Strain identifier

BacDive ID: 5675

Type strain: Yes

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)

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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

@refhistory
6707<- J. Chun; AT 1013
67770J. Chun AT1013.
116404CIP <- 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

    @refsynonym
    20215Kaistella antarctica
    20215Sejongia 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

@refnamegrowthlinkcomposition
6707R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
34203MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116404CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6707positivegrowth10-15psychrophilic
34203positivegrowth22psychrophilic
67770positivegrowth15psychrophilic
116404positivegrowth5-25psychrophilic
116404nogrowth30mesophilic
116404nogrowth37mesophilic
116404nogrowth41thermophilic
116404nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6707aerobe
116404obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116404NaClpositivegrowth0-2 %
116404NaClnogrowth4 %
116404NaClnogrowth6 %
116404NaClnogrowth8 %
116404NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11640416947citrate-carbon source
1164044853esculin+hydrolysis
116404606565hippurate-hydrolysis
11640417632nitrate-builds gas from
11640417632nitrate-reduction
11640416301nitrite-builds gas from
11640416301nitrite-reduction
11640415792malonate-assimilation

metabolite production

  • @ref: 116404
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11640415688acetoin-
11640417234glucose-

enzymes

@refvalueactivityec
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
116404oxidase+
116404beta-galactosidase-3.2.1.23
116404alcohol dehydrogenase-1.1.1.1
116404gelatinase+
116404amylase-
116404DNase+
116404caseinase+3.4.21.50
116404catalase+1.11.1.6
116404tween esterase-
116404gamma-glutamyltransferase+2.3.2.2
116404lecithinase-
116404lipase-
116404lysine decarboxylase-4.1.1.18
116404ornithine decarboxylase-4.1.1.17
116404phenylalanine ammonia-lyase-4.3.1.24
116404tryptophan deaminase-
116404urease-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
116404-+++-++---++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116404----------------------+---------------------+-++------++--------+-++--++++-+------+----++--+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
6707soilKing Sejong StationAustralia and Oceania
67770Soil of penguin habitats near the King Sejong Station on King George IslandKing George IslandAntarcticaAntarcticaATA
116404Terrestrial samplesAntarcticaAntarcticaATA

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

@refbiosafety levelbiosafety level comment
67071Risk group (German classification)
1164041Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium antarcticum strain DSM 17047266748.16wgspatric266748
66792Kaistella antarctica DSM 170472687453776draftimg266748
67770Kaistella antarctica DSM 17047GCA_900109615contigncbi266748

GC content

@refGC-contentmethod
670736.1sequence analysis
6777034high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.091no
gram-positiveno98.069no
anaerobicno99.013yes
aerobicyes87.24yes
halophileno87.558no
spore-formingno95.256no
glucose-utilyes84.107no
flagellatedno96.576no
thermophileno99.821no
glucose-fermentno92.842no

External links

@ref: 6707

culture collection no.: DSM 17047, IMSNU 14040, JCM 12381, KCTC 12225, CIP 108669

straininfo link

  • @ref: 75157
  • straininfo: 130940

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653910Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic.Yi H, Yoon HI, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63273-02005Antarctic 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 MicrobiologyGenetics
Phylogeny19620362Transfer 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 GInt J Syst Evol Microbiol10.1099/ijs.0.009142-02009Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacteriaceae/*classification/*genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitle
6707Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17047)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17047
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
34203Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6323
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75157Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID130940.1StrainInfo: A central database for resolving microbial strain identifiers
116404Curators of the CIPCollection of Institut Pasteur (CIP 108669)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108669