Strain identifier

BacDive ID: 5686

Type strain: Yes

Species: Chryseobacterium oranimense

Strain Designation: H8

Strain history: CIP <- 2008, DSMZ <- E. Hantsis-Zacharov, Haifa Univ., Haifa, Israel: strain H8

NCBI tax ID(s): 421058 (species)

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General

@ref: 7785

BacDive-ID: 5686

DSM-Number: 19055

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

description: Chryseobacterium oranimense H8 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from raw cow’s milk.

NCBI tax id

  • NCBI tax id: 421058
  • Matching level: species

strain history

@refhistory
7785<- M. Halpern, Dept. Biol., Faculty of Sci. and Sci. Education, Univ. Haifa, Oranim, Tivon, Israel; H8 <- E. Hantsis-Zacharov and M. Halpern, Dept. Evolutionary and Environmental Biol., Faculty Sci. and Sci. Education, Univ. Haifa, Mount Carmel, Haifa, Israel
121430CIP <- 2008, DSMZ <- E. Hantsis-Zacharov, Haifa Univ., Haifa, Israel: strain H8

doi: 10.13145/bacdive5686.20230509.8.1

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 oranimense
  • full scientific name: Chryseobacterium oranimense Hantsis-Zacharov et al. 2008

@ref: 7785

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium oranimense

full scientific name: Chryseobacterium oranimense Hantsis-Zacharov et al. 2008

strain designation: H8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32632negative1.2-2 µm0.7-1.2 µmrod-shapedno
69480negative99.995
121430negativerod-shapedno

pigmentation

  • @ref: 32632
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7785NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37882MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121430CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7785positivegrowth28mesophilic
32632positivegrowth05-37
32632positiveoptimum30-33mesophilic
37882positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32632positivegrowth04-08acidophile
32632positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32632aerobe
121430obligate aerobe

spore formation

@refspore formationconfidence
32632no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
32632NaClpositivegrowth0-3 %
32632NaClpositiveoptimum0-1 %

observation

  • @ref: 32632
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263222599arabinose+carbon source
3263216947citrate+carbon source
3263217234glucose+carbon source
3263217306maltose+carbon source
3263237684mannose+carbon source
326324853esculin+hydrolysis
12143017632nitrate-reduction
12143016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3263235581indoleyes
12143035581indoleyes

metabolite tests

  • @ref: 32632
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32632gelatinase+
32632cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121430oxidase+
121430catalase+1.11.1.6
121430urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121430-+++-++-++++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7785raw cow’s milknorthern partIsraelISRAsia
121430Food, Cow, raw milkIsraelISRAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3017.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_753;97_1893;98_2323;99_3017&stattab=map
  • Last taxonomy: Chryseobacterium oranimense
  • 16S sequence: EF204451
  • Sequence Identity:
  • Total samples: 64
  • soil counts: 10
  • aquatic counts: 5
  • animal counts: 40
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77851Risk group (German classification)
1214301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7785
  • description: Chryseobacterium oranimense strain H8 16S ribosomal RNA gene, partial sequence
  • accession: EF204451
  • length: 1453
  • database: ena
  • NCBI tax ID: 421058

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium oranimense DSM 19055GCA_900129755contigncbi421058
66792Chryseobacterium oranimense strain DSM 19055421058.6wgspatric421058
66792Chryseobacterium oranimense DSM 190552684623028draftimg421058

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.067no
anaerobicno99.448yes
halophileno93.317yes
spore-formingno94.53no
glucose-utilyes85.644no
aerobicyes89.503yes
flagellatedno95.293no
thermophileno99.755yes
motileno90.462yes
glucose-fermentno92.366no

External links

@ref: 7785

culture collection no.: DSM 19055, CIP 109920, LMG 24030

straininfo link

  • @ref: 75168
  • straininfo: 360129

literature

  • topic: Phylogeny
  • Pubmed-ID: 18984706
  • title: Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk.
  • authors: Hantsis-Zacharov E, Shaked T, Senderovich Y, Halpern M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65819-0
  • year: 2008
  • mesh: Animals, Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification/physiology, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lipolysis/*physiology, Milk/*microbiology, Molecular Sequence Data, Peptide Hydrolases/*metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7785Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19055)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19055
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
32632Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2884328776041
37882Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7718
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)
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.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
75168Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360129.1StrainInfo: A central database for resolving microbial strain identifiers
121430Curators of the CIPCollection of Institut Pasteur (CIP 109920)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109920