Strain identifier
BacDive ID: 23023
Type strain:
Species: Chryseobacterium vrystaatense
Strain history: CIP <- 2005, CCUG <- 2005, LMG <- H. De Beer, Central Univ., Vrystaat, South Africa
NCBI tax ID(s): 307480 (species)
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
@ref | history |
---|---|
19030 | <- CCUG <- P. Vandamme, LMG <- H. de Beer, Central University of Technology, Bloemfontein, South Africa |
123886 | CIP <- 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
@ref | gram stain | motility | cell shape |
---|---|---|---|
31527 | negative | no | |
123886 | negative | no | rod-shaped |
colony morphology
@ref | incubation period | hemolysis ability |
---|---|---|
59067 | 1 day | |
123886 | 1 |
pigmentation
- @ref: 31527
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
19030 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
33267 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123886 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19030 | positive | growth | 28 | mesophilic |
31527 | positive | growth | 04-32 | |
31527 | positive | optimum | 18 | psychrophilic |
33267 | positive | growth | 25 | mesophilic |
59067 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
59067 | aerobe |
123886 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31527 | NaCl | positive | growth | 01-04 % |
31527 | NaCl | positive | optimum | 1.5 % |
observation
- @ref: 31527
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31527 | 30089 | acetate | + | carbon source |
31527 | 22653 | asparagine | + | carbon source |
31527 | 35391 | aspartate | + | carbon source |
31527 | 23652 | dextrin | + | carbon source |
31527 | 17234 | glucose | + | carbon source |
31527 | 29987 | glutamate | + | carbon source |
31527 | 17754 | glycerol | + | carbon source |
31527 | 17596 | inosine | + | carbon source |
31527 | 29864 | mannitol | + | carbon source |
31527 | 37684 | mannose | + | carbon source |
31527 | 17822 | serine | + | carbon source |
31527 | 30031 | succinate | + | carbon source |
31527 | 26986 | threonine | + | carbon source |
31527 | 17748 | thymidine | + | carbon source |
31527 | 27082 | trehalose | + | carbon source |
31527 | 53423 | tween 40 | + | carbon source |
31527 | 53426 | tween 80 | + | carbon source |
31527 | 16704 | uridine | + | carbon source |
31527 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
123886 | 17632 | nitrate | - | reduction |
123886 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
31527 | 16136 | hydrogen sulfide | yes |
31527 | 35581 | indole | yes |
123886 | 35581 | indole | yes |
metabolite tests
- @ref: 31527
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
31527 | catalase | + | 1.11.1.6 |
31527 | cytochrome oxidase | + | 1.9.3.1 |
31527 | urease | + | 3.5.1.5 |
123886 | oxidase | + | |
123886 | alcohol dehydrogenase | - | 1.1.1.1 |
123886 | catalase | + | 1.11.1.6 |
123886 | lysine decarboxylase | - | 4.1.1.18 |
123886 | ornithine decarboxylase | - | 4.1.1.17 |
123886 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123886 | - | + | + | + | - | + | + | - | + | + | + | + | - | - | - | + | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123886 | +/- | - | - | - | - | - | - | - | - | - | +/- | +/- | +/- | - | - | - | - | +/- | - | - | - | - | +/- | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19030 | raw chicken | Vrystaat, chicken-processing plant | South Africa | ZAF | Africa |
59067 | Chicken | Vrystaat | South Africa | ZAF | Africa |
123886 | Chicken | Vrystaat | South Africa | ZAF | Africa |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
19030 | 1 | Risk group (German classification) |
123886 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chryseobacterium vrystaatense LMG 22846 | GCA_000737765 | contig | ncbi | 307480 |
66792 | Chryseobacterium vrystaatense strain LMG 22846 | 307480.5 | wgs | patric | 307480 |
66792 | Chryseobacterium vrystaatense LMG 22846 | 2617271207 | draft | img | 307480 |
GC content
- @ref: 31527
- GC-content: 37.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 96.768 | no |
anaerobic | no | 99.401 | yes |
halophile | no | 94.409 | yes |
spore-forming | no | 91.319 | no |
glucose-util | yes | 85.362 | yes |
flagellated | no | 95.717 | no |
aerobic | yes | 93.516 | yes |
thermophile | no | 99.933 | yes |
motile | no | 91.485 | yes |
glucose-ferment | no | 91.811 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19030 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25206) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25206 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31527 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27821 | 28776041 | |
33267 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6619 | ||||
59067 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50970) | https://www.ccug.se/strain?id=50970 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
87263 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131389.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123886 | Curators of the CIP | Collection of Institut Pasteur (CIP 108934) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108934 |