Strain identifier

BacDive ID: 5557

Type strain: Yes

Species: Flavobacterium antarcticum

Strain Designation: AT1026

Strain history: CIP <- 2005, JCM <- J. Chun, Seoul, Korea: strain AT1026

NCBI tax ID(s): 1111730 (strain), 271155 (species)

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General

@ref: 8265

BacDive-ID: 5557

DSM-Number: 19726

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped

description: Flavobacterium antarcticum AT1026 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from soil sample of a penguin habitat.

NCBI tax id

NCBI tax idMatching level
1111730strain
271155species

strain history

@refhistory
8265<- JCM/RIKEN <- J. Chun, Seoul Nat. Univ.; AT1026
67770J. Chun AT1026.
67771<- J Chun, Seoul Nat. Univ.
116406CIP <- 2005, JCM <- J. Chun, Seoul, Korea: strain AT1026

doi: 10.13145/bacdive5557.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium antarcticum
  • full scientific name: Flavobacterium antarcticum Yi et al. 2005

@ref: 8265

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium antarcticum

full scientific name: Flavobacterium antarcticum Yi et al. 2005 emend. Hahnke et al. 2016

strain designation: AT1026

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31373negative0.9 µm0.35 µmrod-shapedno
67771negative
69480negative99.983
116406negativerod-shapedno

colony morphology

  • @ref: 116406

pigmentation

  • @ref: 31373
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8265TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
37576MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116406CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8265positivegrowth15psychrophilic
31373positivegrowth5-24.1psychrophilic
31373positiveoptimum21.2psychrophilic
37576positivegrowth15psychrophilic
67770positivegrowth15psychrophilic
67771positivegrowth15psychrophilic

culture pH

@refabilitytypepHPH range
31373positivegrowth06-10alkaliphile
31373positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31373aerobe
67771aerobe
116406obligate aerobe

spore formation

@refspore formationconfidence
31373no
69481no100
69480no99.982

halophily

  • @ref: 31373
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3137317234glucose+carbon source
3137317306maltose+carbon source
11640617632nitrate-reduction
11640616301nitrite-reduction

enzymes

@refvalueactivityec
31373acid phosphatase+3.1.3.2
31373alkaline phosphatase+3.1.3.1
31373catalase+1.11.1.6
31373cytochrome oxidase+1.9.3.1
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
116406oxidase+
116406alcohol dehydrogenase+1.1.1.1
116406catalase+1.11.1.6
116406lysine decarboxylase-4.1.1.18
116406ornithine decarboxylase-4.1.1.17
116406urease-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
116406-+++-++---++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
8265soil sample of a penguin habitatKing George Island, King Sejong StationAustralia and Oceania
67771From soil, a habit of penguinnear the King Sejong Station on King George Island, AntarctiaAustralia and OceaniaAntarcticaATA
67770Soil of penguin habitats near the King Sejong Station on King George IslandKing George IslandAntarcticaAntarcticaATA
116406Terrestrial sampleAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Birds

taxonmaps

  • @ref: 69479
  • File name: preview.99_5801.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2779;97_3417;98_4315;99_5801&stattab=map
  • Last taxonomy: Flavobacterium antarcticum subclade
  • 16S sequence: FM163401
  • Sequence Identity:
  • Total samples: 10350
  • soil counts: 1414
  • aquatic counts: 4266
  • animal counts: 1590
  • plant counts: 3080

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82651Risk group (German classification)
1164061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium antarcticum 16S rRNA gene, type strain DSM19726TFM1634011550ena1111730
8265Flavobacterium antarcticum DSM 19726 strain AT1026 16S ribosomal RNA gene, partial sequenceAY5811131438ena1111730

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium antarcticum DSM 197261111730.5wgspatric1111730
66792Flavobacterium antarcticum DSM 197262513237111draftimg1111730
67771Flavobacterium antarcticum DSM 19726GCA_000419685contigncbi1111730

GC content

@refGC-contentmethod
826538.0
3137338
826535.0sequence analysis
6777038high performance liquid chromatography (HPLC)
6777138.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.381yes
flagellatedno94.895no
gram-positiveno98.783yes
anaerobicno98.733no
aerobicyes86.489no
halophileno78.665no
spore-formingno96.109yes
thermophileno99.605yes
glucose-utilyes82.493no
glucose-fermentno93.247no

External links

@ref: 8265

culture collection no.: DSM 19726, CIP 108750, IMSNU 14042, JCM 12383, KCTC 12222, KCTC 23290, KCTC 52532, LMG 25319

straininfo link

  • @ref: 75039
  • straininfo: 106541

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774636Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic.Yi H, Oh HM, Lee JH, Kim SJ, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63423-02005Antarctic Regions, Bacterial Typing Techniques, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23064352Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater.Zhu L, Liu Q, Liu H, Zhang J, Dong X, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.045534-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Ice Cover/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8265Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19726)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19726
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31373Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127686
37576Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6413
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75039Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID106541.1StrainInfo: A central database for resolving microbial strain identifiers
116406Curators of the CIPCollection of Institut Pasteur (CIP 108750)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108750