Strain identifier

BacDive ID: 5687

Type strain: Yes

Species: Chryseobacterium haifense

Strain Designation: H38

Strain history: CIP <- 2010, DSMZ <- M. Halpern, Haifa Univ., Oranim, Tivon, Israel: strain H38

NCBI tax ID(s): 1450526 (strain), 421525 (species)

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General

@ref: 7786

BacDive-ID: 5687

DSM-Number: 19056

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

description: Chryseobacterium haifense H38 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from raw milk.

NCBI tax id

NCBI tax idMatching level
421525species
1450526strain

strain history

@refhistory
7786<- M. Halpern, Dept. Biol., Faculty of Sci. and Sci. Education, Univ. Haifa, Oranim, Tivon, Israel; H38 <- E. Hantsis-Zacharov and M. Halpern, Dept. Evolutionary and Environmental Biol., Faculty Sci. and Sci. Education, Univ. Haifa, Mount Carmel, Haifa, Israel
119785CIP <- 2010, DSMZ <- M. Halpern, Haifa Univ., Oranim, Tivon, Israel: strain H38

doi: 10.13145/bacdive5687.20230509.8.1

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 haifense
  • full scientific name: Chryseobacterium haifense Hantsis-Zacharov and Halpern 2007

  • synonyms

    • @ref: 20215
    • synonym: Kaistella haifensis

@ref: 7786

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium haifense

full scientific name: Chryseobacterium haifense Hantsis-Zacharov and Halpern 2007

strain designation: H38

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32203negative1.9 µm0.75 µmrod-shapedno
119785negativerod-shapedno

pigmentation

  • @ref: 32203
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7786NUTRIENT 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
37588MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119785CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7786positivegrowth28mesophilic
32203positivegrowth04-41
32203positiveoptimum32mesophilic
37588positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32203positivegrowth6.5-10.5alkaliphile
32203positiveoptimum7-9.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32203aerobe
119785obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
32203NaClpositivegrowth0-2.5 %
32203NaClpositiveoptimum0-1.5 %

observation

  • @ref: 32203
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3220322599arabinose+carbon source
3220328757fructose+carbon source
3220317234glucose+carbon source
3220317716lactose+carbon source
3220325115malate+carbon source
3220317306maltose+carbon source
3220337684mannose+carbon source
3220317992sucrose+carbon source
322034853esculin+hydrolysis
11978517632nitrate-reduction
11978516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3220335581indoleyes
11978535581indoleyes

metabolite tests

  • @ref: 32203
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32203acid phosphatase+3.1.3.2
32203alkaline phosphatase+3.1.3.1
32203catalase+1.11.1.6
32203cytochrome 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
119785oxidase+
119785catalase+1.11.1.6
119785urease-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
119785-+++-+++--++-+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7786raw milkIsraelISRAsia
119785Food, Raw milkIsraelISRAsia

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Host#Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_17752.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_497;97_569;98_654;99_17752&stattab=map
  • Last taxonomy: Weeksellaceae
  • 16S sequence: EF204450
  • Sequence Identity:
  • Total samples: 953
  • soil counts: 137
  • aquatic counts: 207
  • animal counts: 578
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77861Risk group (German classification)
1197851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7786
  • description: Chryseobacterium haifense strain H38 16S ribosomal RNA gene, partial sequence
  • accession: EF204450
  • length: 1480
  • database: ena
  • NCBI tax ID: 421525

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistella haifensis DSM 19056GCA_000735695contigncbi1450526
66792Chryseobacterium haifense DSM 190561450526.3wgspatric1450526
66792Chryseobacterium haifense DSM 190562600255101draftimg1450526

GC content

  • @ref: 7786
  • GC-content: 37.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.14yes
gram-positiveno98.092yes
anaerobicno98.723no
halophileno88.444yes
spore-formingno97.273no
thermophileno99.193yes
glucose-utilyes85.246yes
aerobicyes87.63yes
flagellatedno96.946yes
glucose-fermentno92.264no

External links

@ref: 7786

culture collection no.: DSM 19056, LMG 24029, CIP 110174

straininfo link

  • @ref: 75169
  • straininfo: 310967

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911308Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk.Hantsis-Zacharov E, Halpern MInt J Syst Evol Microbiol10.1099/ijs.0.65115-02007Aerobiosis/physiology, Animals, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Milk/*microbiology, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny19622666Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium.Kampfer P, Vaneechoutte M, Lodders N, De Baere T, Avesani V, Janssens M, Busse HJ, Wauters GInt J Syst Evol Microbiol10.1099/ijs.0.008250-02009Bacterial Typing Techniques, Chryseobacterium/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacteriaceae/*classification/genetics/isolation & purification, Flavobacteriaceae Infections/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny19767354Chryseobacterium solincola sp. nov., isolated from soil.Benmalek Y, Cayol JL, Bouanane NA, Hacene H, Fauque G, Fardeau MLInt J Syst Evol Microbiol10.1099/ijs.0.008631-02009Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny27412503Chryseobacterium montanum sp. nov. isolated from mountain soil.Guo W, Li J, Shi M, Yuan K, Li N, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0013092016Bacterial Typing Techniques, Base Composition, China, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34988667Kaistella soli sp. nov., isolated from oil-contaminated experimental soil.Chaudhary DK, Dahal RH, Park JH, Hong YArch Microbiol10.1007/s00203-021-02734-42022Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil MicrobiologyTranscriptome
Phylogeny35639593Chryseobacterium faecale sp. nov., isolated from camel feces.Son Y, Min J, Park WInt J Syst Evol Microbiol10.1099/ijsem.0.0054052022Animals, Bacterial Typing Techniques, Base Composition, Camelus, *Chryseobacterium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7786Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19056)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19056
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
32203Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2844528776041
37588Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8004
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
75169Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310967.1StrainInfo: A central database for resolving microbial strain identifiers
119785Curators of the CIPCollection of Institut Pasteur (CIP 110174)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110174