Strain identifier

BacDive ID: 24023

Type strain: Yes

Species: Flavobacterium cutihirudinis

Strain Designation: E89

Strain history: CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain E89

NCBI tax ID(s): 1265740 (species)

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General

@ref: 20570

BacDive-ID: 24023

DSM-Number: 25795

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

description: Flavobacterium cutihirudinis E89 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from skin of a juvenile medical leech from a leech farm.

NCBI tax id

  • NCBI tax id: 1265740
  • Matching level: species

strain history

@refhistory
379402012, P. Kämpfer, J.L. Univ., Giessen, Germany: strain E89
20570<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; E89 <- L. Kaiser
118826CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain E89

doi: 10.13145/bacdive24023.20230509.8.1

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 cutihirudinis
  • full scientific name: Flavobacterium cutihirudinis Glaeser et al. 2013

@ref: 20570

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium cutihirudinis

full scientific name: Flavobacterium cutihirudinis Glaeser et al. 2013

strain designation: E89

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
30971negative2.5 µm0.9 µmrod-shapedyesgliding
69480negative99.987
118826negativerod-shapedyes

pigmentation

  • @ref: 30971
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37940MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
20570R2A MEDIUM (DSMZ Medium 830)yesName: 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 waterhttps://mediadive.dsmz.de/medium/830
118826CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
20570positivegrowth28mesophilic
30971positivegrowth10-30
30971positiveoptimum26.5mesophilic
37940positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30971positivegrowth6.5-9.5alkaliphile
30971positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30971aerobe
118826obligate aerobe

spore formation

@refspore formationconfidence
30971no
69481no100
69480no99.998

halophily

  • @ref: 30971
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

  • @ref: 30971
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3097122599arabinose+carbon source
3097117057cellobiose+carbon source
3097128260galactose+carbon source
3097117234glucose+carbon source
3097117306maltose+carbon source
3097137684mannose+carbon source
30971506227N-acetylglucosamine+carbon source
3097115361pyruvate+carbon source
3097130911sorbitol+carbon source
3097117992sucrose+carbon source
3097127082trehalose+carbon source
3097118222xylose+carbon source
309714853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11882617632nitrate+reduction
11882616301nitrite+reduction

metabolite production

  • @ref: 118826
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30971gelatinase+
30971cytochrome oxidase+1.9.3.1
118826oxidase-
118826catalase+1.11.1.6
118826urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118826-+---++---++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118826---+-+/----++++--------++-+-++--+/--+/--+/-+/-+/--+/-----+/------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
20570skin of a juvenile medical leech (Hirudo verbana) from a leech farmHirudo verbanaHessen, BiebertalGermanyDEUEurope
118826Animal, Surface of a juvenile leech, Hirudo verbanaLeech farm , Biebertal, HessenGermanyDEUEurope2009

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Annelida
#Host Body-Site#Organ#Skin, Nail, Hair

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
205701Risk group (German classification)
1188261Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20570
  • description: Flavobacterium cutihirudinis strain E89 16S ribosomal RNA gene, partial sequence
  • accession: JX966231
  • length: 1373
  • database: ena
  • NCBI tax ID: 1265740

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium cutihirudinis DSM 25795GCA_003385895scaffoldncbi1265740
66792Flavobacterium cutihirudinis strain DSM 257951265740.4wgspatric1265740
66792Flavobacterium cutihirudinis DSM 257952695421040draftimg1265740

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.016yes
gram-positiveno98.2yes
anaerobicno99.685no
aerobicyes88.792no
halophileno96.45no
spore-formingno94.544yes
glucose-utilyes93.233yes
thermophileno99.602yes
motileno77.983no
glucose-fermentno87.964no

External links

@ref: 20570

culture collection no.: DSM 25795, CIP 110384, LMG 26922

straininfo link

  • @ref: 87997
  • straininfo: 379501

literature

  • topic: Phylogeny
  • Pubmed-ID: 23315416
  • title: Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana.
  • authors: Glaeser SP, Galatis H, Martin K, Kampfer P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.048736-0
  • year: 2013
  • mesh: Animals, 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/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20570Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25795Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25795)
30971Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172730128776041
37940Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8238
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
87997Reimer, 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-ID379501.1
118826Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110384Collection of Institut Pasteur (CIP 110384)