Strain identifier

BacDive ID: 5566

Type strain: Yes

Species: Flavobacterium glaciei

Strain Designation: 0499, 499

Strain history: CIP <- 2007, JCM <- 2006, D. Zhang and P. Zhou, Chinese Acad. Sci., Beijing, China: strain 0499

NCBI tax ID(s): 386300 (species)

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General

@ref: 8267

BacDive-ID: 5566

DSM-Number: 19728

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

description: Flavobacterium glaciei 0499 is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from frozen soil from the China No.1 glacier.

NCBI tax id

  • NCBI tax id: 386300
  • Matching level: species

strain history

@refhistory
8267<- JCM/RIKEN <- D. Zhang and P. Zhou, Chinese Acad. Sci. (CAS), Beijing; 0499
67770D.-C. Zhang and P.-J. Zhou 0499.
119633CIP <- 2007, JCM <- 2006, D. Zhang and P. Zhou, Chinese Acad. Sci., Beijing, China: strain 0499

doi: 10.13145/bacdive5566.20230509.8.1

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 glaciei
  • full scientific name: Flavobacterium glaciei Zhang et al. 2006

@ref: 8267

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium glaciei

full scientific name: Flavobacterium glaciei Zhang et al. 2006

strain designation: 0499, 499

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.993
119633negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8267PYG MEDIUM (E) (DSMZ Medium 1140)yeshttps://mediadive.dsmz.de/medium/1140Name: PYG MEDIUM (E) (DSMZ Medium 1140) Composition: Agar 15.0 g/l Glucose 5.0 g/l Bacto peptone 5.0 g/l Beef extract 3.0 g/l MgSO4 x 7 H2O 1.5 g/l NaCl 0.5 g/l Yeast extract 0.2 g/l Distilled water
37571MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119633CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119633CIP Medium 691yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=691

culture temp

@refgrowthtypetemperaturerange
8267positivegrowth21psychrophilic
37571positivegrowth20psychrophilic
67770positivegrowth21psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119633
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11963317632nitrate-reduction
11963316301nitrite-reduction

metabolite production

  • @ref: 119633
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
119633oxidase+
119633catalase+1.11.1.6
119633urease-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
119633-+++-++++-++-+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8267frozen soil from the China No.1 glaciernorth-west China, Xinjiang Uygur Autonomous RegionChinaCHNAsia
62463GlacierNo.1 glacier,Xinjiang Uygur RegionChinaCHNAsia2006
67770China No.1 glacier in the Xinjiang Uygur Autonomous Region
119633China N°1 glacierChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82671Risk group (German classification)
1196331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8267
  • description: Flavobacterium glaciei strain 0499 16S ribosomal RNA gene, partial sequence
  • accession: DQ515962
  • length: 1424
  • database: ena
  • NCBI tax ID: 386300

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium glaciei DSM 19728GCA_003350545scaffoldncbi386300
66792Flavobacterium glaciei CGMCC 1.5380GCA_007994155scaffoldncbi386300
66792Flavobacterium glaciei strain CGMCC 1.5380386300.6wgspatric386300
66792Flavobacterium glaciei strain DSM 19728386300.4wgspatric386300
66792Flavobacterium glaciei DSM 197282770939517draftimg386300
66792Flavobacterium glaciei CGMCC 1.53802596583583draftimg386300

GC content

@refGC-contentmethod
826736.5
6777036.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.913no
flagellatedno94.01no
gram-positiveno98.706no
anaerobicno99.422no
aerobicyes93.718no
halophileno95.492no
spore-formingno95.529no
glucose-utilyes86.733no
thermophileno99.461yes
glucose-fermentno94.002no

External links

@ref: 8267

culture collection no.: DSM 19728, CGMCC 1.5380, JCM 13953, CCUG 60844, CIP 109489, BCRC 81081

straininfo link

@refstraininfo
75048376998
75049411903

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158999Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier.Zhang DC, Wang HX, Liu HC, Dong XZ, Zhou PJInt J Syst Evol Microbiol10.1099/ijs.0.64564-02006Bacterial Typing Techniques, China, Cold Temperature, DNA, Bacterial/analysis, Flavobacterium/chemistry/*classification/genetics/isolation & purification, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny21186289Flavobacterium chungbukense sp. nov., isolated from soil.Lim CS, Oh YS, Lee JK, Park AR, Yoo JS, Rhee SK, Roh DHInt J Syst Evol Microbiol10.1099/ijs.0.028563-02010Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny27469138Flavobacterium terriphilum sp. nov., isolated from soil.Zhang G, Xian W, Chu Q, Yang J, Liu W, Yang L, Xiao M, Jiang H, Li WInt J Syst Evol Microbiol10.1099/ijsem.0.0013472016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31483240Flavobacterium ranwuense sp. nov., isolated from glacier.Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0036872019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Ice Cover/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
8267Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19728)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19728
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
37571Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7239
62463Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60844)https://www.ccug.se/strain?id=60844
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
75048Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID376998.1StrainInfo: A central database for resolving microbial strain identifiers
75049Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID411903.1StrainInfo: A central database for resolving microbial strain identifiers
119633Curators of the CIPCollection of Institut Pasteur (CIP 109489)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109489