Strain identifier

BacDive ID: 24022

Type strain: Yes

Species: Flavobacterium fontis

Strain history: K. Y. Jahng MIC3010.

NCBI tax ID(s): 1124188 (species)

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General

@ref: 20569

BacDive-ID: 24022

DSM-Number: 25660

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

description: Flavobacterium fontis DSM 25660 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh water pond.

NCBI tax id

  • NCBI tax id: 1124188
  • Matching level: species

strain history

@refhistory
20569<- J. Chun, Chonbuk National Univ., Dept. of Life Scs., Jeonju-si, Korea; MIC3010
67770K. Y. Jahng MIC3010.

doi: 10.13145/bacdive24022.20250331.9.3

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 fontis
  • full scientific name: Flavobacterium fontis Chun et al. 2013

@ref: 20569

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium fontis

full scientific name: Flavobacterium fontis Chun et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30818negativerod-shapedno
125438no94.5
125438negative98.5
125439negative99.8

pigmentation

  • @ref: 30818
  • production: no

Culture and growth conditions

culture medium

  • @ref: 20569
  • 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

@refgrowthtypetemperature
20569positivegrowth25
30818positivegrowth15-42
30818positiveoptimum25
67770positivegrowth25

culture pH

@refabilitytypepH
30818positivegrowth5.5-8
30818positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30818aerobe
125439obligate aerobe96.1

spore formation

@refspore formationconfidence
125438no94.803
125439no99.5

halophily

  • @ref: 30818
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.5 %

observation

  • @ref: 30818
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3081821217L-alaninamide+carbon source
30818286442-oxopentanoate+carbon source
3081823652dextrin+carbon source
3081824148galactonate+carbon source
3081829987glutamate+carbon source
3081815428glycine+carbon source
3081828087glycogen+carbon source
3081826271proline+carbon source
3081826546rhamnose+carbon source
3081853423tween 40+carbon source
308184853esculin+hydrolysis

enzymes

@refvalueactivityec
30818gelatinase+
30818cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20569fresh water pondJeonju (35° 50' N 127° 07' E)Republic of KoreaKORAsia35.8333127.117
67770Freshwater pond in JeonjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4326.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2169;97_2625;98_3255;99_4326&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: JN873147
  • Sequence Identity:
  • Total samples: 6484
  • soil counts: 410
  • aquatic counts: 5359
  • animal counts: 496
  • plant counts: 219

Safety information

risk assessment

  • @ref: 20569
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20569
  • description: Flavobacterium fontis strain MIC3010 16S ribosomal RNA gene, partial sequence
  • accession: JN873147
  • length: 1378
  • database: nuccore
  • NCBI tax ID: 1124188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium fontis strain DSM 256601124188.3wgspatric1124188
66792Flavobacterium fontis DSM 256602695420946draftimg1124188
67770Flavobacterium fontis DSM 25660GCA_900129405contigncbi1124188

GC content

@refGC-contentmethod
2056941.0high performance liquid chromatography (HPLC)
3081841

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.707yes
125438spore-formingspore-formingAbility to form endo- or exosporesno94.803no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.589yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.108yes
125438motile2+flagellatedAbility to perform flagellated movementno94.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.5
125439BacteriaNetmotilityAbility to perform movementno72.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.1

External links

@ref: 20569

culture collection no.: DSM 25660, JCM 18212, KACC 16593, MIC 3010

straininfo link

  • @ref: 87996
  • straininfo: 408227

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904217Flavobacterium fontis sp. nov., isolated from freshwater.Chun J, Kang JY, Jahng KYInt J Syst Evol Microbiol10.1099/ijs.0.045203-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny26769164Flavobacterium lutivivi sp. nov., isolated from activated sludge.Feng Q, Han L, Nogi Y, Hong Q, Lv JInt J Syst Evol Microbiol10.1099/ijsem.0.0008922016
Phylogeny31157614Flavobacterium stagni sp. nov., isolated from a freshwater reservoir.Chen WM, Guo YP, Kwon SW, Sheu C, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0034882019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
20569Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25660Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25660)
30818Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172714928776041
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/
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/
87996Reimer, 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-ID408227.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG