Strain identifier

BacDive ID: 141119

Type strain: Yes

Species: Ichthyobacterium seriolicida

Strain Designation: JBKA-6

Strain history: T. Takano JBKA-6.

NCBI tax ID(s): 242600 (species)

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General

@ref: 44031

BacDive-ID: 141119

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, rod-shaped, animal pathogen

description: Ichthyobacterium seriolicida JBKA-6 is a Gram-negative, motile, rod-shaped animal pathogen that was isolated from blood sample from a jaundiced farmed yellowtail.

NCBI tax id

  • NCBI tax id: 242600
  • Matching level: species

strain history

  • @ref: 67770
  • history: T. Takano JBKA-6.

doi: 10.13145/bacdive141119.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Ichthyobacteriaceae
  • genus: Ichthyobacterium
  • species: Ichthyobacterium seriolicida
  • full scientific name: Ichthyobacterium seriolicida Takano et al. 2016

@ref: 44031

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Ichthyobacteriaceae

genus: Ichthyobacterium

species: Ichthyobacterium seriolicida

strain designation: JBKA-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
44031negative4-6 µm0.3 µmrod-shapedyesgliding
69480negative99.999

Culture and growth conditions

culture medium

@refnamegrowthcomposition
44031L-15yeswith fetal bovine serum
44031Marine agar (MA)no
44031solid mediano

culture temp

@refgrowthtypetemperaturerange
44031positivegrowth18-28
44031positiveoptimum26mesophilic
67770positivegrowth25mesophilic

culture pH

  • @ref: 44031
  • ability: positive
  • type: optimum
  • pH: 7.0-7.5

Physiology and metabolism

spore formation

@reftype of sporespore formationconfidence
44031sporeno
69481no100
69480no99.998

halophily

  • @ref: 44031
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1.6 %(w/v)

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4403128971ampicillinyesyes0.125 µg/mL
4403117698chloramphenicolyesyes1-2 µg/mL
4403159066oxolinateyesyes0.5-1 µg/mL
4403127701oxytetracyclineyesyes0.063-0.125 µg/mL
4403128915fosfomycinyesyes128 µg/mL
440316104kanamycinyesyes128 µg/mL
4403132164sulfamonomethoxineyesyes128 µg/mL

enzymes

@refvalueactivityec
44031catalase-1.11.1.6
44031cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturehost species
44031blood sample from a jaundiced farmed yellowtail1991-10Aji-cho, Kagawa PrefectureJapanJPNAsiaLeibovitz's L-15 (L-15) mediumwith 10% Fetal bovine serum2 weeks25
67770Farmed yellowtail (Seriola quinqueradiata) showing symptoms of bacterial haemolytic jaundiceAji-cho, Kagawa Pref.JapanJPNAsiaSeriola quinqueradiata

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body Product#Fluids#Blood
#Infection#Disease

taxonmaps

  • @ref: 69479
  • File name: preview.99_25921.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2852;96_12969;97_15745;98_19483;99_25921&stattab=map
  • Last taxonomy: Ichthyobacterium seriolicida subclade
  • 16S sequence: AB713897
  • Sequence Identity:
  • Total samples: 84
  • soil counts: 3
  • aquatic counts: 40
  • animal counts: 41

Safety information

risk assessment

  • @ref: 44031
  • pathogenicity animal: yes

Sequence information

16S sequences

  • @ref: 44031
  • description: 16S rRNA gene sequence
  • accession: AB713897
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ichthyobacterium seriolicida JBKA-6GCA_002369955completencbi242600
66792Ichthyobacterium seriolicida JBKA-62775506813completeimg242600

GC content

  • @ref: 67770
  • GC-content: 33.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.453yes
gram-positiveno98.657yes
anaerobicno90.065no
aerobicno72.314no
halophileno52.9no
spore-formingno96.735yes
glucose-utilyes78.256no
thermophileno82.126no
motileno92.848no
glucose-fermentno78.297no

External links

@ref: 44031

culture collection no.: ATCC BAA 2465, JCM 18228

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26554606Ichthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum 'Bacteroidetes', isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.Takano T, Matsuyama T, Sakai T, Nakamura Y, Kamaishi T, Nakayasu C, Kondo H, Hirono I, Fukuda Y, Sorimachi M, Iida TInt J Syst Evol Microbiol10.1099/ijsem.0.0007572015Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fish Diseases/microbiology, Jaundice/microbiology, Perciformes/*microbiology, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics28183761Complete Genome Sequence of Ichthyobacterium seriolicida JBKA-6(T), Isolated from Yellowtail (Seriola quinqueradiata) Affected by Bacterial Hemolytic Jaundice.Takano T, Nakamura Y, Matsuyama T, Sakai T, Shigenobu Y, Sugaya T, Yasuike M, Fujiwara A, Kondo H, Hirono I, Fukuda Y, Nakayasu CGenome Announc10.1128/genomeA.01574-162017Phylogeny

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
44031Tomokazu Takano, Tomomasa Matsuyama, Takamitsu Sakai, Yoji Nakamura, Takashi Kamaishi, Chihaya Nakayasu, Hidehiro Kondo, Ikuo Hirono, Yutaka Fukuda, Minoru Sorimachi and Takaji IidaIchthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum 'Bacteroidetes', isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.10.1099/ijsem.0.000757IJSEM 66: 580-586 201626554606
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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