Strain identifier

BacDive ID: 5695

Type strain: Yes

Species: Chryseobacterium hominis

Strain Designation: P2K6

Strain history: CIP <- 2007, S. Campbell, Hawaï Univ., Honolulu, Hawaï, USA: strain P2K6

NCBI tax ID(s): 420404 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8040

BacDive-ID: 5695

DSM-Number: 19326

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

description: Chryseobacterium hominis P2K6 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from kidneys of the pufferfish Arothron hispidus.

NCBI tax id

  • NCBI tax id: 420404
  • Matching level: species

strain history

@refhistory
377712007, S. Campbell, Hawaï Univ., Honolulu, Hawaï, USA: strain P2K6
8040<- S. Campbell, Dept. Molecular Biosci. and Bioengineering, Univ. Hawai‘i at Manoa, Honolulu; P2K6
116503CIP <- 2007, S. Campbell, Hawaï Univ., Honolulu, Hawaï, USA: strain P2K6

doi: 10.13145/bacdive5695.20230509.8.1

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 hominis
  • full scientific name: Chryseobacterium hominis Vaneechoutte et al. 2007

  • synonyms

    @refsynonym
    20215Chryseobacterium arothri
    20215Epilithonimonas hominis

@ref: 8040

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium hominis

full scientific name: Chryseobacterium hominis Vaneechoutte et al. 2007

strain designation: P2K6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32296negative1 µm0.5 µmrod-shapedno
69480negative99.993
116503negativerod-shapedno

pigmentation

  • @ref: 32296
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8040TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
37771MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116503CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8040positivegrowth28mesophilic
32296positivegrowth20-37
32296positiveoptimum28.5mesophilic
37771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32296facultative anaerobe
116503obligate aerobe

antibiogram

  • @ref: 8040
  • medium: Mueller-Hinton Agar
  • Penicillin G: 30
  • oxacillin: 8
  • ampicillin: 28
  • ticarcillin: >50
  • mezlocillin: >50
  • cefalotin: 32-34
  • cefazolin: 30-32
  • cefotaxime: 50
  • aztreonam: 38
  • imipenem: 26
  • tetracycline: 40
  • chloramphenicol: 30
  • gentamycin: 10-12
  • amikacin: 10-12
  • vancomycin: 28
  • erythromycin: 20-22
  • lincomycin: 32-34
  • ofloxacin: 50
  • norfloxacin: 38
  • colistin: 8-10
  • pipemidic acid: 24
  • nitrofurantoin: >50
  • bacitracin: 30
  • polymyxin b: 12-14
  • kanamycin: 26-28
  • neomycin: 12
  • doxycycline: 40
  • ceftriaxone: 44
  • clindamycin: 50
  • fosfomycin: 0
  • moxifloxacin: >50
  • linezolid: 24
  • nystatin: 0
  • quinupristin/dalfopristin: 18-20
  • teicoplanin: 18-20
  • piperacillin/tazobactam: >50

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
32296NaClpositivegrowth0.5-3 %
32296NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3229630089acetate+carbon source
3229621217L-alaninamide+carbon source
3229616449alanine+carbon source
3229640585alpha-cyclodextrin+carbon source
32296286442-oxopentanoate+carbon source
3229622653asparagine+carbon source
3229617057cellobiose+carbon source
3229623652dextrin+carbon source
3229628757fructose+carbon source
3229624265gluconate+carbon source
3229617234glucose+carbon source
3229629987glutamate+carbon source
3229628087glycogen+carbon source
3229625017leucine+carbon source
3229617306maltose+carbon source
3229637684mannose+carbon source
3229626271proline+carbon source
3229617272propionate+carbon source
3229651850methyl pyruvate+carbon source
3229626490quinate+carbon source
3229617822serine+carbon source
3229617992sucrose+carbon source
3229626986threonine+carbon source
3229653423tween 40+carbon source
3229653426tween 80+carbon source
3229617151xylitol+carbon source
11650317632nitrate-reduction
11650316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3229616136hydrogen sulfideyes
11650335581indoleyes

enzymes

@refvalueactivityec
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
116503oxidase+
116503catalase+1.11.1.6
116503urease-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
116503-+++-++-+-++---+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
8040kidneys of the pufferfish Arothron hispidusArothron hispidusHawaii, island of Oahu, Kaneohe BayUSAUSANorth America
116503Pufferfish, kidneyKaneone, HawaiiUnited States of AmericaUSANorth America2006

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Urogenital tract#Kidney

taxonmaps

  • @ref: 69479
  • File name: preview.99_9647.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_497;97_5674;98_7129;99_9647&stattab=map
  • Last taxonomy: Epilithonimonas
  • 16S sequence: EF554408
  • Sequence Identity:
  • Total samples: 30673
  • soil counts: 2926
  • aquatic counts: 7775
  • animal counts: 18269
  • plant counts: 1703

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80402Risk group (German classification)
1165031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8040
  • description: Chryseobacterium arothri strain P2K6 16S ribosomal RNA gene, partial sequence
  • accession: EF554408
  • length: 1399
  • database: ena
  • NCBI tax ID: 420404

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Epilithonimonas hominis DSM 19326GCA_900108525contigncbi420404
66792Chryseobacterium hominis strain DSM 19326420404.16wgspatric420404
66792Chryseobacterium hominis DSM 193262684622847draftimg420404

GC content

  • @ref: 8040
  • GC-content: 36.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.474yes
anaerobicno99.292yes
halophileno95.532no
spore-formingno96.864no
glucose-utilyes80.033no
aerobicyes85.814yes
flagellatedno95.403no
thermophileno99.472no
motileno92.494no
glucose-fermentno93.417no

External links

@ref: 8040

culture collection no.: DSM 19326, CIP 109575

straininfo link

  • @ref: 75177
  • straininfo: 323953

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175724Chryseobacterium arothri sp. nov., isolated from the kidneys of a pufferfish.Campbell S, Harada RM, Li QXInt J Syst Evol Microbiol10.1099/ijs.0.65276-02008Animals, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Kidney/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Tetraodontiformes/*microbiologyGenetics
Phylogeny19329590Chryseobacterium arothri Campbell et al. 2008 is a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007.Kampfer P, Vaneechoutte M, Wauters GInt J Syst Evol Microbiol10.1099/ijs.0.004093-02009Bacterial Typing Techniques, Chryseobacterium/chemistry/*classification/genetics/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8040Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19326)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19326
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
32296Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2853628776041
37771Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7333
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
75177Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323953.1StrainInfo: A central database for resolving microbial strain identifiers
116503Curators of the CIPCollection of Institut Pasteur (CIP 109575)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109575