Strain identifier

BacDive ID: 24010

Type strain: Yes

Species: Flammeovirga yaeyamensis

Strain Designation: IR25-3

Strain history: CIP <- 2006, NBRC <- Y. Nakagawa, IFO: strain IR25-3

NCBI tax ID(s): 367791 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 20562

BacDive-ID: 24010

DSM-Number: 25626

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

description: Flammeovirga yaeyamensis IR25-3 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from seaweed Digenea simplex.

NCBI tax id

  • NCBI tax id: 367791
  • Matching level: species

strain history

@refhistory
20562<- CIP <- BRRC <- Y. Nakagawa, IFO; IR25-3
124007CIP <- 2006, NBRC <- Y. Nakagawa, IFO: strain IR25-3

doi: 10.13145/bacdive24010.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flammeovirgaceae
  • genus: Flammeovirga
  • species: Flammeovirga yaeyamensis
  • full scientific name: Flammeovirga yaeyamensis Takahashi et al. 2006

@ref: 20562

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flammeovirgaceae

genus: Flammeovirga

species: Flammeovirga yaeyamensis

full scientific name: Flammeovirga yaeyamensis Takahashi et al. 2006

strain designation: IR25-3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.991
124007negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20562BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
40121Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
124007CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
20562positivegrowth25mesophilic
40121positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 124007
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.901

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12400717632nitrate-reduction
12400716301nitrite-reduction

metabolite production

  • @ref: 124007
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
124007oxidase+
124007alcohol dehydrogenase-1.1.1.1
124007catalase+1.11.1.6
124007lysine decarboxylase-4.1.1.18
124007ornithine decarboxylase-4.1.1.17
124007urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124007-+++-++-+-+++--+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
20562seaweed Digenea simplexDigenea simplexOkinawa Pref., Yaeyama IslandsJapanJPNAsia
124007Seaweed, Digenea simplexUehara, Iriomote Island, OkinawaJapanJPNAsia2001

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Aquatic plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_2487.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16066;96_1341;97_1592;98_1936;99_2487&stattab=map
  • Last taxonomy: Flammeovirga yaeyamensis subclade
  • 16S sequence: AB247554
  • Sequence Identity:
  • Total samples: 1757
  • soil counts: 58
  • aquatic counts: 1080
  • animal counts: 614
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
205621Risk group (German classification)
1240071Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20562
  • description: Flammeovirga yaeyamensis gene for 16S ribosomal RNA, partial sequence, strain: NBRC 100898
  • accession: AB247554
  • length: 1451
  • database: ena
  • NCBI tax ID: 367791

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flammeovirga yaeyamensis NBRC:100898GCA_018736045completencbi367791
66792Flammeovirga yaeyamensis DSM 25626GCA_014195575scaffoldncbi367791
66792Flammeovirga yaeyamensis NBRC 100898GCA_012844325scaffoldncbi367791
66792Flammeovirga yaeyamensis strain DSM 25626367791.5wgspatric367791
66792Flammeovirga yaeyamensis strain NBRC 100898367791.4wgspatric367791
66792Flammeovirga yaeyamensis strain NBRC:100898367791.6completepatric367791
66792Flammeovirga yaeyamensis DSM 256262827971030draftimg367791

GC content

  • @ref: 20562
  • GC-content: 33.4-35.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
flagellatedno92.806no
gram-positiveno98.051no
anaerobicno97.936no
aerobicyes76.393no
halophileno76.986no
spore-formingno91.145no
thermophileno97.997yes
motileno86.284no
glucose-utilyes89.718no
glucose-fermentno81.594no

External links

@ref: 20562

culture collection no.: DSM 25626, CIP 109099, NBRC 100898

straininfo link

  • @ref: 87984
  • straininfo: 297160

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957105Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov.Takahashi M, Suzuki KI, Nakagawa YInt J Syst Evol Microbiol10.1099/ijs.0.64324-02006Bacterial Typing Techniques, Bacteroidetes/classification/genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis, Sphingobacterium/*classification/genetics, *Terminology as TopicGenetics
Phylogeny17473242Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family 'Flammeovirgaceae' isolated from sediment.Yoon J, Ishikawa S, Kasai H, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64845-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Microscopy, Electron, Transmission, Molecular Sequence Data, Palau, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny21669915Flammeovirga pacifica sp. nov., isolated from deep-sea sediment.Xu H, Fu Y, Yang N, Ding Z, Lai Q, Zeng RInt J Syst Evol Microbiol10.1099/ijs.0.030676-02011Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Cadaverine/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Phylogeny33095697Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater.Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu WInt J Syst Evol Microbiol10.1099/ijsem.0.0044972020Agar/*metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics, Base Composition, China, Fatty Acids/chemistry, Genes, Bacterial/genetics, Glycolipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity, Water MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20562Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25626Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25626)
40121Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6803
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87984Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID297160.1
124007Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109099Collection of Institut Pasteur (CIP 109099)