Strain identifier

BacDive ID: 5586

Type strain: Yes

Species: Flavobacterium chilense

Strain Designation: LM-09-Fp

Strain history: <- P. Kämpfer, Univ. Giessen, Germany; LM09-FP <- R. Avendano-Herrera

NCBI tax ID(s): 946677 (species)

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General

@ref: 17744

BacDive-ID: 5586

DSM-Number: 24724

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

description: Flavobacterium chilense LM-09-Fp is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from external lesion on a diseased rainbow trout from a fish farm.

NCBI tax id

  • NCBI tax id: 946677
  • Matching level: species

strain history

  • @ref: 17744
  • history: <- P. Kämpfer, Univ. Giessen, Germany; LM09-FP <- R. Avendano-Herrera

doi: 10.13145/bacdive5586.20230509.8.1

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 chilense
  • full scientific name: Flavobacterium chilense Kämpfer et al. 2012

@ref: 17744

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium chilense

full scientific name: Flavobacterium chilense Kämpfer et al. 2012

strain designation: LM-09-Fp

type strain: yes

Morphology

cell morphology

  • @ref: 30323
  • gram stain: negative
  • cell length: 2.5 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: gliding

colony morphology

  • @ref: 62523
  • incubation period: 2-3 days

pigmentation

  • @ref: 30323
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17744
  • 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
17744positivegrowth28mesophilic
30323positivegrowth4-30
30323positiveoptimum26.5mesophilic
62523positivegrowth20-30

culture pH

@refabilitytypepHPH range
30323positivegrowth6.5-8.5alkaliphile
30323positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30323aerobe
62523aerobe

spore formation

  • @ref: 30323
  • spore formation: no

halophily

  • @ref: 30323
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3032316449alanine+carbon source
3032322599arabinose+carbon source
3032317057cellobiose+carbon source
3032328757fructose+carbon source
3032328260galactose+carbon source
3032324265gluconate+carbon source
3032317234glucose+carbon source
3032325115malate+carbon source
3032317306maltose+carbon source
3032329864mannitol+carbon source
3032337684mannose+carbon source
3032328053melibiose+carbon source
30323506227N-acetylglucosamine+carbon source
3032318257ornithine+carbon source
3032315361pyruvate+carbon source
3032326546rhamnose+carbon source
3032333942ribose+carbon source
3032330911sorbitol+carbon source
3032317992sucrose+carbon source
3032327082trehalose+carbon source
3032318222xylose+carbon source

enzymes

@refvalueactivityec
30323gelatinase+
30323cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17744external lesion on a diseased rainbow trout (Oncorhynchus mykiss) from a fish farmOncorhynchus mykissnear AysenChileCHLMiddle and South America
62523External lesion,Rainbow trout(Oncorhynchus mykiss)near AysenChileCHLMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Host#Fishes
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_2122.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_352;97_396;98_1656;99_2122&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: FR774915
  • Sequence Identity:
  • Total samples: 432
  • soil counts: 64
  • aquatic counts: 134
  • animal counts: 215
  • plant counts: 19

Safety information

risk assessment

  • @ref: 17744
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17744
  • description: Flavobacterium chilense partial 16S rRNA gene, type strain LM-09-FpT
  • accession: FR774915
  • length: 1388
  • database: ena
  • NCBI tax ID: 946677

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium chilense DSM 24724GCA_900142685contigncbi946677
66792Flavobacterium chilense LMG 26360GCA_001602525contigncbi946677
66792Flavobacterium chilense strain DSM 24724946677.8wgspatric946677
66792Flavobacterium chilense strain LMG 26360946677.7wgspatric946677
66792Flavobacterium chilense LMG 263602724679197draftimg946677
66792Flavobacterium chilense DSM 247242700988709draftimg946677

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno84.927no
flagellatedno93.714yes
gram-positiveno98.044yes
anaerobicno99.737yes
halophileno95.233no
spore-formingno91.089yes
thermophileno99.808yes
glucose-utilyes90.376no
aerobicyes91.673no
glucose-fermentno88.711no

External links

@ref: 17744

culture collection no.: DSM 24724, CCM 7940, LMG 26360, CCUG 61032

straininfo link

  • @ref: 75068
  • straininfo: 376904

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21828008Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish.Kampfer P, Lodders N, Martin K, Avendano-Herrera RInt J Syst Evol Microbiol10.1099/ijs.0.033431-02011Animals, Chile, DNA, Bacterial/genetics, Fatty Acids/metabolism, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Oncorhynchus mykiss/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny23315416Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana.Glaeser SP, Galatis H, Martin K, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.048736-02013Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Germany, Leeches/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skin/microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27120464Flavobacterium panacisoli sp. nov., isolated from soil of a ginseng field.Jung SY, Kim YJ, Hoang VA, Jin Y, Nguyen NL, Oh KH, Yang DCArch Microbiol10.1007/s00203-016-1216-62016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/*analysis, *Flavobacterium/classification/genetics/isolation & purification, Panax/microbiology, Phosphatidylethanolamines/*analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/*analogs & derivatives/analysisTranscriptome
Phylogeny27357576Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.Kim DH, Singh P, Farh Mel-A, Kim YJ, Nguyen NL, Lee HA, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-016-0720-72016Base Composition, Cell Wall/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Panax/*microbiology, Phosphatidylethanolamines/metabolism, Phosphatidylserines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Soil Microbiology, Species Specificity, Vitamin K 2/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17744Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24724)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24724
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
30323Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2666428776041
62523Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 61032)https://www.ccug.se/strain?id=61032
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)
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
75068Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID376904.1StrainInfo: A central database for resolving microbial strain identifiers