Strain identifier

BacDive ID: 5668

Type strain: Yes

Species: Chryseobacterium defluvii

Strain Designation: B2, B2T

Strain history: CIP <- 2001, P. Kämpfer, Giessen Univ., Giessen, Germany: strain B2T <- U. Dreyer

NCBI tax ID(s): 160396 (species)

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General

@ref: 5257

BacDive-ID: 5668

DSM-Number: 14219

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

description: Chryseobacterium defluvii B2 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from wastewater.

NCBI tax id

  • NCBI tax id: 160396
  • Matching level: species

strain history

@refhistory
5257<- P. Kämpfer; B2 <- U. Dreyer
67771<- CIP <- 2001, P Kampfer, Univ., Giessen, Germany, strain B2 U. Dreyer
118866CIP <- 2001, P. Kämpfer, Giessen Univ., Giessen, Germany: strain B2T <- U. Dreyer

doi: 10.13145/bacdive5668.20230509.8.1

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 defluvii
  • full scientific name: Chryseobacterium defluvii Kämpfer et al. 2003

@ref: 5257

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium defluvii

full scientific name: Chryseobacterium defluvii Kämpfer et al. 2003 emend. Montero-Calasanz et al. 2013

strain designation: B2, B2T

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771negative
69480no93.924
69480negative99.983
118866rod-shapednonegative

colony morphology

  • @ref: 118866
  • hemolysis ability: 1

pigmentation

  • @ref: 118866
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5257NUTRIENT 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
40560MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118866CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5257positivegrowth28mesophilic
40560positivegrowth30mesophilic
57814positivegrowth30-42
67771positivegrowth28mesophilic
118866positivegrowth15-41
118866nogrowth5psychrophilic
118866nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57814aerobe
67771aerobe
118866obligate aerobe

spore formation

@refspore formationconfidence
67771no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
118866NaClpositivegrowth0 %
118866NaClnogrowth2 %
118866NaClnogrowth4 %
118866NaClnogrowth6 %
118866NaClnogrowth8 %
118866NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11886616947citrate-carbon source
1188664853esculin+hydrolysis
118866606565hippurate+hydrolysis
11886617632nitrate-builds gas from
11886617632nitrate-reduction
11886616301nitrite-builds gas from
11886616301nitrite-reduction
11886615792malonate-assimilation
11886617632nitrate-respiration

antibiotic resistance

  • @ref: 118866
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118866
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11886615688acetoin-
11886617234glucose-

enzymes

@refvalueactivityec
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
118866oxidase+
118866beta-galactosidase+3.2.1.23
118866alcohol dehydrogenase-1.1.1.1
118866gelatinase+
118866amylase-
118866DNase-
118866caseinase+3.4.21.50
118866catalase+1.11.1.6
118866tween esterase+
118866gamma-glutamyltransferase+2.3.2.2
118866lecithinase+
118866lipase-
118866lysine decarboxylase-4.1.1.18
118866ornithine decarboxylase-4.1.1.17
118866phenylalanine ammonia-lyase-4.3.1.24
118866protease+
118866tryptophan deaminase-
118866urease+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
118866-+-+-++-+-++---+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118866+--++----++-----+-+-++----------------------------------------+--+--------------------+---++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
5257wastewaterBerlinGermanyDEUEurope
57814WastewaterBerlinGermanyDEUEurope1998
67771From WastewaterBerlinGermanyDEUEurope
118866Environment, WastewaterBerlinGermanyDEUEurope1998

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_174411.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_1573;98_20005;99_174411&stattab=map
  • Last taxonomy: Chryseobacterium defluvii
  • 16S sequence: AJ309324
  • Sequence Identity:
  • Total samples: 19
  • soil counts: 8
  • aquatic counts: 4
  • animal counts: 2
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52571Risk group (German classification)
1188661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5257
  • description: Chryseobacterium defluvium 16S rRNA gene, isolate B2
  • accession: AJ309324
  • length: 1415
  • database: ena
  • NCBI tax ID: 160396

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium defluvii DSM 14219GCA_003634775scaffoldncbi160396
66792Chryseobacterium defluvii strain DSM 14219160396.5wgspatric160396
66792Chryseobacterium defluvii DSM 142192681812957draftimg160396

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.258yes
gram-positiveno98.261yes
anaerobicno99.608no
aerobicyes89.389yes
halophileno96.138no
spore-formingno94.881yes
glucose-utilyes83.101no
thermophileno99.284no
motileno90.175no
glucose-fermentno93.714no

External links

@ref: 5257

culture collection no.: DSM 14219, CIP 107207, CCUG 47675, KCTC 12434

straininfo link

  • @ref: 75150
  • straininfo: 20512

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656158Chryseobacterium defluvii sp. nov., isolated from wastewater.Kampfer P, Dreyer U, Neef A, Dott W, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.02073-02003Bacteroides/*classification/genetics/*isolation & purification/metabolism, Bioreactors, Cytophaga/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiologyEnzymology
Phylogeny15653865Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment.Kim KK, Bae HS, Schumann P, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02931-02005Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitle
5257Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14219)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14219
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
40560Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4618
57814Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47675)https://www.ccug.se/strain?id=47675
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
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
75150Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID20512.1StrainInfo: A central database for resolving microbial strain identifiers
118866Curators of the CIPCollection of Institut Pasteur (CIP 107207)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107207