Strain identifier

BacDive ID: 5510

Type strain: Yes

Species: Chryseobacterium halperniae

Strain Designation: H1

Strain history: <- M. Halpern, Dept. Biol., Faculty of Sci. and Sci. Education, Univ. Haifa, Oranim, Tivon, Israel; H1 <- E. Hantsis-Zacharov

NCBI tax ID(s): 421072 (species)

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General

@ref: 8390

BacDive-ID: 5510

DSM-Number: 19921

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

description: Chryseobacterium halperniae H1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from raw cow milk.

NCBI tax id

  • NCBI tax id: 421072
  • Matching level: species

strain history

  • @ref: 8390
  • history: <- M. Halpern, Dept. Biol., Faculty of Sci. and Sci. Education, Univ. Haifa, Oranim, Tivon, Israel; H1 <- E. Hantsis-Zacharov

doi: 10.13145/bacdive5510.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium halperniae
  • full scientific name: Chryseobacterium halperniae Hahnke et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Epilithonimonas lactis

@ref: 8390

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium halperniae

full scientific name: Chryseobacterium halperniae Hahnke et al. 2017

strain designation: H1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29410negative1.65 µm0.8 µmrod-shapedno
69480no93.267
69480negative99.983

pigmentation

  • @ref: 29410
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8390
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8390positivegrowth28mesophilic
29410positivegrowth05-33
29410positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
29410positivegrowth04-08acidophile
29410positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29410
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
29410NaClpositivegrowth0-2 %
29410NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2941017234glucose+carbon source
2941017306maltose+carbon source
294104853esculin+hydrolysis

metabolite production

  • @ref: 29410
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29410
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29410acid phosphatase+3.1.3.2
29410alkaline phosphatase+3.1.3.1
29410catalase+1.11.1.6
29410cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 8390
  • sample type: raw cow milk
  • geographic location: Northern Israel
  • country: Israel
  • origin.country: ISR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_7255.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_3036;97_3731;98_4731;99_7255&stattab=map
  • Last taxonomy: Chryseobacterium halperniae
  • 16S sequence: EF204460
  • Sequence Identity:
  • Total samples: 990
  • soil counts: 88
  • aquatic counts: 199
  • animal counts: 620
  • plant counts: 83

Safety information

risk assessment

  • @ref: 8390
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8390
  • description: Chryseobacterium halperniae strain H1 16S ribosomal RNA gene, partial sequence
  • accession: EF204460
  • length: 1497
  • database: ena
  • NCBI tax ID: 421072

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Epilithonimonas lactis DSM 19921GCA_900110605scaffoldncbi421072
66792Epilithonimonas lactis LMG 24401GCA_000735105contigncbi421072
66792Chryseobacterium halperniae strain DSM 19921421072.12wgspatric421072
66792Epilithonimonas lactis strain LMG 24401421072.8wgspatric421072
66792Chryseobacterium halperniae LMG 244012619619117draftimg421072
66792Chryseobacterium halperniae DSM 199212622736498draftimg421072

GC content

@refGC-contentmethod
839038.0high performance liquid chromatography (HPLC)
2941038

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno92.325no
motileno92.147yes
flagellatedno96.614yes
gram-positiveno98.176yes
anaerobicno99.681yes
aerobicyes90.623yes
halophileno94.14yes
spore-formingno96.549no
thermophileno99.52yes
glucose-utilyes88.143yes

External links

@ref: 8390

culture collection no.: DSM 19921, LMG 24401

straininfo link

  • @ref: 74995
  • straininfo: 401993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656919Epilithonimonas lactis sp. nov., isolated from raw cow's milk.Shaked T, Hantsis-Zacharov E, Halpern MInt J Syst Evol Microbiol10.1099/ijs.0.012575-02009Animals, Cattle, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Milk/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny25298379Epilithonimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.Hoang VA, Kim YJ, Ponnuraj SP, Nguyen NL, Hwang KH, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.065466-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8390Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19921)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19921
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
29410Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2581728776041
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74995Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401993.1StrainInfo: A central database for resolving microbial strain identifiers