Strain identifier

BacDive ID: 5704

Type strain: Yes

Species: Chryseobacterium piscicola

Strain Designation: VQ-6316s

Strain history: CIP <- 2010, DSMZ <- R. Avendano-Herrera, Lab. Veterquimica, Santiago, Chile: strain VQ-6316s

NCBI tax ID(s): 551459 (species)

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General

@ref: 15541

BacDive-ID: 5704

DSM-Number: 21068

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, psychrophilic, Gram-negative, rod-shaped, animal pathogen

description: Chryseobacterium piscicola VQ-6316s is an obligate aerobe, psychrophilic, Gram-negative animal pathogen that was isolated from diseased Atlantic salmon Salmo salar.

NCBI tax id

  • NCBI tax id: 551459
  • Matching level: species

strain history

@refhistory
15541<- R. Avendaño-Herrera, Lab. Veterquímica, Santiago, Chile; VQ-6316s
121840CIP <- 2010, DSMZ <- R. Avendano-Herrera, Lab. Veterquimica, Santiago, Chile: strain VQ-6316s

doi: 10.13145/bacdive5704.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium piscicola
  • full scientific name: Chryseobacterium piscicola Ilardi et al. 2009

@ref: 15541

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium piscicola

full scientific name: Chryseobacterium piscicola Ilardi et al. 2009

strain designation: VQ-6316s

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29135negative2.55 µm1 µmrod-shapedno
69480no92.902
69480negative99.987
121840negativerod-shapedyes

pigmentation

  • @ref: 29135
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15541NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39757MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121840CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
15541positivegrowth15psychrophilic
29135positivegrowth04-28
29135positiveoptimum15psychrophilic
39757positivegrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121840
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
29135NaClpositivegrowth0-3 %
29135NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
291354853esculin+hydrolysis
12184017632nitrate-reduction
12184016301nitrite-reduction

metabolite production

  • @ref: 121840
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29135acid phosphatase+3.1.3.2
29135alkaline phosphatase+3.1.3.1
29135catalase+1.11.1.6
29135gelatinase+
29135cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121840oxidase+
121840catalase+1.11.1.6
121840urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121840-+++++++--++-----+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15541diseased Atlantic salmon Salmo salarSalmo salarRegion Los Lagos, OsornoChileCHLMiddle and South America
121840Animal, Diseased Atlantic Salmon, Salmo salarLos Lagos, OsornoChileCHLMiddle and South America

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes
  • Cat3: #Salmonidae

taxonmaps

  • @ref: 69479
  • File name: preview.99_6864.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_1157;98_5054;99_6864&stattab=map
  • Last taxonomy: Chryseobacterium piscicola subclade
  • 16S sequence: EU869190
  • Sequence Identity:
  • Total samples: 2274
  • soil counts: 322
  • aquatic counts: 564
  • animal counts: 1185
  • plant counts: 203

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
15541yes1Risk group (German classification)
1218401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15541
  • description: Chryseobacterium piscicola strain VQ-6316s 16S ribosomal RNA gene, partial sequence
  • accession: EU869190
  • length: 1401
  • database: ena
  • NCBI tax ID: 551459

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium piscicola DSM 21068GCA_900156685contigncbi551459
66792Chryseobacterium piscicola DSM 21068GCA_002943675scaffoldncbi551459
66792Chryseobacterium piscicola strain DSM 21068551459.6wgspatric551459
66792Chryseobacterium piscicola strain DSM 21068551459.4wgspatric551459
66792Chryseobacterium piscicola DSM 210682681813514draftimg551459

GC content

@refGC-contentmethod
1554132.5high performance liquid chromatography (HPLC)
2913532.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.649no
gram-positiveno98.242yes
anaerobicno99.29no
aerobicyes91.434no
halophileno96.174no
spore-formingno95.636no
glucose-utilyes88.073no
motileno92.051no
glucose-fermentno93.15no
thermophileno99.355yes

External links

@ref: 15541

culture collection no.: DSM 21068, CECT 7357, CIP 110179

straininfo link

  • @ref: 75186
  • straininfo: 364829

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643904Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish.Ilardi P, Fernandez J, Avendano-Herrera RInt J Syst Evol Microbiol10.1099/ijs.0.007021-02009Animals, Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Salmonidae/microbiologyMetabolism
Phylogeny34232119Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola.Chhetri G, Kim J, Kim I, Kang M, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0048542021Bacterial Typing Techniques, Base Composition, Caseins/metabolism, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Phosphatidylethanolamines, *Phylogeny, Pigmentation, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15541Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21068)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21068
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29135Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2556028776041
39757Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8009
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75186Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364829.1StrainInfo: A central database for resolving microbial strain identifiers
121840Curators of the CIPCollection of Institut Pasteur (CIP 110179)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110179