Strain identifier

BacDive ID: 24017

Type strain: Yes

Species: Wocania ichthyoenteri

Strain Designation: Th78

Strain history: <- X-H Zhang, Ocean Univ. of China

NCBI tax ID(s): 1230531 (species)

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General

@ref: 20565

BacDive-ID: 24017

DSM-Number: 26285

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

description: Wocania ichthyoenteri Th78 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from From intestine of a cultured flounder, `Paralichthys olivaceus`, fish farm.

NCBI tax id

  • NCBI tax id: 1230531
  • Matching level: species

strain history

@refhistory
20565<- X.-H. Zhang, Ocean Univ. China, Dept. of Marine Biology, Qingdao, P. R. China; Th78 <- K. Tang
67770X.-H. Zhang and Y. Zhang <-- K. Tang Th78.
67771<- X-H Zhang, Ocean Univ. of China

doi: 10.13145/bacdive24017.20230509.8.1

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 ichthyoenteri
  • full scientific name: Wocania ichthyoenteri (Zhang et al. 2013) He et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Flaviramulus ichthyoenteri

@ref: 20565

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Wocania

species: Wocania ichthyoenteri

full scientific name: Wocania ichthyoenteri (Zhang et al. 2013) He et al. 2020

strain designation: Th78

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
31152negative2.5 µm0.4 µmrod-shapedyesgliding
67771rod-shapedgliding
67771negative

pigmentation

  • @ref: 31152
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20565
  • 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
20565positivegrowth28mesophilic
31152positivegrowth04-37
31152positiveoptimum28mesophilic
67770positivegrowth30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31152positivegrowth7.0-9.0alkaliphile
31152positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31152aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
31152NaClpositivegrowth0.5-6 %
31152NaClpositiveoptimum2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3115216449alanine+carbon source
3115240585alpha-cyclodextrin+carbon source
31152286442-oxopentanoate+carbon source
3115228087glycogen+carbon source
31152506227N-acetylglucosamine+carbon source
3115226271proline+carbon source
3115230031succinate+carbon source
311524853esculin+hydrolysis

enzymes

@refvalueactivityec
31152acid phosphatase+3.1.3.2
31152alkaline phosphatase+3.1.3.1
31152catalase+1.11.1.6
31152cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
67771From intestine of a cultured flounder, `Paralichthys olivaceus`, fish farmShandong ProvinceChinaCHNAsia
20565intestine of a cultured flounder (Paralichthys olivaceus)ChinaCHNAsiaParalichthys olivaceus
67770Intestine of a cultured flounder (Paralichthys olivaceus) in Shandong ProvinceChinaCHNAsiaParalichthys olivaceus

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Host#Fishes
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3500.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_1821;97_2185;98_2682;99_3500&stattab=map
  • Last taxonomy: Flaviramulus ichthyoenteri subclade
  • 16S sequence: JX412958
  • Sequence Identity:
  • Total samples: 1090
  • soil counts: 22
  • aquatic counts: 945
  • animal counts: 117
  • plant counts: 6

Safety information

risk assessment

  • @ref: 20565
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20565
  • description: Flaviramulus ichthyoenteri Th78 16S ribosomal RNA gene, partial sequence
  • accession: JX412958
  • length: 1484
  • database: ena
  • NCBI tax ID: 1380600

Genome sequences

  • @ref: 67771
  • description: Wocania ichthyoenteri Th78
  • accession: GCA_000789235
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1380600

GC content

@refGC-contentmethod
2056531.5high performance liquid chromatography (HPLC)
3115231.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.437no
flagellatedno94.467no
gram-positiveno98.208yes
anaerobicno99.532no
aerobicyes87.933no
halophileno78.467no
spore-formingno96.294no
thermophileno98.524yes
glucose-utilyes85.024no
glucose-fermentno89.297no

External links

@ref: 20565

culture collection no.: DSM 26285, JCM 18634, KCTC 32142

straininfo link

  • @ref: 87991
  • straininfo: 405050

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23859948Flaviramulus ichthyoenteri sp. nov., an N-acylhomoserine lactone-degrading bacterium isolated from the intestine of a flounder (Paralichthys olivaceus), and emended descriptions of the genus Flaviramulus and Flaviramulus basaltis.Zhang Y, Tang K, Shi X, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.053744-02013Animals, Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Flounder/*microbiology, Intestines/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny32886593Wocania indica gen. nov., sp. nov., isolated from deep sea hydrothermal sulfide in the northwest Indian Ocean, and proposal to reclassify Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov.He Y, Zeng X, Xiong J, Lai Q, Li J, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0044392020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Hydrothermal Vents/*microbiology, Indian Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
20565Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26285Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26285)
31152Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172748028776041
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/
87991Reimer, 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-ID405050.1