Strain identifier

BacDive ID: 5693

Type strain: Yes

Species: Chryseobacterium luteum

Strain Designation: P 456/04

Strain history: CIP <- 2008, DSMZ

NCBI tax ID(s): 421531 (species)

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General

@ref: 7619

BacDive-ID: 5693

DSM-Number: 18605

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

description: Chryseobacterium luteum P 456/04 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from phyllosphere of grasses.

NCBI tax id

  • NCBI tax id: 421531
  • Matching level: species

strain history

@refhistory
7619<- U. Behrendt, Leibniz-Centre Agricult. Landscape Res. (ZALF), Inst. Landscape Matter Dynamics, Müncheberg; P 456/04
333262008, DSMZ
120700CIP <- 2008, DSMZ

doi: 10.13145/bacdive5693.20230509.8.1

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 luteum
  • full scientific name: Chryseobacterium luteum Behrendt et al. 2007

@ref: 7619

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium luteum

full scientific name: Chryseobacterium luteum Behrendt et al. 2007 emend. Montero-Calasanz et al. 2014 emend. Hahnke et al. 2016

strain designation: P 456/04

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32196negativerod-shapedno
69480negative99.991
120700negativerod-shapedno

pigmentation

  • @ref: 32196
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7619TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
33326MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120700CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7619positivegrowth21-30
32196positivegrowth4.0-37
32196positiveoptimum21psychrophilic
33326positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32196aerobe
120700obligate aerobe

spore formation

@refspore formationconfidence
32196no
69481no100
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3219622599arabinose+carbon source
3219628757fructose+carbon source
3219617234glucose+carbon source
3219617754glycerol+carbon source
3219628087glycogen+carbon source
3219617306maltose+carbon source
3219637684mannose+carbon source
32196506227N-acetylglucosamine+carbon source
3219617814salicin+carbon source
3219617992sucrose+carbon source
3219627082trehalose+carbon source
321964853esculin+hydrolysis
12070017632nitrate-reduction
12070016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3219635581indoleyes
12070035581indoleyes

metabolite tests

  • @ref: 32196
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32196catalase+1.11.1.6
32196gelatinase+
32196cytochrome 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
120700oxidase+/-
120700catalase+1.11.1.6
120700urease-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
120700-+-+-+++++++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7619phyllosphere of grassesBrandenburg, Havelland, PaulinenaueGermanyDEUEurope
120700Phyllosphere of grassesPaulinenaueGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76191Risk group (German classification)
1207001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7619
  • description: Chryseobacterium luteum partial 16S rRNA gene, type strain DSM 18605T
  • accession: AM489609
  • length: 1465
  • database: ena
  • NCBI tax ID: 421531

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium luteum DSM 18605GCA_000737785contigncbi421531
66792Chryseobacterium luteum strain DSM 18605421531.5wgspatric421531
66792Chryseobacterium luteum DSM 186052617271211draftimg421531

GC content

  • @ref: 7619
  • GC-content: 37.3
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.199no
anaerobicno99.363yes
halophileno93.86no
spore-formingno94.335no
glucose-utilyes85.531no
aerobicyes89.495no
flagellatedno94.782yes
thermophileno99.559no
motileno89.858yes
glucose-fermentno92.511no

External links

@ref: 7619

culture collection no.: DSM 18605, CIP 109792, LMG 23785

straininfo link

  • @ref: 75175
  • straininfo: 309444

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684275Chryseobacterium luteum sp. nov., associated with the phyllosphere of grasses.Behrendt U, Ulrich A, Sproer C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65104-02007Chryseobacterium/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny23456810Chryseobacterium carnipullorum sp. nov., isolated from raw chicken.Charimba G, Jooste P, Albertyn J, Hugo CInt J Syst Evol Microbiol10.1099/ijs.0.049445-02013Animals, Bacterial Typing Techniques, Base Composition, Chickens/*microbiology, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Food Contamination, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Poultry/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/analysisBiotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7619Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18605)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18605
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
32196Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2843828776041
33326Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7575
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
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
75175Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309444.1StrainInfo: A central database for resolving microbial strain identifiers
120700Curators of the CIPCollection of Institut Pasteur (CIP 109792)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109792