Strain identifier

BacDive ID: 158549

Type strain: Yes

Species: Wocania arenilitoris

Strain Designation: HMF6543

Strain history: <- Kiseoung Joh, Hankuk Univ. of Foreign Studies.

NCBI tax ID(s): 2044858 (species)

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General

@ref: 65242

BacDive-ID: 158549

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

description: Wocania arenilitoris HMF6543 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sand sample.

NCBI tax id

  • NCBI tax id: 2044858
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Kiseoung Joh, Hankuk Univ. of Foreign Studies.

doi: 10.13145/bacdive158549.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Wocania
  • species: Wocania arenilitoris
  • full scientific name: Wocania arenilitoris (Kang et al. 2017) Liu et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Sabulilitoribacter arenilitoris

@ref: 65242

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Sabulilitoribacter

species: Sabulilitoribacter arenilitoris

strain designation: HMF6543

type strain: yes

Morphology

cell morphology

  • @ref: 65242
  • gram stain: negative
  • cell length: 1.8-2.1 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65242
  • colony size: 0.7 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 3 days
  • medium used: marine agar 2216

pigmentation

  • @ref: 65242
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

@refnamegrowth
65242Reasoner's 2A agar (R2A)no
65242Nutrient agar (NA)no
65242tryptic soy agarno
65242blood agarno
65242MacConkey agarno
65242Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
65242positivegrowth10-30
65242positiveoptimum30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
65242positivegrowth6-8
65242positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65242aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65242NaClpositivegrowth0.5-5 %
65242NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65242167632-oxobutanoate+carbon source
65242309162-oxoglutarate+carbon source
65242286442-oxopentanoate+carbon source
65242182404-hydroxy-L-proline+carbon source
6524217128adipate-assimilation
6524217925alpha-D-glucose+carbon source
6524227689decanoate-assimilation
6524285146carboxymethylcellulose-hydrolysis
65242casein-hydrolysis
6524262968cellulose-hydrolysis
6524217634D-glucose-assimilation
6524216899D-mannitol-assimilation
6524216024D-mannose-assimilation
6524223652dextrin-hydrolysis
6524223652dextrin+carbon source
6524216991dna-hydrolysis
652424853esculin-hydrolysis
6524217234glucose-fermentation
6524230849L-arabinose-assimilation
6524216857L-threonine+carbon source
6524225115malate-assimilation
6524217306maltose-assimilation
6524251850methyl pyruvate+carbon source
65242506227N-acetylglucosamine-assimilation
6524217632nitrate+reduction
6524218401phenylacetate-assimilation
6524232032potassium gluconate-assimilation
6524253258sodium citrate-assimilation
6524228017starch-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6524228971ampicillinyesyes10 µg (disc)
6524218208penicillin gyesyes10 Unit (disc)
6524248923erythromycinyesyes15 µg (disc)
6524217698chloramphenicolyesyes30 µg (disc)
6524228077rifampicinyesyes30 µg (disc)
6524228001vancomycinyesyes30 µg (disc)
6524217833gentamicinyesyes10 µg (disc)
6524217076streptomycinyesyes10 µg (disc)
652426104kanamycinyesyes30 µg (disc)
6524227902tetracyclineyesyes30 µg (disc)

metabolite production

  • @ref: 65242
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65242cytochrome oxidase+1.9.3.1
65242catalase+1.11.1.6
65242arginine dihydrolase+3.5.3.6
65242urease+3.5.1.5
65242gelatinase-
65242alkaline phosphatase+3.1.3.1
65242esterase (C 4)+
65242esterase Lipase (C 8)+
65242leucine arylamidase+3.4.11.1
65242valine arylamidase+
65242cystine arylamidase+3.4.11.3
65242trypsin+3.4.21.4
65242acid phosphatase+3.1.3.2
65242naphthol-AS-BI-phosphohydrolase+
65242N-acetyl-beta-glucosaminidase+3.2.1.52
65242alpha-fucosidase+3.2.1.51
65242lipase (C 14)-
65242alpha-chymotrypsin-3.4.21.1
65242alpha-galactosidase-3.2.1.22
65242beta-glucuronidase-3.2.1.31
65242alpha-glucosidase-3.2.1.20
65242beta-glucosidase-3.2.1.21
65242alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65242C16:02.3
    65242C12:0 iso2.9
    65242C15:0 iso19.6
    65242C15:0 anteiso4.7
    65242C15:1 iso G25.4
    65242C15:1 anteiso A1.6
    65242C16:0 iso1.3
    65242C15:0 2OH1.5
    65242C17:0 2OH1.3
    65242C15:0 iso 3OH7.9
    65242C16:0 iso 3OH1.7
    65242C17:0 iso 3OH13
    65242C16:1ω7c and/or C16:1ω6c8.9
  • type of FA analysis: whole cell analysis
  • incubation medium: marine agar
  • agar/liquid: agar
  • incubation temperature: 30
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65242sand sampleseashore sand of the South Sea located on Boseong in Jeollanam-doRepublic of KoreaKORAsia34.67127.094marine agar 22167 days30The sand sample (1 g) was suspended in 10 ml sterile 2 % (w/v) NaCl solution and vortexed for 1 min. The dispersed suspension was dilutedserially in 2 % (w/v) saline water, spread on marine agar (MA; BD) plates and incubated at 30°C for 7 days. Orange-coloured colonies were picked from the plates and purified by streaking three times on MA.
67771From sand of seashoreBoseong-gun, Jeollanam-do ProvinceRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_49524.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_6916;97_27934;98_35595;99_49524&stattab=map
  • Last taxonomy: Sabulilitoribacter arenilitoris subclade
  • 16S sequence: KX343046
  • Sequence Identity:
  • Total samples: 10
  • aquatic counts: 9
  • animal counts: 1

Sequence information

16S sequences

  • @ref: 65242
  • description: 16S rRNA gene sequence
  • accession: KX343046
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Wocania arenilitoris HMF6543
  • accession: GCA_021728535
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2044858

GC content

  • @ref: 65242
  • GC-content: 31.9
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno95.587yes
gram-positiveno98.383no
anaerobicno98.737yes
aerobicyes76.823no
halophileno83.134no
spore-formingno96.618no
motileno92.067yes
glucose-fermentno89.795yes
thermophileno94.294yes
glucose-utilyes89.948no

External links

@ref: 65242

culture collection no.: KCTC 52401, NBRC 112674, HME 6543

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984564
  • title: Sabulilitoribacter arenilitoris sp. nov., isolated from seashore sand.
  • authors: Kang H, Cha I, Kim H, Joh K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002378
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Glycolipids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
65242Heeyoung Kang, Inseong Cha, Haneul Kim, Kiseong JohSabulilitoribacter arenilitoris sp. nov., isolated from seashore sand10.1099/ijsem.0.002378IJSEM 67: 4796-4800 201728984564
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
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/