Strain identifier

BacDive ID: 5542

Type strain: Yes

Species: Flavobacterium xanthum

Strain Designation: 5-O-C

Strain history: CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain ACAM 81 <- NCIMB 2069

NCBI tax ID(s): 69322 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1445

BacDive-ID: 5542

DSM-Number: 3661

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

description: Flavobacterium xanthum 5-O-C is a psychrophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69322
  • Matching level: species

strain history

@refhistory
1445<- H. Reichenbach <- NCMB <- K. Yamasoto <- K. Inoue, 5-O-C (Cytophaga xantha)
67770IAM 12026 <-- K. Inoue and K. Komagata 5-O-c.
123969CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain ACAM 81 <- NCIMB 2069

doi: 10.13145/bacdive5542.20230509.8.1

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 xanthum
  • full scientific name: Flavobacterium xanthum (ex Inoue and Komagata 1976) McCammon and Bowman 2000

@ref: 1445

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium xanthum

full scientific name: Flavobacterium xanthum (ex Inoue and Komagata 1976) McCammon and Bowman 2000

strain designation: 5-O-C

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.997
123969negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1445CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
34273Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123969CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
123969CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
1445positivegrowth10-20psychrophilic
34273positivegrowth20psychrophilic
67770positivegrowth10psychrophilic
123969positivegrowth5-25psychrophilic
123969nogrowth30mesophilic
123969nogrowth37mesophilic
123969nogrowth41thermophilic
123969nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
123969NaClnogrowth0 %
123969NaClnogrowth2 %
123969NaClnogrowth4 %
123969NaClnogrowth6 %
123969NaClnogrowth8 %
123969NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1239694853esculin-hydrolysis
12396917632nitrate-builds gas from
12396917632nitrate+reduction
12396916301nitrite-builds gas from
12396916301nitrite-reduction
12396915792malonate-assimilation

metabolite production

  • @ref: 123969
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12396915688acetoin-
12396917234glucose+

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
123969oxidase+
123969beta-galactosidase-3.2.1.23
123969alcohol dehydrogenase-1.1.1.1
123969gelatinase-
123969amylase-
123969DNase-
123969caseinase+3.4.21.50
123969catalase+1.11.1.6
123969tween esterase+
123969gamma-glutamyltransferase-2.3.2.2
123969lecithinase-
123969lipase-
123969lysine decarboxylase-4.1.1.18
123969ornithine decarboxylase-4.1.1.17
123969protease+
123969tryptophan deaminase-
123969urease-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
123969-+++-++---++---+----

Isolation, sampling and environmental information

isolation

@refsample typecontinentcountryorigin.countryisolation date
1445soilAustralia and Oceania
67770Soil at Showa StationAntarcticaAntarcticaATA
123969Environment, Pond, mudAntarcticaAntarcticaATA1975

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
14451Risk group (German classification)
1239691Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium xanthum 16S ribosomal RNA gene, partial sequenceAF0303801454ena69322
20218Flavobacterium xanthum O31 16S ribosomal RNA gene, partial sequenceAF312005472ena69322
20218Flavobacterium xanthum axD2 16S ribosomal RNA gene, partial sequenceAF312006459ena69322
20218Flavobacterium xanthum gene for 16S rRNA, partial sequence, strain: NBRC 14972AB6807271439ena69322

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium xanthum strain DSM 366169322.3wgspatric69322
66792Flavobacterium xanthum DSM 36612700988712draftimg69322
67770Flavobacterium xanthum DSM 3661GCA_900142695contigncbi69322

GC content

  • @ref: 67770
  • GC-content: 39
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.507no
anaerobicno99.313no
halophileno92.869no
spore-formingno93.883no
glucose-utilyes82.283no
thermophileno99.794yes
flagellatedno94.253no
motileno91.464no
aerobicyes91.808no
glucose-fermentno94.687no

External links

@ref: 1445

culture collection no.: DSM 3661, ACAM 81, IAM 12026, NCMB 2069, JCM 20358, DSM 3312, IFO 14972, LMG 8372, NBRC 14972, NCIMB 2069, CIP 107448

straininfo link

  • @ref: 75025
  • straininfo: 10830

literature

  • topic: Enzymology
  • Pubmed-ID: 17369961
  • title: A novel, intracellular antifreeze protein in an antarctic bacterium, Flavobacterium xanthum.
  • authors: Kawahara H, Iwanaka Y, Higa S, Muryoi N, Sato M, Honda M, Omura H, Obata H
  • journal: Cryo Letters
  • year: 2007
  • mesh: Acclimatization/physiology, Antarctic Regions, Antifreeze Proteins/chemistry/*isolation & purification/*metabolism, Bacterial Proteins/chemistry/isolation & purification/metabolism, Cold Temperature, Electrophoresis, Polyacrylamide Gel, Flavobacterium/classification/*metabolism, Microbiological Techniques, Molecular Weight
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1445Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3661)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3661
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
34273Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4885
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
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
75025Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10830.1StrainInfo: A central database for resolving microbial strain identifiers
123969Curators of the CIPCollection of Institut Pasteur (CIP 107448)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107448