Strain identifier
BacDive ID: 5674
Type strain:
Species: Chryseobacterium joostei
Strain Designation: Ix 5a
Strain history: CIP <- 1998, J.F. Bernardet, INRA, Jouy-en-Josas, France <- C.J. Hugo: strain Ix 5a <- P.J. Jooste
NCBI tax ID(s): 112234 (species)
General
@ref: 6648
BacDive-ID: 5674
DSM-Number: 16927
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Chryseobacterium joostei Ix 5a is an aerobe, mesophilic bacterium that was isolated from raw milk, tanker.
NCBI tax id
- NCBI tax id: 112234
- Matching level: species
strain history
@ref | history |
---|---|
6648 | <- CCUG <- LMG <- C. Hugo University of the Orange Free State Bloemfontein South Africa <- P. J. Jooste |
120362 | CIP <- 1998, J.F. Bernardet, INRA, Jouy-en-Josas, France <- C.J. Hugo: strain Ix 5a <- P.J. Jooste |
doi: 10.13145/bacdive5674.20230509.8.1
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 joostei
- full scientific name: Chryseobacterium joostei Hugo et al. 2003
@ref: 6648
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium joostei
full scientific name: Chryseobacterium joostei Hugo et al. 2003 emend. Montero-Calasanz et al. 2014
strain designation: Ix 5a
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 93.39 | ||
69480 | 99.996 | negative | ||
120362 | no | negative | rod-shaped |
colony morphology
- @ref: 120362
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6648 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
6648 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf | |
6648 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
38560 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
120362 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
120362 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6648 | positive | growth | 30 | mesophilic |
38560 | positive | growth | 25 | mesophilic |
57298 | positive | growth | 28 | mesophilic |
6648 | positive | growth | 28 | mesophilic |
120362 | positive | growth | 5-37 | |
120362 | no | growth | 41 | thermophilic |
120362 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
57298 | aerobe |
120362 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120362 | NaCl | positive | growth | 0-2 % |
120362 | NaCl | no | growth | 4 % |
120362 | NaCl | no | growth | 6 % |
120362 | NaCl | no | growth | 8 % |
120362 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120362 | 16947 | citrate | - | carbon source |
120362 | 4853 | esculin | + | hydrolysis |
120362 | 606565 | hippurate | - | hydrolysis |
120362 | 17632 | nitrate | - | builds gas from |
120362 | 17632 | nitrate | - | reduction |
120362 | 16301 | nitrite | - | builds gas from |
120362 | 16301 | nitrite | - | reduction |
120362 | 15792 | malonate | - | assimilation |
120362 | 17234 | glucose | + | degradation |
antibiotic resistance
- @ref: 120362
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 120362
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120362 | 15688 | acetoin | - | |
120362 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
120362 | oxidase | + | |
120362 | beta-galactosidase | - | 3.2.1.23 |
120362 | alcohol dehydrogenase | - | 1.1.1.1 |
120362 | gelatinase | + | |
120362 | amylase | - | |
120362 | DNase | - | |
120362 | caseinase | + | 3.4.21.50 |
120362 | catalase | + | 1.11.1.6 |
120362 | tween esterase | - | |
120362 | gamma-glutamyltransferase | + | 2.3.2.2 |
120362 | lecithinase | + | |
120362 | lipase | - | |
120362 | lysine decarboxylase | - | 4.1.1.18 |
120362 | ornithine decarboxylase | - | 4.1.1.17 |
120362 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120362 | protease | + | |
120362 | tryptophan deaminase | - | |
120362 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120362 | - | + | + | + | - | + | + | - | + | - | + | + | - | - | - | + | - | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120362 | + | + | - | + | + | - | - | - | - | + | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
6648 | raw milk, tanker | Ixopo Kwazulu-Natal | South Africa | ZAF | Africa | ||
57298 | Raw milk,tanker | Ixopo Kwazulu-Natal | South Africa | ZAF | Africa | 1981 | |
120362 | Food, Cow, milk | South Africa | ZAF | Africa | 1981 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Built environment | #Container (Reservoir) |
#Host Body Product | #Fluids | #Milk |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6648 | 1 | Risk group (German classification) |
120362 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6648
- description: Chryseobacterium joosteii 16S rRNA gene, strain LMG 18212
- accession: AJ271010
- length: 1469
- database: ena
- NCBI tax ID: 112234
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chryseobacterium joostei DSM 16927 | GCA_003815775 | complete | ncbi | 112234 |
66792 | Chryseobacterium joostei DSM 16927 | GCA_900156585 | scaffold | ncbi | 112234 |
66792 | Chryseobacterium joostei strain DSM 16927 | 112234.4 | wgs | patric | 112234 |
66792 | Chryseobacterium joostei DSM 16927 | 2681813505 | draft | img | 112234 |
GC content
- @ref: 6648
- GC-content: 36.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.338 | no |
gram-positive | no | 98.096 | no |
anaerobic | no | 99.425 | no |
aerobic | yes | 90.475 | no |
halophile | no | 94.809 | no |
spore-forming | no | 94.929 | no |
thermophile | no | 99.658 | yes |
glucose-util | yes | 85.727 | no |
motile | no | 93.717 | no |
glucose-ferment | no | 93.437 | no |
External links
@ref: 6648
culture collection no.: DSM 16927, CCM 7154, CCUG 46665, LMG 18212, CIP 105533
straininfo link
- @ref: 75156
- straininfo: 11460
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12807199 | Chryseobacterium joostei sp. nov., isolated from the dairy environment. | Hugo CJ, Segers P, Hoste B, Vancanneyt M, Kersters K | Int J Syst Evol Microbiol | 10.1099/ijs.0.02232-0 | 2003 | Animals, DNA, Ribosomal/analysis, *Dairying, Fatty Acids/analysis, Gram-Negative Bacteria/chemistry/*classification/genetics, Milk/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, South Africa | Genetics |
Phylogeny | 24958763 | Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer. | Venil CK, Nordin N, Zakaria ZA, Ahmad WA | Int J Syst Evol Microbiol | 10.1099/ijs.0.063594-0 | 2014 | Artocarpus/*microbiology, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 34748473 | Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity. | Keum DH, Yeon JM, Yun CS, Lee SY, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005086 | 2021 | Bacterial Typing Techniques, Base Composition, *Chryseobacterium/classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ginsenosides/metabolism, Glycolipids/chemistry, Nucleic Acid Hybridization, *Panax/microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
6648 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16927) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16927 | |
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 | |
38560 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17563 | ||
57298 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 46665) | https://www.ccug.se/strain?id=46665 | |
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) | |
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
75156 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID11460.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
120362 | Curators of the CIP | Collection of Institut Pasteur (CIP 105533) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105533 |