Strain identifier

BacDive ID: 24471

Type strain: Yes

Species: Kaistia hirudinis

Strain Designation: E94

Strain history: CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain E94

NCBI tax ID(s): 1293440 (species)

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General

@ref: 20615

BacDive-ID: 24471

DSM-Number: 25966

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

description: Kaistia hirudinis E94 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from skin of a juvenile medicinal leech .

NCBI tax id

  • NCBI tax id: 1293440
  • Matching level: species

strain history

@refhistory
342232012, P. Kämpfer, J.L. Univ., Giessen, Germany: strain E94
20615<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; E94 <- L. Kaiser
119914CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain E94

doi: 10.13145/bacdive24471.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Kaistiaceae
  • genus: Kaistia
  • species: Kaistia hirudinis
  • full scientific name: Kaistia hirudinis Glaeser et al. 2013

@ref: 20615

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Kaistiaceae

genus: Kaistia

species: Kaistia hirudinis

full scientific name: Kaistia hirudinis Glaeser et al. 2013

strain designation: E94

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
31006negative1 µm0.5 µmrod-shaped
69480negative99.992
119914negativeoval-shapedyes

colony morphology

  • @ref: 20615
  • incubation period: 2-3 days

pigmentation

  • @ref: 31006
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34223MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
20615R2A 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
119914CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
20615positivegrowth25mesophilic
31006positivegrowth15-37
34223positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31006positivegrowth4.5-10.5alkaliphile
31006positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31006aerobe
119914obligate aerobe

spore formation

@refspore formationconfidence
31006no
69481no100
69480no99.989

halophily

  • @ref: 31006
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 01-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31006370543-hydroxybutyrate+carbon source
3100630089acetate+carbon source
3100616449alanine+carbon source
3100624996lactate+carbon source
3100618401phenylacetate+carbon source
3100626271proline+carbon source
3100617632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
683714853esculin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-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
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11991417632nitrate+reduction
11991416301nitrite-reduction

metabolite production

  • @ref: 119914
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31006catalase+1.11.1.6
31006cytochrome oxidase+1.9.3.1
119914oxidase+
119914catalase+1.11.1.6
119914urease+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
119914--+--+--+-++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119914--+/-+/-+/-+/----+/-+/-+/-+/--+/------+/---+/--+/-+/-+/---+/-+/--+/-+/----+/-+/-+/--+/-+/-+/-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
20615skin of a juvenile medicinal leech (Hirudo verbana)Hirudo verbanaHessen, Biebertal, Leech Breeding StationGermanyDEUEurope
119914Animal, Surface of a juvenile leech, Hirudo verbanaBiebertal, HessenGermanyDEUEurope2009

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_74944.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_31789;97_40222;98_52404;99_74944&stattab=map
  • Last taxonomy: Hyphomicrobiales
  • 16S sequence: KC254734
  • Sequence Identity:
  • Total samples: 311
  • soil counts: 34
  • aquatic counts: 150
  • animal counts: 22
  • plant counts: 105

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
206151Risk group (German classification)
1199141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20615
  • description: Kaistia hirudinis strain E94 16S ribosomal RNA gene, partial sequence
  • accession: KC254734
  • length: 1308
  • database: ena
  • NCBI tax ID: 1293440

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistia hirudinis DSM 25966GCA_014196455contigncbi1293440
66792Kaistia hirudinis strain DSM 259661293440.3wgspatric1293440
66792Kaistia hirudinis DSM 259662829893694draftimg1293440

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.248no
gram-positiveno97.633yes
anaerobicno98.595yes
aerobicyes90.699yes
halophileno90.94no
spore-formingno96.635yes
glucose-utilyes92.365no
flagellatedno97.011no
thermophileno96.777yes
glucose-fermentno91.606no

External links

@ref: 20615

culture collection no.: DSM 25966, CCM 8401, CIP 110381, LMG 26925

straininfo link

  • @ref: 88340
  • straininfo: 379504

literature

  • topic: Phylogeny
  • Pubmed-ID: 23456803
  • title: Kaistia hirudinis sp. nov., isolated from the skin of Hirudo verbana.
  • authors: Glaeser SP, Galatis H, Martin K, Kampfer P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.049619-0
  • year: 2013
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Leeches/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Skin/microbiology, Ubiquinone/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
20615Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25966Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25966)
31006Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172733628776041
34223Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8233
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
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
88340Reimer, 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-ID379504.1
119914Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110381Collection of Institut Pasteur (CIP 110381)