Strain identifier

BacDive ID: 24021

Type strain: Yes

Species: Flavobacterium aciduliphilum

Strain Designation: JJ013

Strain history: K. Y. Jahng JJ013.

NCBI tax ID(s): 1101402 (species)

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General

@ref: 20568

BacDive-ID: 24021

DSM-Number: 25663

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

description: Flavobacterium aciduliphilum JJ013 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from artificial lake.

NCBI tax id

  • NCBI tax id: 1101402
  • Matching level: species

strain history

@refhistory
20568<- J.Y. Kang, Chonbuk National Univ., Dept. of Life Scs., Jeonju-si, Korea; JJ013
67770K. Y. Jahng JJ013.

doi: 10.13145/bacdive24021.20230509.8.1

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 aciduliphilum
  • full scientific name: Flavobacterium aciduliphilum Kang et al. 2013

@ref: 20568

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium aciduliphilum

full scientific name: Flavobacterium aciduliphilum Kang et al. 2013

strain designation: JJ013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30796negative1.75 µm0.35 µmrod-shapedno
69480no93.998
69480negative99.996

pigmentation

  • @ref: 30796
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20568
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
20568positivegrowth25mesophilic
30796positivegrowth20-30
30796positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
30796positivegrowth05-07
30796positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 30796
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

observation

  • @ref: 30796
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30796620642,3-butanediol+carbon source
3079615963ribitol+carbon source
3079621217L-alaninamide+carbon source
3079616449alanine+carbon source
30796286442-oxopentanoate+carbon source
3079622599arabinose+carbon source
3079618403L-arabitol+carbon source
3079622653asparagine+carbon source
3079635391aspartate+carbon source
3079617126DL-carnitine+carbon source
3079616947citrate+carbon source
3079623652dextrin+carbon source
3079615740formate+carbon source
3079624148galactonate+carbon source
307965417glucosamine+carbon source
3079617234glucose+carbon source
3079632323glucuronamide+carbon source
3079629987glutamate+carbon source
3079617716lactose+carbon source
3079615792malonate+carbon source
3079629864mannitol+carbon source
3079637657methyl D-glucoside+carbon source
30796506227N-acetylglucosamine+carbon source
3079618257ornithine+carbon source
3079626271proline+carbon source
3079617272propionate+carbon source
3079651850methyl pyruvate+carbon source
3079616634raffinose+carbon source
3079626546rhamnose+carbon source
3079617822serine+carbon source
3079630031succinate+carbon source
3079617748thymidine+carbon source
3079627082trehalose+carbon source
3079653423tween 40+carbon source
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source

metabolite production

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30796acid phosphatase+3.1.3.2
30796alkaline phosphatase+3.1.3.1
30796catalase+1.11.1.6
30796cytochrome oxidase+1.9.3.1
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
20568--++--+-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20568artificial lakeJeollabuk-do, Jinan-gunRepublic of KoreaKORAsia
67770Artificial lake in Jeollabuk-doRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Aquatic#Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_25317.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_11869;97_15359;98_19028;99_25317&stattab=map
  • Last taxonomy: Flavobacterium aciduliphilum subclade
  • 16S sequence: JN712178
  • Sequence Identity:
  • Total samples: 612
  • soil counts: 4
  • aquatic counts: 530
  • animal counts: 76
  • plant counts: 2

Safety information

risk assessment

  • @ref: 20568
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20568
  • description: Flavobacterium aciduliphilum strain JJ013 16S ribosomal RNA gene, partial sequence
  • accession: JN712178
  • length: 1377
  • database: ena
  • NCBI tax ID: 1101402

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium aciduliphilum strain DSM 256631101402.3wgspatric1101402
66792Flavobacterium aciduliphilum DSM 256632728369510draftimg1101402
67770Flavobacterium aciduliphilum DSM 25663GCA_003268855scaffoldncbi1101402

GC content

@refGC-contentmethod
2056833.9high performance liquid chromatography (HPLC)
3079633.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.602yes
flagellatedno96.84no
gram-positiveno98.265yes
anaerobicno97.769yes
aerobicyes79.45yes
halophileno94.928no
spore-formingno94.663no
glucose-utilyes76.097no
thermophileno93.636yes
glucose-fermentno88.759no

External links

@ref: 20568

culture collection no.: DSM 25663, JCM 18211, KACC 16594

straininfo link

  • @ref: 87995
  • straininfo: 399969

literature

  • topic: Phylogeny
  • Pubmed-ID: 22904226
  • title: Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium.
  • authors: Kang JY, Chun J, Jahng KY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044495-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Glycolipids/analysis, Molecular Sequence Data, *Phylogeny, Polyenes/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
20568Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25663Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25663)
30796Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172712728776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
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
87995Reimer, 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-ID399969.1