Strain identifier

BacDive ID: 23024

Type strain: Yes

Species: Chryseobacterium piscium

Strain history: CIP <- 2006, CCUG <- 2005, LMG

NCBI tax ID(s): 333702 (species)

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General

@ref: 19029

BacDive-ID: 23024

DSM-Number: 25207

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

description: Chryseobacterium piscium CCUG 51923 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fish, freshly caught.

NCBI tax id

  • NCBI tax id: 333702
  • Matching level: species

strain history

@refhistory
19029<- CCUG <- P. A. R. Vandamme, LMG
121842CIP <- 2006, CCUG <- 2005, LMG

doi: 10.13145/bacdive23024.20230509.8.1

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 piscium
  • full scientific name: Chryseobacterium piscium de Beer et al. 2006

@ref: 19029

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium piscium

full scientific name: Chryseobacterium piscium de Beer et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31670negative1 µm0.5 µmrod-shaped
69480no90.207
69480negative99.969
121842negativerod-shapedno

pigmentation

  • @ref: 31670
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19029CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40029MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121842CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
121842CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19029positivegrowth28mesophilic
31670positivegrowth04-32
31670positiveoptimum30mesophilic
40029positivegrowth30mesophilic
59364positivegrowth30mesophilic

culture pH

@refabilitytypepH
31670positivegrowth7
31670positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31670aerobe
59364aerobe

spore formation

@refspore formationconfidence
31670no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
31670NaClpositivegrowth5 %
31670NaClpositiveoptimum5 %

observation

  • @ref: 31670
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3167030089acetate+carbon source
3167037684mannose+carbon source
3167017632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12184217632nitrate-reduction
12184216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3167035581indoleyes
12184235581indoleno

metabolite tests

  • @ref: 31670
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31670catalase+1.11.1.6
31670cytochrome oxidase+1.9.3.1
31670urease+3.5.1.5
121842oxidase+
121842catalase+1.11.1.6
121842urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121842-+++-+----++----++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121842----------+/--+/----------+/--+--+/--------+/---+/-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountryisolation date
19029fish, freshly caughtSouth African coastline
59364Fish,freshly caughtSouth1996Atlantic Ocean
121842Animal, FishSouthAtlantic Ocean1996

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_299.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_254;99_299&stattab=map
  • Last taxonomy: Chryseobacterium
  • 16S sequence: AM040439
  • Sequence Identity:
  • Total samples: 1234
  • soil counts: 131
  • aquatic counts: 174
  • animal counts: 665
  • plant counts: 264

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
190291Risk group (German classification)
1218421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19029
  • description: Chryseobacterium piscium partial 16S rRNA gene, strain LMG 23089T
  • accession: AM040439
  • length: 1469
  • database: ena
  • NCBI tax ID: 333702

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium piscium CCUG 51923GCA_003385415contigncbi333702
66792Chryseobacterium piscium strain CCUG 51923333702.10wgspatric333702
66792Chryseobacterium piscium CCUG 519232905984197draftimg333702

GC content

  • @ref: 31670
  • GC-content: 33.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.24yes
anaerobicno99.241yes
halophileno92.382no
spore-formingno95.163yes
glucose-utilyes84.674no
motileno90.817no
flagellatedno96.204no
thermophileno99.732no
aerobicyes90.03yes
glucose-fermentno92.084no

External links

@ref: 19029

culture collection no.: CCUG 51923, CIP 109277, DSM 25207, CCUG 5192, LMG 23089

straininfo link

  • @ref: 87264
  • straininfo: 131341

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738109Chryseobacterium piscium sp. nov., isolated from fish of the South Atlantic Ocean off South Africa.de Beer H, Hugo CJ, Jooste PJ, Vancanneyt M, Coenye T, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.64014-02006Animals, Atlantic Ocean, Chryseobacterium/*classification/genetics/growth & development/*isolation & purification, Culture Media, DNA, Bacterial/genetics, Fishes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, South AfricaCultivation
Phylogeny19819990Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater.Joung Y, Song J, Lee K, Oh HM, Joh K, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.017707-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Genetics30637405Draft Genome Sequences of Seven Chryseobacterium Type Strains.Matu A, Lum Nde A, Oosthuizen L, Hitzeroth A, Badenhorst M, Duba L, Gidaga M, Klinck J, Kriek IM, Lekoma PJ, Nel L, Dos Ramos SM, Rossouw J, Salomane N, Segone N, Serobe S, Tiyani T, Hugo CJ, Newman JDMicrobiol Resour Announc10.1128/MRA.01518-182019
Phylogeny36410095Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey.Saticioglu IB, Ay H, Altun S, Duman MSyst Appl Microbiol10.1016/j.syapm.2022.1263852022

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19029Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25207)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25207
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
31670Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794928776041
40029Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7000
59364Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51923)https://www.ccug.se/strain?id=51923
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)
68371Automatically annotated from API 50CH acid
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
87264Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131341.1StrainInfo: A central database for resolving microbial strain identifiers
121842Curators of the CIPCollection of Institut Pasteur (CIP 109277)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109277