Strain identifier

BacDive ID: 5555

Type strain: Yes

Species: Flavobacterium omnivorum

Strain Designation: ZF-8

Strain history: CIP <- 2003, JCM <- 2001, F. Zhu: strain ZF-8

NCBI tax ID(s): 178355 (species)

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General

@ref: 8276

BacDive-ID: 5555

DSM-Number: 19742

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

description: Flavobacterium omnivorum ZF-8 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: 178355
  • Matching level: species

strain history

@refhistory
8276<- JCM/RIKEN <- F. Zhu, Chinese Acad. Sci. (CAS), Beijing; ZF-8
67770F. Zhu ZF-8.
121418CIP <- 2003, JCM <- 2001, F. Zhu: strain ZF-8

doi: 10.13145/bacdive5555.20230509.8.1

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

@ref: 8276

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium omnivorum

full scientific name: Flavobacterium omnivorum Zhu et al. 2003

strain designation: ZF-8

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.996
121418negativerod-shapedno

colony morphology

  • @ref: 121418

pigmentation

  • @ref: 121418
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8276PYG 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
39767MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121418CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
121418CIP Medium 469yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=469
121418CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8276positivegrowth11psychrophilic
39767positivegrowth10psychrophilic
67770positivegrowth11psychrophilic
121418positivegrowth5-15psychrophilic
121418nogrowth25mesophilic
121418nogrowth30mesophilic
121418nogrowth37mesophilic
121418nogrowth41thermophilic
121418nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121418
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
121418NaClpositivegrowth0 %
121418NaClnogrowth2 %
121418NaClnogrowth4 %
121418NaClnogrowth6 %
121418NaClnogrowth8 %
121418NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12141816947citrate-carbon source
1214184853esculin+hydrolysis
121418606565hippurate+hydrolysis
12141817632nitrate-builds gas from
12141817632nitrate-reduction
12141816301nitrite-builds gas from
12141816301nitrite-reduction
12141835020tributyrin+hydrolysis
12141815792malonate-assimilation

antibiotic resistance

  • @ref: 121418
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121418
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12141815688acetoin-
12141817234glucose-

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
121418oxidase-
121418beta-galactosidase+3.2.1.23
121418alcohol dehydrogenase-1.1.1.1
121418gelatinase+/-
121418amylase+
121418DNase-
121418caseinase+3.4.21.50
121418catalase+1.11.1.6
121418tween esterase-
121418gamma-glutamyltransferase+2.3.2.2
121418lecithinase-
121418lipase-
121418lysine decarboxylase-4.1.1.18
121418ornithine decarboxylase-4.1.1.17
121418phenylalanine ammonia-lyase-4.3.1.24
121418tryptophan deaminase-
121418urease-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
121418-+++-++---++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121418+-+++--+++++++-+++-------------+---+---------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8276frozen soil from the China No. 1 glacierNorth-West China, Xinjiang provinceChinaCHNAsia
67770Frozen soil from the China No. 1 glacier (Xinjiang Province)
121418Environment, Frozen soil from the China n°1 glacierXinjiangChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82761Risk group (German classification)
1214181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8276
  • description: Flavobacterium omnivorum As1.2747 16S ribosomal RNA gene, partial sequence
  • accession: AF433174
  • length: 1466
  • database: ena
  • NCBI tax ID: 178355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium omnivorum strain CGMCC 1.2747178355.3wgspatric178355
66792Flavobacterium omnivorum CGMCC 1.27472617270789draftimg178355
67770Flavobacterium omnivorum CGMCC 1.2747GCA_900099915scaffoldncbi178355

GC content

  • @ref: 8276
  • GC-content: 35.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.029no
gram-positiveno97.873no
anaerobicno99.433no
aerobicyes92.671no
halophileno93.046no
spore-formingno94.044no
thermophileno99.61yes
glucose-utilyes86.733no
flagellatedno93.524no
glucose-fermentno93.847no

External links

@ref: 8276

culture collection no.: DSM 19742, AS 1.2747, JCM 11313, CGMCC 1.2747, CIP 108050, KCTC 12490

straininfo link

  • @ref: 75037
  • straininfo: 88291

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
8276Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19742)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19742
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
39767Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5630
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
75037Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88291.1StrainInfo: A central database for resolving microbial strain identifiers
121418Curators of the CIPCollection of Institut Pasteur (CIP 108050)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108050