

BacDive ID: 133649

Type strain: Yes

Species: Kordia algicida

Strain Designation: OT-1

NCBI tax ID(s): 221066 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 29928

BacDive-ID: 133649

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

description: Kordia algicida OT-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from seawater.

NCBI tax id

  • NCBI tax id: 221066
  • Matching level: species

doi: 10.13145/bacdive133649.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Kordia
  • species: Kordia algicida
  • full scientific name: Kordia algicida Sohn et al. 2004

@ref: 29928

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Kordia

species: Kordia algicida

strain designation: OT-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29928negative3.5 µm0.4 µmrod-shapedno
26299negative2-5 µm0.3-0.5 µmrod-shapedno
69480negative97.481
69480no93

colony morphology

  • @ref: 26299
  • colony color: Yellow
  • colony shape: circular
  • medium used: ZoBell 2216e

pigmentation

@refproductionname
29928yes
26299noFlexirubin
26299yesCarotenoid

Culture and growth conditions

culture medium

@refnamegrowth
26299ZoBell 2216eyes
26299Aux mediumno
26299TSA plus sea wateryes

culture temp

@refgrowthtypetemperature
29928positivegrowth04-30
29928positiveoptimum30
26299positiveoptimum30
26299positivegrowth5-40

culture pH

@refabilitytypepHPH range
29928positiveoptimum7.5
26299positivegrowth6-10alkaliphile
26299positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29928aerobe
26299obligate aerobe

halophily

@refsaltgrowthtested relationconcentrationhalophily level
29928NaClpositivegrowth01-05 %
29928NaClpositiveoptimum3 %
26299NaClpositivegrowth1-5 %halophilic
26299NaClpositiveoptimum3 %halophilic

observation

@refobservation
26299abilty to kill and lyse several marine microalgal species
26299requires sea salts (Na+, Ca2+, Mg2+) and organic nitrogen

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2992815963ribitol+carbon source
2992821217L-alaninamide+carbon source
2992835391aspartate+carbon source
2992817126DL-carnitine+carbon source
2992816947citrate+carbon source
2992823652dextrin+carbon source
299285291gelatin+carbon source
2992817234glucose+carbon source
2992829987glutamate+carbon source
2992828087glycogen+carbon source
2992824996lactate+carbon source
2992817306maltose+carbon source
2992829864mannitol+carbon source
2992837684mannose+carbon source
29928506227N-acetylglucosamine+carbon source
2992818257ornithine+carbon source
2992826271proline+carbon source
2992816634raffinose+carbon source
2992830031succinate+carbon source
2992817992sucrose+carbon source
2992826986threonine+carbon source
2992816704uridine+carbon source
2992817632nitrate+reduction
26299645522-hydroxybutyrate-oxidation
26299167632-oxobutanoate-oxidation
26299309162-oxoglutarate+oxidation
26299286442-oxopentanoate-oxidation
26299620642,3-butanediol-oxidation
26299370543-hydroxybutyrate-oxidation
2629916865gamma-aminobutyric acid-oxidation
26299167244-hydroxybutyrate-oxidation
26299181014-hydroxyphenylacetic acid-oxidation
2629930089acetate-oxidation
2629915963ribitol+oxidation
262992509agar-degradation
2629958187alginate-degradation
2629940585alpha-cyclodextrin+oxidation
2629917925alpha-D-glucose+oxidation
2629936219alpha-lactose-oxidation
2629928938ammonium-nitrogen source
2629973706bromosuccinate-oxidation
2629985146carboxymethylcellulose-degradation
2629917057cellobiose-oxidation
2629962968cellulose-degradation
2629917029chitin-degradation
2629916383cis-aconitate-oxidation
2629916947citrate+oxidation
2629915570D-alanine-oxidation
2629918333D-arabitol-oxidation
2629915824D-fructose-oxidation
2629915895D-galactonic acid lactone-oxidation
2629912936D-galactose-oxidation
2629918024D-galacturonic acid-oxidation
262998391D-gluconate-oxidation
2629917784D-glucosaminic acid-oxidation
2629914314D-glucose 6-phosphate+oxidation
2629915748D-glucuronate+oxidation
2629916899D-mannitol+oxidation
2629916024D-mannose+oxidation
2629928053melibiose-oxidation
2629927605D-psicose-oxidation
2629916634raffinose+oxidation
2629933801D-saccharate-oxidation
2629916523D-serine-oxidation
2629917924D-sorbitol-oxidation
2629916551D-trehalose-oxidation
2629923652dextrin+oxidation
2629917126DL-carnitine+oxidation
2629917113erythritol+oxidation
2629916000ethanolamine-oxidation
2629915740formate-oxidation
262995291gelatin+degradation
2629928066gentiobiose+oxidation
2629917234glucose-builds acid from
2629929042glucose 1-phosphate+oxidation
2629932323glucuronamide-oxidation
2629917754glycerol-oxidation
2629914336glycerol 1-phosphate-oxidation
2629928087glycogen+oxidation
2629924741hydroxyproline-oxidation
2629917596inosine-oxidation
2629915443inulin-degradation
2629917240itaconate-oxidation
2629921217L-alaninamide+oxidation
2629916977L-alanine-oxidation
2629973786L-alanylglycine-oxidation
2629930849L-arabinose-oxidation
2629917196L-asparagine-oxidation
2629929991L-aspartate+oxidation
2629918287L-fucose-oxidation
2629929985L-glutamate+oxidation
2629915971L-histidine-oxidation
2629915603L-leucine-oxidation
2629915729L-ornithine+oxidation
2629917295L-phenylalanine-oxidation
2629917203L-proline+oxidation
2629918183L-pyroglutamic acid-oxidation
2629962345L-rhamnose-oxidation
2629917115L-serine-oxidation
2629916857L-threonine+oxidation
2629924996lactate+oxidation
262996359lactulose-oxidation
2629915792malonate-oxidation
26299maltose hydrate+oxidation
2629937657methyl D-glucoside-oxidation
2629951850methyl pyruvate-oxidation
2629975146monomethyl succinate-oxidation
2629917268myo-inositol-oxidation
2629928037N-acetylgalactosamine-oxidation
26299506227N-acetylglucosamine+oxidation
2629917632nitrate-nitrogen source
2629917632nitrate+reduction
2629917309pectin-degradation
2629950048phenylethylamine-oxidation
2629917272propionate-oxidation
2629917148putrescine-oxidation
2629926490quinate+oxidation
2629941865sebacic acid-oxidation
26299skimmed milk+degradation
2629928017starch+degradation
26299143136succinamate-oxidation
2629930031succinate+oxidation
2629917992sucrose+oxidation
2629917748thymidine-oxidation
2629932528turanose-oxidation
2629953423tween 40-oxidation
2629953426tween 80-oxidation
2629916199urea-nitrogen source
2629916704uridine+oxidation
2629927248urocanic acid-oxidation
2629917151xylitol-oxidation

metabolite production

@refChebi-IDmetaboliteproduction
2629916136hydrogen sulfideno
2629935581indoleno

enzymes

@refvalueactivityec
29928gelatinase+
29928cytochrome oxidase+1.9.3.1
26299catalase-1.11.1.6
26299cytochrome oxidase+1.9.3.1
26299urease-3.5.1.5
26299agarase-3.2.1.81
26299amylase+
26299beta-galactosidase-3.2.1.23
26299caseinase+3.4.21.50
26299beta-glucosidase-3.2.1.21
26299gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29928seawater
26299sea water of Masan Bay, during an outbreak of red tideMasan BayRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Protozoa#Dinoflagellate

taxonmaps

  • @ref: 69479
  • File name: preview.99_4016.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16095;96_2041;97_2462;98_3044;99_4016&stattab=map
  • Last taxonomy: Kordia algicida subclade
  • 16S sequence: AY195836
  • Sequence Identity:
  • Total samples: 136
  • soil counts: 4
  • aquatic counts: 127
  • animal counts: 3
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 26299
  • description: Kordia algicida 16S ribosomal RNA gene, partial sequence
  • accession: AY195836
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kordia algicida OT-1GCA_000154725scaffoldncbi391587
66792Kordia algicida OT-1391587.3wgspatric391587
66792Kordia algicida OT-1641380434draftimg391587

GC content

@refGC-contentmethod
2992834
2629934high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.481yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.293yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.718no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.333no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.424yes
69480flagellatedmotile2+Ability to perform flagellated movementno93yes

External links

@ref: 29928

culture collection no.: KCTC 8814P, NBRC 1000336

straininfo link

  • @ref: 91542
  • straininfo: 132019

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143006Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide.Sohn JH, Lee JH, Yi H, Chun J, Bae KS, Ahn TY, Kim SJInt J Syst Evol Microbiol10.1099/ijs.0.02689-02004Animals, Base Composition, Carbohydrate Metabolism, Cytophagaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Dinoflagellida/*microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny18599714Fulvibacter tottoriensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment.Khan ST, Nakagawa Y, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.65554-02008Fatty Acids/metabolism, Flavobacteriaceae/chemistry/*classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Genetics21622754Genome sequence of the algicidal bacterium Kordia algicida OT-1.Lee HS, Kang SG, Kwon KK, Lee JH, Kim SJJ Bacteriol10.1128/JB.05241-112011Antibiosis, Flavobacteriaceae/*genetics/isolation & purification/*physiology, *Genome, Bacterial, Microalgae/*microbiology/physiology, Molecular Sequence DataEnzymology
Phylogeny23606478Kordia antarctica sp. nov., isolated from Antarctic seawater.Baek K, Choi A, Kang I, Lee K, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.052738-02013Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27098380Kordiaulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp.Qi F, Huang Z, Lai Q, Li D, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0010982016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ulva/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
28790980Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes.Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sanchez P, Salazar G, Stepanauskas R, Gonzalez JM, Sieracki ME, Speich S, Stemmann L, Pedros-Alio C, Acinas SGFront Microbiol10.3389/fmicb.2017.013172017
Metabolism29757599Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins.Hespen CW, Bruegger JJ, Guo Y, Marletta MAACS Chem Biol10.1021/acschembio.8b002482018Alanine/chemistry, Bacterial Proteins/chemistry/*metabolism, Flavobacteriaceae/*chemistry, Glycine/chemistry, Heme/chemistry, Hemeproteins/chemistry/*metabolism, Ligands, Mutation, Nitric Oxide/*metabolism, Oxidation-Reduction, Pliability, Protein Binding, Protein Conformation

Reference

@idauthorstitledoi/urlpubmedID_cross_reference
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
2629910.1099/ijs.0.02689-015143006
29928Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604126299
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
91542Reimer, 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-ID132019.1