Strain identifier

BacDive ID: 158654

Type strain: Yes

Species: Bizionia berychis

Strain Designation: RA3-3-1

Strain history: <- Jung-Hoon Y00n, Sungkyunkwan Univ.

NCBI tax ID(s): 2036822 (species)

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General

@ref: 65381

BacDive-ID: 158654

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

description: Bizionia berychis RA3-3-1 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from splendid alfonsino .

NCBI tax id

  • NCBI tax id: 2036822
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon Y00n, Sungkyunkwan Univ.

doi: 10.13145/bacdive158654.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Bizionia
  • species: Bizionia berychis
  • full scientific name: Bizionia berychis Kim et al. 2018

@ref: 65381

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Bizionia

species: Bizionia berychis

strain designation: RA3-3-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
65381negative0.8-7 µm0.2-0.4 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 65381
  • colony size: 1-2 mm
  • colony color: strong yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: marine agar 2216

pigmentation

  • @ref: 65381
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65381
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65381positiveoptimum25mesophilic
65381positivegrowth4psychrophilic
65381positivegrowth30mesophilic
65381nogrowth35mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
65381positiveoptimum7-8
65381positivegrowth5.5
65381nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65381aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65381NaClpositivegrowth0.5-9 %(w/v)
65381NaClpositiveoptimum1-3 %(w/v)

observation

@refobservation
65381Growth does not occur under anaerobic conditions on MA and on MA supplemented with nitrate.
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6538130089acetate-carbon source
6538116150benzoate-carbon source
65381casein+hydrolysis
6538117057cellobiose-carbon source
6538116947citrate-carbon source
6538115824D-fructose-carbon source
6538112936D-galactose-carbon source
6538116024D-mannose-carbon source
6538165327D-xylose-carbon source
653814853esculin-hydrolysis
6538115740formate-carbon source
653815291gelatin+hydrolysis
6538117368hypoxanthine-hydrolysis
6538130849L-arabinose-carbon source
6538129985L-glutamate-carbon source
6538115589L-malate-carbon source
6538117895L-tyrosine+hydrolysis
6538118420magnesium(2+)-required for growth
6538117306maltose-carbon source
6538117632nitrate+reduction
6538115361pyruvate-carbon source
6538117814salicin-carbon source
6538128017starch-hydrolysis
6538130031succinate-carbon source
6538117992sucrose-carbon source
6538127082trehalose-carbon source
6538153424tween 20+hydrolysis
6538153423tween 40+hydrolysis
6538153425tween 60+hydrolysis
6538153426tween 80+hydrolysis
6538116199urea-hydrolysis
6538115318xanthine-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6538128368novobiocinyesyes5 µg (disc)
653816472lincomycinyesyes15 µg (disc)
6538116869oleandomycinyesyes15 µg (disc)
653813542cephalothinyesyes30 µg (disc)
6538127902tetracyclineyesyes30 µg (disc)
653813393carbenicillinyesyes100 µg (disc)
6538117698chloramphenicolyesyes100 µg (disc)
6538128971ampicillinyesyes10 µg (disc)
6538118208penicillin gyesyes20 Unit (disc)
6538117833gentamicinyesyes30 µg (disc)
653816104kanamycinyesyes30 µg (disc)
6538117076streptomycinyesyes50 µg (disc)
653818309polymyxin byesyes100 Unit (disc)

enzymes

@refvalueactivityec
65381catalase+1.11.1.6
65381cytochrome oxidase+1.9.3.1
65381alkaline phosphatase+3.1.3.1
65381esterase (C 4)+
65381esterase Lipase (C 8)+
65381leucine arylamidase+3.4.11.1
65381valine arylamidase+
65381acid phosphatase+3.1.3.2
65381naphthol-AS-BI-phosphohydrolase+
65381lipase (C 14)-
65381cystine arylamidase-3.4.11.3
65381trypsin-3.4.21.4
65381alpha-chymotrypsin-3.4.21.1
65381alpha-galactosidase-3.2.1.22
65381beta-galactosidase-3.2.1.23
65381beta-glucuronidase-3.2.1.31
65381alpha-glucosidase-3.2.1.20
65381beta-glucosidase-3.2.1.21
65381N-acetyl-beta-glucosaminidase-3.2.1.52
65381alpha-mannosidase-3.2.1.24
65381alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryenrichment cultureenrichment culture compositionenrichment culture temperatureisolation proceduregeographic location
65381splendid alfonsino (Beryx splendens)2016-03Northwest PacificR2A/marine agar 2216(1 : 1, v/v) of Reasoner's 2A agar and marine agar 221620standard dilution plating technique
67771From splendid alfonsino, `Beryx splendens`Pacific Oceanthe North Pacific Ocean

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_13487.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_6917;97_8293;98_10186;99_13487&stattab=map
  • Last taxonomy: Bizionia berychis
  • 16S sequence: MF962574
  • Sequence Identity:
  • Total samples: 21
  • aquatic counts: 19
  • animal counts: 2

Sequence information

16S sequences

  • @ref: 65381
  • description: 16S rRNA gene sequence
  • accession: MF962574
  • database: nuccore

GC content

@refGC-contentmethod
6538134.1high performance liquid chromatography (HPLC)
6777134.1

External links

@ref: 65381

culture collection no.: KCTC 62140, NBRC 113024

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29469688Bizionia berychis sp. nov., isolated from intestinal tract of a splendid alfonsino (Beryx splendens).Kim YO, Park IS, Park S, Nam BH, Kim DG, Choi SG, Bae JW, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0026562018Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fishes/*microbiology, Flavobacteriaceae/*classification/genetics/isolation & purification, Intestines/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
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/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
65381Young-Ok Kim, In-Suk Park, Sooyeon Park, Bo-Hye Nam, Dong-Gyun Kim, Seok-Gwan Choi, Jin-Woo Bae, Jung-Hoon YoonBizionia berychis sp. nov., isolated from intestinal tract of a splendid alfonsino (Beryx splendens)10.1099/ijsem.0.002656IJSEM 68: 1227-1232 201829469688
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/