Strain identifier

BacDive ID: 133395

Type strain: Yes

Species: Flavobacterium crassostreae

Strain Designation: LPB0076

Strain history: H. Yi; Korea Univ., South Korea; LPB0076.

NCBI tax ID(s): 1763534 (species)

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General

@ref: 25263

BacDive-ID: 133395

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

description: Flavobacterium crassostreae LPB0076 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and has a brown diffusible pigmentation.

NCBI tax id

  • NCBI tax id: 1763534
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Yi; Korea Univ., South Korea; LPB0076.

doi: 10.13145/bacdive133395.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 25263

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium crassostreae

strain designation: LPB0076

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25263negative1.8-4.0 µm0.4-0.5 µmrod-shapedno
69480negative99.997
69480no93.168

colony morphology

  • @ref: 25263
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

pigmentation

@refproductioncolorname
25263nobrown diffusible
25263noFlexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
25263Marine agar (MA)yes
25263Trypticase Soy Agar (TSA)yes
25263Reasoner's 2A agar (R2A)yes
25263NA (nutrient agar)yes

culture temp

@refgrowthtypetemperaturerange
25263positivegrowth15-30
25263positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
25263positivegrowth5.5-8.0
25263positiveoptimum6.5-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25263
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
25263NaClpositivegrowth0-4 %
25263NaCloptimum2-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2526317128adipate-carbon source
252632509agar-degradation
2526358187alginate-degradation
2526327613amygdalin-builds acid from
2526385146carboxymethylcellulose-degradation
2526317029chitin-degradation
2526316947citrate-assimilation
2526317634D-glucose-builds acid from
2526317924D-sorbitol-builds acid from
2526327689decanoate-carbon source
2526316991dna-degradation
252634853esculin-degradation
252635291gelatin-degradation
2526317368hypoxanthine-degradation
2526317268myo-inositol-builds acid from
2526330849L-arabinose-carbon source
2526330849L-arabinose-builds acid from
2526362345L-rhamnose-builds acid from
2526317895L-tyrosine-degradation
2526325115malate-carbon source
2526317306maltose-carbon source
2526328053melibiose-builds acid from
25263506227N-acetylglucosamine-carbon source
2526317632nitrate-reduction
2526318401phenylacetate-carbon source
2526332032potassium gluconate-carbon source
2526353258sodium citrate-carbon source
2526328017starch-degradation
2526317992sucrose-builds acid from
2526353424tween 20-degradation
2526353423tween 40-degradation
2526353425tween 60-degradation
2526353426tween 80-degradation
2526315318xanthine-degradation
25263casein+degradation
2526329864mannitol+carbon source
2526329864mannitol+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
2526315688acetoinno
2526316136hydrogen sulfideno
2526335581indoleno

enzymes

@refvalueactivityec
252636-phospho-beta-galactosidase-3.2.1.85
25263acid phosphatase+3.1.3.2
25263alkaline phosphatase+3.1.3.1
25263alpha-chymotrypsin-3.4.21.1
25263alpha-fucosidase-3.2.1.51
25263alpha-galactosidase-3.2.1.22
25263alpha-glucosidase-3.2.1.20
25263alpha-mannosidase-3.2.1.24
25263arginine dihydrolase-3.5.3.6
25263beta-glucosidase-3.2.1.21
25263beta-glucuronidase-3.2.1.31
25263catalase+1.11.1.6
25263cystine arylamidase-3.4.11.3
25263cytochrome oxidase+1.9.3.1
25263esterase (C 4)-
25263esterase Lipase (C 8)-
25263leucine arylamidase+3.4.11.1
25263lipase (C 14)-
25263lysine decarboxylase-4.1.1.18
25263N-acetyl-beta-glucosaminidase-3.2.1.52
25263naphthol-AS-BI-phosphohydrolase+
25263ornithine decarboxylase-4.1.1.17
25263trypsin-3.4.21.4
25263tryptophan deaminase-4.1.99.1
25263urease-3.5.1.5
25263valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation datehost species
25263a gut sample of a Pacific oyster (C. gigas) caught at Yeongheung Island, KoreaYeongheung Island, KoreaRepublic of KoreaKORAsia371262016-02-27
67770Pacific oyster (Crassostrea gigas) caught off Yeongheung IslandRepublic of KoreaKORAsiaCrassostrea gigas

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_1300.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_163;97_175;98_1028;99_1300&stattab=map
  • Last taxonomy: Flavobacterium crassostreae subclade
  • 16S sequence: KU057346
  • Sequence Identity:
  • Total samples: 411
  • soil counts: 124
  • aquatic counts: 204
  • animal counts: 59
  • plant counts: 24

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
2526316S rRNA gene sequence and the whole-genome sequenceKU0573461405ena1763534
2526316S rRNA gene sequence and the whole-genome sequenceCP017688nuccore1763534

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium crassostreae LPB0076GCA_001831475completencbi1763534
66792Flavobacterium crassostreae LPB0076GCA_001686945contigncbi1763534
66792Flavobacterium crassostreae LPB00762772190676draftimg1763534
66792Flavobacterium crassostreae LPB00762721755704completeimg1763534

GC content

@refGC-contentmethod
2526335.9
6777036genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno92.521yes
gram-positiveno98.452yes
anaerobicno99.551yes
aerobicyes85.547yes
halophileno95.847no
spore-formingno95.012no
thermophileno96.426yes
glucose-utilyes78.018no
motileno88.079no
glucose-fermentno93.648no

External links

@ref: 25263

culture collection no.: KACC 18706, JCM 31219

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27959776Flavobacterium crassostreae sp. nov., isolated from Pacific oyster.Choi S, Shin SK, Kim E, Yi HInt J Syst Evol Microbiol10.1099/ijsem.0.0017282017Animals, Bacterial Typing Techniques, Base Composition, Crassostrea/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome
Phylogeny34296991Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout.Duman M, Ay H, Altun S, Sahin N, Saticioglu IBInt J Syst Evol Microbiol10.1099/ijsem.0.0049032021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oncorhynchus mykiss/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

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
25263S. S. Choi, S. K.,Kim, E.,Yi, H.Flavobacterium crassostreae sp. nov., isolated from Pacific oyster10.1099/ijsem.0.001728IJSEM 67: 988-992 201727959776
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/
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