Strain identifier

BacDive ID: 5562

Type strain: Yes

Species: Flavobacterium croceum

Strain Designation: EMB 47, EMB47

Strain history: CIP <- 2009, DSMZ <- C.O. Jeon, GSNU, Jinju, Korea: strain EMB47

NCBI tax ID(s): 1121886 (strain), 370975 (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: 7292

BacDive-ID: 5562

DSM-Number: 17960

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped

description: Flavobacterium croceum EMB 47 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
370975species
1121886strain

strain history

@refhistory
7292<- C. O. Jeon, Gyeongsang Natl. Univ. (GSNU), Jinju, Korea; EMB 47
67771<- CO Jeon, Gyungsang Univ.
118789CIP <- 2009, DSMZ <- C.O. Jeon, GSNU, Jinju, Korea: strain EMB47

doi: 10.13145/bacdive5562.20230509.8.1

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 croceum
  • full scientific name: Flavobacterium croceum Park et al. 2006

@ref: 7292

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium croceum

full scientific name: Flavobacterium croceum Park et al. 2006

strain designation: EMB 47, EMB47

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedno
67771negative
118789rod-shapednonegative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7292R2A 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
41934MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118789CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7292positivegrowth25mesophilic
41934positivegrowth25mesophilic
67771positivegrowth25-32mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
118789facultative anaerobe

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11878917632nitrate+reduction
11878916301nitrite-reduction

metabolite production

  • @ref: 118789
  • 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
118789oxidase+
118789catalase-1.11.1.6
118789urease-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
118789-+++-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7292activated sludgePohangRepublic of KoreaKORAsia
67771From activated sludgeRepublic of KoreaKORAsia
118789Environment, Activated sludgePohangRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_73347.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_31202;97_39469;98_51359;99_73347&stattab=map
  • Last taxonomy: Flavobacterium croceum subclade
  • 16S sequence: DQ372982
  • Sequence Identity:
  • Total samples: 743
  • soil counts: 19
  • aquatic counts: 673
  • animal counts: 27
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72921Risk group (German classification)
1187891Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7292
  • description: Flavobacterium croceum strain EMB47 16S ribosomal RNA gene, partial sequence
  • accession: DQ372982
  • length: 1439
  • database: ena
  • NCBI tax ID: 370975

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium croceum DSM 17960GCA_002917885contigncbi1121886
66792Flavobacterium croceum DSM 179601121886.3wgspatric1121886
66792Flavobacterium croceum DSM 179602734482249draftimg1121886

GC content

@refGC-contentmethod
729240.8high performance liquid chromatography (HPLC)
6777140.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.637no
flagellatedno97.081yes
gram-positiveno98.783no
anaerobicno99.014no
halophileno96.964no
spore-formingno95.401no
thermophileno92.744yes
glucose-utilyes70.855no
aerobicyes83.317yes
glucose-fermentno92.99no

External links

@ref: 7292

culture collection no.: DSM 17960, CIP 109940, KCTC 12611

straininfo link

  • @ref: 75044
  • straininfo: 297163

literature

  • topic: Phylogeny
  • Pubmed-ID: 17012577
  • title: Flavobacterium croceum sp. nov., isolated from activated sludge.
  • authors: Park M, Lu S, Ryu SH, Chung BS, Park W, Kim CJ, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64436-0
  • year: 2006
  • mesh: Bacterial Typing Techniques, Base Composition, Bioreactors, DNA, Bacterial, DNA, Ribosomal, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Molecular Sequence Data, Phenotype, Phosphorus/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7292Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17960)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17960
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
41934Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7740
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75044Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297163.1StrainInfo: A central database for resolving microbial strain identifiers
118789Curators of the CIPCollection of Institut Pasteur (CIP 109940)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109940