Strain identifier

BacDive ID: 133363

Type strain: Yes

Species: Chryseobacterium cucumeris

Strain history: K. D. Kim; Korea Univ., South Korea; GSE06.

NCBI tax ID(s): 1813611 (species)

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General

@ref: 25237

BacDive-ID: 133363

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped, colony-forming

description: Chryseobacterium cucumeris KACC 18798 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root of cucumber .

NCBI tax id

  • NCBI tax id: 1813611
  • Matching level: species

strain history

  • @ref: 67770
  • history: K. D. Kim; Korea Univ., South Korea; GSE06.

doi: 10.13145/bacdive133363.20230509.8.1

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 cucumeris
  • full scientific name: Chryseobacterium cucumeris Jeong et al. 2017

@ref: 25237

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Chryseobacterium

species: Chryseobacterium cucumeris

type strain: yes

Morphology

cell morphology

  • @ref: 25237
  • gram stain: negative
  • cell length: 1.1-2.0 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25237
  • colony color: yellow
  • colony shape: circular
  • medium used: NA

Culture and growth conditions

culture medium

@refnamegrowth
25237Nutrient agar (NA)yes
25237TSByes
25237NB (Nutrient broth)yes
25237MacConkey agaryes

culture temp

@refgrowthtypetemperaturerange
25237positivegrowth10-38
25237positiveoptimum25mesophilic
25237positivegrowth15psychrophilic
25237positivegrowth28mesophilic
25237positivegrowth37mesophilic
25237nogrowth5psychrophilic
25237nogrowth45thermophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
25237positivegrowth5.0-8.0
25237positiveoptimum6.0-8.0

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
25237NaClpositivegrowth1-3 %
25237NaCloptimum1-2 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2523727613amygdalin-builds acid from
2523717057cellobiose-builds acid from
2523716947citrate-assimilation
2523717634D-glucose-builds acid from
2523716899D-mannitol-builds acid from
2523716024D-mannose-builds acid from
2523728053melibiose-builds acid from
2523717924D-sorbitol-builds acid from
2523765327D-xylose-builds acid from
2523717268myo-inositol-builds acid from
2523730849L-arabinose-builds acid from
2523762345L-rhamnose-builds acid from
2523717632nitrate-reduction
2523716301nitrite-reduction
2523717992sucrose-builds acid from
25237casein+hydrolysis
2523715824D-fructose+builds acid from
252374853esculin+degradation
2523717306maltose+builds acid from
2523728017starch+hydrolysis
2523727082trehalose+builds acid from
2523753424tween 20+hydrolysis
2523753426tween 80+hydrolysis
2523718186tyrosine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2523715688acetoinno
2523716136hydrogen sulfideno
2523735581indoleyes

enzymes

@refvalueactivityec
25237arginine dihydrolase-3.5.3.6
25237beta-galactosidase+3.2.1.23
25237catalase+1.11.1.6
25237cytochrome oxidase+1.9.3.1
25237gelatinase+
25237lysine decarboxylase-4.1.1.18
25237ornithine decarboxylase-4.1.1.17
25237tryptophan deaminase-4.1.99.1
25237urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25237C16:1ω7c / C16:1ω6c14.3
    25237C13:0 iso1.3
    25237C15:0 iso46.5
    25237C15:0 iso 3OH4.3
    25237C17:0 iso1.4
    25237C17:0 iso 3OH14.2
    25237C17:1 iso ω9c17.2
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar (TSA)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 1
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25237surface-sterilized root of cucumber (Cucumis sativus L.)Gunsan, Jeonbuk Province, KoreaRepublic of KoreaKORAsia
67770Surface-sterilized root of a cucumber plant grown in a field in GunsanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Sequence information

16S sequences

  • @ref: 25237
  • description: 16S rRNA gene sequence and the whole-genome shotgun
  • accession: KX146463
  • length: 1426
  • database: ena
  • NCBI tax ID: 1813611

Genome sequences

  • @ref: 67770
  • description: Chryseobacterium cucumeris GSE06
  • accession: GCA_001593385
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1813611

GC content

@refGC-contentmethod
2523736.1
6777036.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.882yes
gram-positiveno97.664no
anaerobicno99.392no
aerobicyes92.056no
halophileno94.801no
spore-formingno93.713no
glucose-utilyes85.752no
motileno89.022yes
thermophileno99.724no
glucose-fermentno92.195no

External links

@ref: 25237

culture collection no.: KACC 18798, JCM 31422, GSE 06

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902284
  • title: Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae.
  • authors: Jeong JJ, Lee DW, Park B, Sang MK, Choi IG, Kim KD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001670
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Enzymology

Reference

@idauthorstitledoi/urljournalpubmed
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
25237J.-J. L. Jeong, Dong Wan,Park, Byeonghyeok,Sang, Mee Kyung,Choi, In-Geol,Kim, Ki DeokChryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae10.1099/ijsem.0.001670IJSEM 67: 610-616 201727902284
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/