Strain identifier

BacDive ID: 134064

Type strain: Yes

Species: Chryseobacterium nakagawai

Strain Designation: F91

NCBI tax ID(s): 1241982 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 31161

BacDive-ID: 134064

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

description: Chryseobacterium nakagawai F91 is an aerobe, Gram-negative bacterium that was isolated from human kidney.

NCBI tax id

  • NCBI tax id: 1241982
  • Matching level: species

doi: 10.13145/bacdive134064.20230509.8.1

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 nakagawai
  • full scientific name: Chryseobacterium nakagawai Holmes et al. 2013

@ref: 31161

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Chryseobacterium

species: Chryseobacterium nakagawai

strain designation: F91

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
31161negativeno
69480no92.018
69480negative99.987

pigmentation

  • @ref: 31161
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31161positivegrowth18-37
62358positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 62358
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

observation

  • @ref: 31161
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3116117234glucose+carbon source
3116117306maltose+carbon source
3116127082trehalose+carbon source

enzymes

@refvalueactivityec
31161catalase+1.11.1.6
31161gelatinase+
31161cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
31161human kidney
62358Human,kidney abscessEngland,GloucesterUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Urogenital tract#Kidney
#Infection#Patient

Sequence information

16S sequences

  • @ref: 31161
  • description: Chryseobacterium nakagawai strain G41 16S ribosomal RNA gene, partial sequence
  • accession: JX100822
  • length: 1439
  • database: nuccore
  • NCBI tax ID: 1241982

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium nakagawai NCTC13529GCA_900637665completencbi1241982
66792Chryseobacterium nakagawai strain NCTC135291241982.8completepatric1241982
66792Chryseobacterium nakagawai NCTC 135292888289149completeimg1241982

GC content

  • @ref: 31161
  • GC-content: 35

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.594yes
gram-positiveno97.963yes
anaerobicno99.352no
aerobicyes89.227yes
halophileno93.359no
spore-formingno93.818no
thermophileno99.825no
glucose-utilyes82.535yes
motileno92.757yes
glucose-fermentno93.485no

External links

@ref: 31161

culture collection no.: CCUG 60563, CDC G41, NCTC 13529

straininfo link

  • @ref: 91691
  • straininfo: 410528

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23934253DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov.Holmes B, Steigerwalt AG, Nicholson ACInt J Syst Evol Microbiol10.1099/ijs.0.054353-02013Bacterial Typing Techniques, Chryseobacterium/*classification/genetics, DNA, Bacterial/genetics, Flavobacteriaceae/*classification/genetics, Humans, Indoles/metabolism, Molecular Sequence Data, *Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny24958763Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer.Venil CK, Nordin N, Zakaria ZA, Ahmad WAInt J Syst Evol Microbiol10.1099/ijs.0.063594-02014Artocarpus/*microbiology, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30272541Chryseobacterium aurantiacum sp. nov., isolated from a freshwater pond used for Murray cod (Maccullochella peelii peelii) culture.Luo T, Liu Y, Chen C, Luo Q, Rao Q, Huang M, Tu J, Lin Q, Weng BInt J Syst Evol Microbiol10.1099/ijsem.0.0029872018Animals, Aquaculture, Bacterial Typing Techniques, Base Composition, China, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Perciformes, *Phylogeny, Pigmentation, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny32515727Chryseobacterium vaccae sp. nov., isolated from raw cow's milk.Lee JE, Yoon SH, Lee GY, Lee DH, Huh CS, Kim GBInt J Syst Evol Microbiol10.1099/ijsem.0.0042502020Animals, Bacterial Typing Techniques, Base Composition, Cattle, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31161Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172748928776041
62358Curators of the CCUGhttps://www.ccug.se/strain?id=60563Culture Collection University of Gothenburg (CCUG) (CCUG 60563)
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
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
91691Reimer, 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-ID410528.1