Strain identifier

BacDive ID: 133365

Type strain: Yes

Species: Chryseobacterium nepalense

Strain Designation: C-5-3

Strain history: J. Kim; Kyonggi Univ., South Korea; C-5-3.

NCBI tax ID(s): 1854498 (species)

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General

@ref: 25219

BacDive-ID: 133365

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

description: Chryseobacterium nepalense C-5-3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from isolated from oil-contaminated soil of Biratnagar.

NCBI tax id

  • NCBI tax id: 1854498
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. Kim; Kyonggi Univ., South Korea; C-5-3.

doi: 10.13145/bacdive133365.20230509.8.1

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 nepalense
  • full scientific name: Chryseobacterium nepalense Chaudhary and Kim 2017

@ref: 25219

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Chryseobacterium

species: Chryseobacterium nepalense

strain designation: C-5-3

type strain: yes

Morphology

cell morphology

  • @ref: 25219
  • gram stain: negative
  • cell length: 1.2-1.8 µm
  • cell width: 0.6-0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25219
  • colony size: 2-4 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

pigmentation

  • @ref: 25219
  • production: yes
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
25219Reasoner's 2A agar (R2A)yes
25219Trypticase Soy Agar (TSA)yes
25219LB (Luria-Bertani) MEDIUMyes
25219Marine agar (MA)yes
25219brain heart infusion agaryes
25219Nutrient agar (NA)yes
25219veal infusion agaryes
25219MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
25219positivegrowth10-45
25219positiveoptimum20-40
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
25219positivegrowth6.0-11.0alkaliphile
25219positiveoptimum6.5-9.0

Physiology and metabolism

tolerance

  • @ref: 25219
  • compound: NaCl
  • percentage: 0-4

oxygen tolerance

  • @ref: 25219
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25219
  • spore formation: no

halophily

  • @ref: 25219
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25219161933-hydroxybenzoate-assimilation
25219370543-hydroxybutyrate-assimilation
25219178794-hydroxybenzoate-assimilation
2521917128adipate-assimilation
25219casein-hydrolysis
2521917029chitin-hydrolysis
2521916899D-mannitol-assimilation
2521916024D-mannose-assimilation
2521916988D-ribose-assimilation
2521917924D-sorbitol-assimilation
2521927689decanoate-assimilation
2521917234glucose-fermentation
2521917368hypoxanthine-hydrolysis
2521917268myo-inositol-assimilation
2521917240itaconate-assimilation
2521916977L-alanine-assimilation
2521916467L-arginine-fermentation
2521918287L-fucose-assimilation
2521917115L-serine-assimilation
2521924996lactate-assimilation
2521925115malate-assimilation
2521928053melibiose-assimilation
25219506227N-acetylglucosamine-assimilation
2521917632nitrate-reduction
2521918401phenylacetate-assimilation
25219potassium 2-dehydro-D-gluconate-assimilation
25219potassium 5-dehydro-D-gluconate-assimilation
2521932032potassium gluconate-assimilation
2521917272propionate-assimilation
2521932954sodium acetate-assimilation
2521953258sodium citrate-assimilation
2521962983sodium malonate-assimilation
252199300suberic acid-assimilation
2521917992sucrose-assimilation
2521953423tween 40-hydrolysis
2521918186tyrosine-hydrolysis
2521916199urea-fermentation
2521931011valerate-assimilation
2521915318xanthine-hydrolysis
252193557154-nitrophenyl beta-D-galactopyranoside+assimilation
2521985146carboxymethylcellulose+hydrolysis
2521917634D-glucose+assimilation
2521916991dna+hydrolysis
252194853esculin+hydrolysis
25219esculin ferric citrate+assimilation
252195291gelatin+hydrolysis
252195291gelatin+assimilation
2521928087glycogen+assimilation
2521930849L-arabinose+assimilation
2521915971L-histidine+assimilation
2521962345L-rhamnose+assimilation
2521916828L-tryptophan+assimilation
2521917306maltose+assimilation
2521917814salicin+assimilation
2521928017starch+hydrolysis
2521953426tween 80+hydrolysis
2521917203L-proline+/-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
2521927902tetracyclineyesyes30 µg
2521917833gentamicinyesyes10 µg
2521928368novobiocinyesyes30 µg
252196104kanamycinyesyes30 µg
2521917076streptomycinyesyes10 µg
2521928077rifampicinyesyes10 µg
25219100147nalidixic acidyesyes30 µg
2521945924trimethoprimyesyes30 µg
2521927641cycloheximideyesyes30 µg
2521928971ampicillinyesyes30 µg
2521917698chloramphenicolyesyes100 µg
2521917334penicillinyesyes10 µg
252197507neomycinyesyes30 µg
252199332sulfamethoxazoleyesyes30 µg

metabolite production

@refChebi-IDmetaboliteproduction
2521916136hydrogen sulfideno
2521935581indoleyes

enzymes

@refvalueactivityec
25219acid phosphatase+3.1.3.2
25219alkaline phosphatase+3.1.3.1
25219alpha-chymotrypsin-3.4.21.1
25219alpha-fucosidase-3.2.1.51
25219alpha-galactosidase-3.2.1.22
25219alpha-glucosidase+3.2.1.20
25219alpha-mannosidase-3.2.1.24
25219beta-galactosidase-3.2.1.23
25219beta-glucosidase+3.2.1.21
25219beta-glucuronidase-3.2.1.31
25219catalase+1.11.1.6
25219cystine arylamidase+/-3.4.11.3
25219cytochrome oxidase+1.9.3.1
25219esterase (C 4)+
25219esterase Lipase (C 8)+
25219leucine arylamidase+3.4.11.1
25219lipase (C 14)-
25219N-acetyl-beta-glucosaminidase+3.2.1.52
25219naphthol-AS-BI-phosphohydrolase+
25219trypsin-3.4.21.4
25219valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25219C16:1ω7c / C16:1ω6c20.68
    25219C15:0 iso29.4
    25219C17:0 iso 3OH17.66
    25219C17:1 iso ω9c / C16:0 10-methyl16.59
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar (TSA)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
25219isolated from oil-contaminated soil of BiratnagarBiratnagar, Morang, NepalNepalNPLAsia2687
67770Oil-contaminated soil of BiratnagarMorangNepalNPLAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 25219
  • description: 16S rRNA gene sequences
  • accession: KX129820
  • length: 1458
  • database: ena
  • NCBI tax ID: 1854498

GC content

  • @ref: 25219
  • GC-content: 38.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 25219

culture collection no.: KEMB 9005-411, KACC 18907, JCM 31469

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902299Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0016802017Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33047174Chryseobacterium cheonjiense sp. nov., isolated from forest soil.Chaudhary DK, Dahal RH, Kim DU, Kim JArch Microbiol10.1007/s00203-020-02065-w2020Base Composition, Chryseobacterium/*classification/genetics, Forests, Nucleic Acid Hybridization, Phosphatidylethanolamines, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Species Specificity

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
25219D. K. K. Chaudhary, J.Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil10.1099/ijsem.0.001680IJSEM 67: 646-652 201727902299
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/