Strain identifier

BacDive ID: 23023

Type strain: Yes

Species: Chryseobacterium vrystaatense

Strain history: CIP <- 2005, CCUG <- 2005, LMG <- H. De Beer, Central Univ., Vrystaat, South Africa

NCBI tax ID(s): 307480 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 19030

BacDive-ID: 23023

DSM-Number: 25206

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

description: Chryseobacterium vrystaatense DSM 25206 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from raw chicken.

NCBI tax id

  • NCBI tax id: 307480
  • Matching level: species

strain history

@refhistory
19030<- CCUG <- P. Vandamme, LMG <- H. de Beer, Central University of Technology, Bloemfontein, South Africa
123886CIP <- 2005, CCUG <- 2005, LMG <- H. De Beer, Central Univ., Vrystaat, South Africa

doi: 10.13145/bacdive23023.20230509.8.1

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 vrystaatense
  • full scientific name: Chryseobacterium vrystaatense de Beer et al. 2005

@ref: 19030

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium vrystaatense

full scientific name: Chryseobacterium vrystaatense de Beer et al. 2005 emend. Montero-Calasanz et al. 2014

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shape
31527negativeno
123886negativenorod-shaped

colony morphology

@refincubation periodhemolysis ability
590671 day
1238861

pigmentation

  • @ref: 31527
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19030CASO 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
33267MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123886CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19030positivegrowth28mesophilic
31527positivegrowth04-32
31527positiveoptimum18psychrophilic
33267positivegrowth25mesophilic
59067positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59067aerobe
123886obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
31527NaClpositivegrowth01-04 %
31527NaClpositiveoptimum1.5 %

observation

  • @ref: 31527
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3152730089acetate+carbon source
3152722653asparagine+carbon source
3152735391aspartate+carbon source
3152723652dextrin+carbon source
3152717234glucose+carbon source
3152729987glutamate+carbon source
3152717754glycerol+carbon source
3152717596inosine+carbon source
3152729864mannitol+carbon source
3152737684mannose+carbon source
3152717822serine+carbon source
3152730031succinate+carbon source
3152726986threonine+carbon source
3152717748thymidine+carbon source
3152727082trehalose+carbon source
3152753423tween 40+carbon source
3152753426tween 80+carbon source
3152716704uridine+carbon source
315274853esculin+hydrolysis
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
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-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
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
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-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
12388617632nitrate-reduction
12388616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3152716136hydrogen sulfideyes
3152735581indoleyes
12388635581indoleyes

metabolite tests

  • @ref: 31527
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31527catalase+1.11.1.6
31527cytochrome oxidase+1.9.3.1
31527urease+3.5.1.5
123886oxidase+
123886alcohol dehydrogenase-1.1.1.1
123886catalase+1.11.1.6
123886lysine decarboxylase-4.1.1.18
123886ornithine decarboxylase-4.1.1.17
123886urease-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
123886-+++-++-++++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123886+/----------+/-+/-+/-----+/-----+/--+/-------+/-------+/-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19030raw chickenVrystaat, chicken-processing plantSouth AfricaZAFAfrica
59067ChickenVrystaatSouth AfricaZAFAfrica
123886ChickenVrystaatSouth AfricaZAFAfrica

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Meat
#Host#Birds#Chicken

taxonmaps

  • @ref: 69479
  • File name: preview.99_2741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_753;97_1740;98_2127;99_2741&stattab=map
  • Last taxonomy: Chryseobacterium vrystaatense subclade
  • 16S sequence: AJ871397
  • Sequence Identity:
  • Total samples: 120
  • soil counts: 35
  • aquatic counts: 24
  • animal counts: 52
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
190301Risk group (German classification)
1238861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19030
  • description: Chryseobacterium vrystaatense 16S rRNA gene, type strain R-23566T
  • accession: AJ871397
  • length: 1469
  • database: ena
  • NCBI tax ID: 307480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium vrystaatense LMG 22846GCA_000737765contigncbi307480
66792Chryseobacterium vrystaatense strain LMG 22846307480.5wgspatric307480
66792Chryseobacterium vrystaatense LMG 228462617271207draftimg307480

GC content

  • @ref: 31527
  • GC-content: 37.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno96.768no
anaerobicno99.401yes
halophileno94.409yes
spore-formingno91.319no
glucose-utilyes85.362yes
flagellatedno95.717no
aerobicyes93.516yes
thermophileno99.933yes
motileno91.485yes
glucose-fermentno91.811no

External links

@ref: 19030

culture collection no.: DSM 25206, CCUG 50970, LMG 22846, CIP 108934

straininfo link

  • @ref: 87263
  • straininfo: 131389

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166723
  • title: Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant.
  • authors: de Beer H, Hugo CJ, Jooste PJ, Willems A, Vancanneyt M, Coenye T, Vandamme PAR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63746-0
  • year: 2005
  • mesh: Animals, Bacterial Typing Techniques, Chickens/*microbiology, Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Food Handling/*methods, *Food-Processing Industry, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19030Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25206)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25206
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
31527Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2782128776041
33267Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6619
59067Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50970)https://www.ccug.se/strain?id=50970
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
87263Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131389.1StrainInfo: A central database for resolving microbial strain identifiers
123886Curators of the CIPCollection of Institut Pasteur (CIP 108934)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108934