Strain identifier
BacDive ID: 5675
Type strain:
Species: Chryseobacterium antarcticum
Strain Designation: AT 1013, AT1013
Strain history: CIP <- 2005, JCM <- 2004, J. Chun, Seoul Nat. Univ., Seoul, Korea: strain AT1013
NCBI tax ID(s): 266748 (species)
General
@ref: 6707
BacDive-ID: 5675
DSM-Number: 17047
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Chryseobacterium antarcticum AT 1013 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 266748
- Matching level: species
strain history
@ref | history |
---|---|
6707 | <- J. Chun; AT 1013 |
67770 | J. Chun AT1013. |
116404 | CIP <- 2005, JCM <- 2004, J. Chun, Seoul Nat. Univ., Seoul, Korea: strain AT1013 |
doi: 10.13145/bacdive5675.20230509.8.1
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 antarcticum
- full scientific name: Chryseobacterium antarcticum (Yi et al. 2005) Kämpfer et al. 2009
synonyms
@ref synonym 20215 Kaistella antarctica 20215 Sejongia antarctica
@ref: 6707
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium antarcticum
full scientific name: Chryseobacterium antarcticum (Yi et al. 2005) Kämpfer et al. 2009 emend. Hahnke et al. 2016
strain designation: AT 1013, AT1013
type strain: yes
Morphology
cell morphology
- @ref: 116404
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 116404
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6707 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
34203 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
116404 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6707 | positive | growth | 10-15 | psychrophilic |
34203 | positive | growth | 22 | psychrophilic |
67770 | positive | growth | 15 | psychrophilic |
116404 | positive | growth | 5-25 | psychrophilic |
116404 | no | growth | 30 | mesophilic |
116404 | no | growth | 37 | mesophilic |
116404 | no | growth | 41 | thermophilic |
116404 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6707 | aerobe |
116404 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116404 | NaCl | positive | growth | 0-2 % |
116404 | NaCl | no | growth | 4 % |
116404 | NaCl | no | growth | 6 % |
116404 | NaCl | no | growth | 8 % |
116404 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116404 | 16947 | citrate | - | carbon source |
116404 | 4853 | esculin | + | hydrolysis |
116404 | 606565 | hippurate | - | hydrolysis |
116404 | 17632 | nitrate | - | builds gas from |
116404 | 17632 | nitrate | - | reduction |
116404 | 16301 | nitrite | - | builds gas from |
116404 | 16301 | nitrite | - | reduction |
116404 | 15792 | malonate | - | assimilation |
metabolite production
- @ref: 116404
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116404 | 15688 | acetoin | - | |
116404 | 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 |
116404 | oxidase | + | |
116404 | beta-galactosidase | - | 3.2.1.23 |
116404 | alcohol dehydrogenase | - | 1.1.1.1 |
116404 | gelatinase | + | |
116404 | amylase | - | |
116404 | DNase | + | |
116404 | caseinase | + | 3.4.21.50 |
116404 | catalase | + | 1.11.1.6 |
116404 | tween esterase | - | |
116404 | gamma-glutamyltransferase | + | 2.3.2.2 |
116404 | lecithinase | - | |
116404 | lipase | - | |
116404 | lysine decarboxylase | - | 4.1.1.18 |
116404 | ornithine decarboxylase | - | 4.1.1.17 |
116404 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116404 | tryptophan deaminase | - | |
116404 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116404 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116404 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | + | - | + | + | - | - | + | + | + | + | - | + | - | - | - | - | - | - | + | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | country | origin.country |
---|---|---|---|---|---|
6707 | soil | King Sejong Station | Australia and Oceania | ||
67770 | Soil of penguin habitats near the King Sejong Station on King George Island | King George Island | Antarctica | Antarctica | ATA |
116404 | Terrestrial samples | Antarctica | Antarctica | ATA |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2059.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_1132;97_1328;98_1610;99_2059&stattab=map
- Last taxonomy: Kaistella antarctica
- 16S sequence: AY553293
- Sequence Identity:
- Total samples: 351
- soil counts: 56
- aquatic counts: 159
- animal counts: 122
- plant counts: 14
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6707 | 1 | Risk group (German classification) |
116404 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6707
- description: Chryseobacterium antarcticum strain AT1013 16S ribosomal RNA gene, partial sequence
- accession: AY553293
- length: 1439
- database: ena
- NCBI tax ID: 266748
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chryseobacterium antarcticum strain DSM 17047 | 266748.16 | wgs | patric | 266748 |
66792 | Kaistella antarctica DSM 17047 | 2687453776 | draft | img | 266748 |
67770 | Kaistella antarctica DSM 17047 | GCA_900109615 | contig | ncbi | 266748 |
GC content
@ref | GC-content | method |
---|---|---|
6707 | 36.1 | sequence analysis |
67770 | 34 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.091 | no |
gram-positive | no | 98.069 | no |
anaerobic | no | 99.013 | yes |
aerobic | yes | 87.24 | yes |
halophile | no | 87.558 | no |
spore-forming | no | 95.256 | no |
glucose-util | yes | 84.107 | no |
flagellated | no | 96.576 | no |
thermophile | no | 99.821 | no |
glucose-ferment | no | 92.842 | no |
External links
@ref: 6707
culture collection no.: DSM 17047, IMSNU 14040, JCM 12381, KCTC 12225, CIP 108669
straininfo link
- @ref: 75157
- straininfo: 130940
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15653910 | Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic. | Yi H, Yoon HI, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63273-0 | 2005 | Antarctic Regions, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/*classification/genetics/isolation & purification, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 19620362 | Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov. | Kampfer P, Lodders N, Vaneechoutte M, Wauters G | Int J Syst Evol Microbiol | 10.1099/ijs.0.009142-0 | 2009 | Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacteriaceae/*classification/*genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
6707 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17047) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17047 | |
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 | |
34203 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6323 | ||
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) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
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 | |
75157 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID130940.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
116404 | Curators of the CIP | Collection of Institut Pasteur (CIP 108669) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108669 |