Strain identifier

BacDive ID: 5583

Type strain: Yes

Species: Flavobacterium phragmitis

Strain Designation: BLN2, BLN_2

Strain history: CIP <- 2012, DSMZ <- Y. Li, College of Life Sci., Capital Normal Univ., Beijing, China: strain BLN2

NCBI tax ID(s): 739143 (species)

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General

@ref: 16785

BacDive-ID: 5583

DSM-Number: 23314

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

description: Flavobacterium phragmitis BLN2 is a mesophilic, Gram-negative bacterium that was isolated from surface-sterilized, crushed roots of reed .

NCBI tax id

  • NCBI tax id: 739143
  • Matching level: species

strain history

@refhistory
16785<- Y. Li, College of Life Sci., Capital Normal Univ., Beijing , PR China; BLN2
121812CIP <- 2012, DSMZ <- Y. Li, College of Life Sci., Capital Normal Univ., Beijing, China: strain BLN2

doi: 10.13145/bacdive5583.20230509.8.1

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 phragmitis
  • full scientific name: Flavobacterium phragmitis Liu et al. 2011

@ref: 16785

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium phragmitis

full scientific name: Flavobacterium phragmitis Liu et al. 2011

strain designation: BLN2, BLN_2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.973
121812negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16785R2A 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
34209MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121812CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16785positivegrowth28mesophilic
34209positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16785surface-sterilized, crushed roots of reed (Phragmites australis)Phragmites australisconstructed Beijing Cuihu Wetland ParkChinaCHNAsia
121812Plant, Surface-sterilized, crushed roots of reed, Phragmites australisCuihu Wetland Park , BeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
167851Risk group (German classification)
1218121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16785
  • description: Flavobacterium phragmitis strain BLN2 16S ribosomal RNA gene, partial sequence
  • accession: GU564236
  • length: 1475
  • database: ena
  • NCBI tax ID: 739143

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium phragmitis CGMCC 1.10370GCA_900112575scaffoldncbi739143
66792Flavobacterium phragmitis strain CGMCC 1.10370739143.3wgspatric739143
66792Flavobacterium phragmitis CGMCC 1.103702667527437draftimg739143

GC content

  • @ref: 16785
  • GC-content: 34.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno79.591no
flagellatedno94.066no
gram-positiveno98.861no
anaerobicno99.418no
aerobicyes82.909no
halophileno97.42no
spore-formingno92.214no
glucose-fermentno88.803no
thermophileno99.608yes
glucose-utilyes92.164no

External links

@ref: 16785

culture collection no.: DSM 23314, CGMCC 1.10370, CIP 110404

straininfo link

  • @ref: 75065
  • straininfo: 374280

literature

  • topic: Phylogeny
  • Pubmed-ID: 21186290
  • title: Flavobacterium phragmitis sp. nov., an endophyte of reed (Phragmites australis).
  • authors: Liu M, Li YH, Liu Y, Zhu JN, Liu QF, Liu Y, Gu JG, Zhang XX, Li CL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.027417-0
  • year: 2010
  • mesh: Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
16785Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23314)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23314
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
34209Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8260
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)
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
75065Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374280.1StrainInfo: A central database for resolving microbial strain identifiers
121812Curators of the CIPCollection of Institut Pasteur (CIP 110404)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110404