Strain identifier

BacDive ID: 5556

Type strain: Yes

Species: Flavobacterium xinjiangense

Strain Designation: ZF-6

Strain history: CIP <- 2004, JCM <- 2001, F. Zhu: strain ZF-6

NCBI tax ID(s): 178356 (species)

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General

@ref: 8277

BacDive-ID: 5556

DSM-Number: 19743

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

description: Flavobacterium xinjiangense ZF-6 is a Gram-negative bacterium that was isolated from frozen soil from the China No. 1 glacier.

NCBI tax id

  • NCBI tax id: 178356
  • Matching level: species

strain history

@refhistory
8277<- JCM/RIKEN <- F. Zhu, Chinese Acad. Sci. (CAS), Beijing; ZF-6
67770F. Zhu ZF-6.
123979CIP <- 2004, JCM <- 2001, F. Zhu: strain ZF-6

doi: 10.13145/bacdive5556.20240916.9.1

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 xinjiangense
  • full scientific name: Flavobacterium xinjiangense Zhu et al. 2003

@ref: 8277

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium xinjiangense

full scientific name: Flavobacterium xinjiangense Zhu et al. 2003

strain designation: ZF-6

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123979negativerod-shapedno
69480no91
69480negative99.455

colony morphology

  • @ref: 123979

pigmentation

  • @ref: 123979
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8277PYG MEDIUM (B) (DSMZ Medium 1139)yeshttps://mediadive.dsmz.de/medium/1139Name: PYG MEDIUM (B) (DSMZ Medium 1139) Composition: Glucose 10.0 g/l Yeast extract 10.0 g/l Polypeptone 5.0 g/l Tryptone 5.0 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.016 g/l CaCl2 0.008 g/l Distilled water
8277R2A 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
34224MEDIUM 469 - for Pseudomonas psychrophilayesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(20.000 g);Yeast extract (10.000 g);Peptone (10.000 g)
123979CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
123979CIP Medium 469yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=469

culture temp

@refgrowthtypetemperature
8277positivegrowth11
34224positivegrowth10
67770positivegrowth11
123979positivegrowth5-15
123979nogrowth25
123979nogrowth30
123979nogrowth37
123979nogrowth41
123979nogrowth45

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no90.958
69481no100

halophily

@refsaltgrowthtested relationconcentration
123979NaClpositivegrowth0 %
123979NaClnogrowth2 %
123979NaClnogrowth4 %
123979NaClnogrowth6 %
123979NaClnogrowth8 %
123979NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12397916947citrate-carbon source
1239794853esculin+hydrolysis
123979606565hippurate+hydrolysis
12397917632nitrate-builds gas from
12397917632nitrate-reduction
12397916301nitrite-builds gas from
12397916301nitrite-reduction
12397915792malonate-assimilation

metabolite production

  • @ref: 123979
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12397915688acetoin-
12397917234glucose-

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
123979oxidase-
123979beta-galactosidase+3.2.1.23
123979alcohol dehydrogenase-1.1.1.1
123979gelatinase-
123979amylase+
123979DNase-
123979caseinase-3.4.21.50
123979catalase-1.11.1.6
123979tween esterase-
123979gamma-glutamyltransferase+2.3.2.2
123979lecithinase-
123979lipase-
123979lysine decarboxylase-4.1.1.18
123979ornithine decarboxylase-4.1.1.17
123979phenylalanine ammonia-lyase+4.3.1.24
123979tryptophan deaminase-
123979urease-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
123979-+++-++++-++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8277frozen soil from the China No. 1 glacierNorth-West China, Xinjiang provinceChinaCHNAsia
67770Frozen soil from the China No. 1 glacier (Xinjiang Province)
123979Environment, Frozen soil from the China No 1 glacierChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_44888.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_19286;97_23931;98_32570;99_44888&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: AF433173
  • Sequence Identity:
  • Total samples: 1978
  • soil counts: 203
  • aquatic counts: 1520
  • animal counts: 90
  • plant counts: 165

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82771Risk group (German classification)
1239791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8277
  • description: Flavobacterium xinjiangense AS1.2749 16S ribosomal RNA gene, partial sequence
  • accession: AF433173
  • length: 1466
  • database: nuccore
  • NCBI tax ID: 178356

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium xinjiangense strain CGMCC 1.2749178356.3wgspatric178356
66792Flavobacterium xinjiangense CGMCC 1.27492663762760draftimg178356
67770Flavobacterium xinjiangense CGMCC 1.2749GCA_900142885scaffoldncbi178356

GC content

  • @ref: 8277
  • GC-content: 34.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.455no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.33no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.958no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.35no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.654yes
69480flagellatedmotile2+Ability to perform flagellated movementno91no

External links

@ref: 8277

culture collection no.: DSM 19743, AS 1.2749, JCM 11314, CGMCC 1.2749, CIP 108285, KCTC 12491

straininfo link

  • @ref: 75038
  • straininfo: 88290

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807212Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier.Zhu F, Wang S, Zhou PInt J Syst Evol Microbiol10.1099/ijs.0.02310-02003Bacterial Typing Techniques, Base Composition, China, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification/physiology, Genotype, *Ice, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny21724953Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice.Dong K, Liu H, Zhang J, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.030049-02011Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification, *Ice, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitle
8277Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19743)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19743
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
34224Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5890
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
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
75038Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88290.1StrainInfo: A central database for resolving microbial strain identifiers
123979Curators of the CIPCollection of Institut Pasteur (CIP 108285)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108285