Strain identifier

BacDive ID: 5681

Type strain: Yes

Species: Chryseobacterium caeni

Strain Designation: N4

Strain history: CIP <- 2007, DSMZ <- Z.X. Quan, Fudan Univ., Shangai, China: strain N4

NCBI tax ID(s): 365343 (species)

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General

@ref: 7152

BacDive-ID: 5681

DSM-Number: 17710

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

description: Chryseobacterium caeni N4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sludge of a nickel-complexed cyanide treatment bioreactor.

NCBI tax id

  • NCBI tax id: 365343
  • Matching level: species

strain history

@refhistory
7152<- Z.-X. Quan, Fudan Univ., Shanghai, China; N4
67771<- ZX Quan, KAIST
117091CIP <- 2007, DSMZ <- Z.X. Quan, Fudan Univ., Shangai, China: strain N4

doi: 10.13145/bacdive5681.20230509.8.1

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 caeni
  • full scientific name: Chryseobacterium caeni Quan et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Epilithonimonas caeni

@ref: 7152

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium caeni

full scientific name: Chryseobacterium caeni Quan et al. 2007 emend. Hahnke et al. 2016

strain designation: N4

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31887negativerod-shapedno
67771rod-shapedno
67771negative
69480negative99.982
117091negativerod-shapedno

pigmentation

  • @ref: 31887
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7152R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
37652MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
117091CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7152positivegrowth28mesophilic
31887positivegrowth05-37
31887positiveoptimum28-30mesophilic
37652positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31887positivegrowth06-10alkaliphile
31887positiveoptimum6.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31887aerobe
67771aerobe
117091obligate aerobe

spore formation

@refspore formationconfidence
31887no
67771no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
31887NaClpositivegrowth0-3 %
31887NaClpositiveoptimum1.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3188722599arabinose+carbon source
3188717234glucose+carbon source
3188728087glycogen+carbon source
3188717306maltose+carbon source
3188717992sucrose+carbon source
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
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+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
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+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
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11709117632nitrate-reduction
11709116301nitrite-reduction

metabolite production

  • @ref: 117091
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31887urease+3.5.1.5
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
117091oxidase+
117091catalase+1.11.1.6
117091urease-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
117091-+++-++--+++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117091---+/--+/-----+++---------++++++--++---++-+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7152sludge of a nickel-complexed cyanide treatment bioreactorDaejeonRepublic of KoreaKORAsia
67771From wastewater treatment bioreactorKAISTRepublic of KoreaKORAsia
117091Environment, Sludge of a nickel-complexed cyanide treatment bioreactorDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Environmental#Terrestrial#Mud (Sludge)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71521Risk group (German classification)
1170911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7152
  • description: Chryseobacterium caeni N4 16S ribosomal RNA gene, partial sequence
  • accession: DQ336714
  • length: 1483
  • database: ena
  • NCBI tax ID: 365343

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Epilithonimonas caeni DSM 17710GCA_000426465scaffoldncbi1121285
66792Chryseobacterium caeni DSM 177101121285.4wgspatric1121285
66792Chryseobacterium caeni DSM 177102524614876draftimg1121285

GC content

@refGC-contentmethod
715238.2
715236.6sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.316yes
flagellatedno95.963yes
gram-positiveno98.318yes
anaerobicno99.398yes
aerobicyes85.999yes
halophileno96.698yes
spore-formingno95.205no
glucose-utilyes88.037yes
thermophileno99.469yes
glucose-fermentno90.819no

External links

@ref: 7152

culture collection no.: DSM 17710, CCBAU 10201, CIP 109625, KCTC 12506

straininfo link

  • @ref: 75163
  • straininfo: 294435

literature

  • topic: Phylogeny
  • Pubmed-ID: 17220456
  • title: Chryseobacterium caeni sp. nov., isolated from bioreactor sludge.
  • authors: Quan ZX, Kim KK, Kim MK, Jin L, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64599-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7152Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17710)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17710
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
31887Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2814728776041
37652Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7389
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
75163Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294435.1StrainInfo: A central database for resolving microbial strain identifiers
117091Curators of the CIPCollection of Institut Pasteur (CIP 109625)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109625