Strain identifier

BacDive ID: 140833

Type strain: Yes

Species: Cupriavidus nantongensis

Strain Designation: X1

NCBI tax ID(s): 1796606 (species)

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General

@ref: 43635

BacDive-ID: 140833

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, coccus-shaped, colony-forming

description: Cupriavidus nantongensis X1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sludge collected from the vicinity of a pesticide manufacturer.

NCBI tax id

  • NCBI tax id: 1796606
  • Matching level: species

doi: 10.13145/bacdive140833.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Cupriavidus
  • species: Cupriavidus nantongensis
  • full scientific name: Cupriavidus nantongensis Sun et al. 2016

@ref: 43635

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus nantongensis

strain designation: X1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43635negative1.3-2.4 µm1.3-1.5 µmcoccus-shapedyesgliding
69480yes95.423
69480negative99.997

colony morphology

  • @ref: 43635
  • colony size: 0.5-1 mm
  • colony color: Pale
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Luria Bertani agar

Culture and growth conditions

culture medium

  • @ref: 43635
  • name: LB (Luria-Bertani) MEDIUM
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43635positivegrowth20-42
43635positiveoptimum30-37mesophilic

culture pH

@refabilitytypepHPH range
43635positivegrowth6-9alkaliphile
43635positiveoptimum7

Physiology and metabolism

tolerance

@refcompoundconcentration
43635Cobalt0.05 mg/ml
43635Cobalt0.1 mg/ml
43635Zinc0.5 mg/ml

oxygen tolerance

  • @ref: 43635
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.973

halophily

  • @ref: 43635
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4363517634D-glucose-assimilation
4363516899D-mannitol-assimilation
4363516024D-mannose-assimilation
4363530849L-arabinose-assimilation
4363517306maltose-assimilation
43635506227N-acetylglucosamine-assimilation
4363518401phenylacetate-assimilation
4363527613amygdalin-builds acid from
4363518305arbutin-builds acid from
4363515963ribitol-builds acid from
4363517108D-arabinose-builds acid from
4363518333D-arabitol-builds acid from
4363517057cellobiose-builds acid from
4363515824D-fructose-builds acid from
4363528847D-fucose-builds acid from
4363512936D-galactose-builds acid from
4363517634D-glucose-builds acid from
4363517716lactose-builds acid from
4363562318D-lyxose-builds acid from
4363517306maltose-builds acid from
4363516899D-mannitol-builds acid from
4363516024D-mannose-builds acid from
436356731melezitose-builds acid from
4363528053melibiose-builds acid from
4363516634raffinose-builds acid from
4363516988D-ribose-builds acid from
4363517924D-sorbitol-builds acid from
4363516443D-tagatose-builds acid from
4363516551D-trehalose-builds acid from
4363532528turanose-builds acid from
4363565327D-xylose-builds acid from
4363516813galactitol-builds acid from
4363517113erythritol-builds acid from
43635esculin ferric citrate-builds acid from
4363528066gentiobiose-builds acid from
4363528087glycogen-builds acid from
4363517268myo-inositol-builds acid from
4363515443inulin-builds acid from
4363530849L-arabinose-builds acid from
4363518403L-arabitol-builds acid from
4363518287L-fucose-builds acid from
4363562345L-rhamnose-builds acid from
4363517266L-sorbose-builds acid from
43635320061methyl alpha-D-glucopyranoside-builds acid from
4363543943methyl alpha-D-mannoside-builds acid from
4363574863methyl beta-D-xylopyranoside-builds acid from
43635506227N-acetylglucosamine-builds acid from
43635potassium 2-dehydro-D-gluconate-builds acid from
43635potassium 5-dehydro-D-gluconate-builds acid from
4363532032potassium gluconate-builds acid from
4363517814salicin-builds acid from
4363528017starch-builds acid from
4363517992sucrose-builds acid from
4363517151xylitol-builds acid from
4363517234glucose-fermentation
436354853esculin-hydrolysis
436355291gelatin-hydrolysis
4363528017starch-hydrolysis
4363516301nitrite-reduction
4363527689decanoate+assimilation
4363525115malate+assimilation
4363532032potassium gluconate+assimilation
4363517754glycerol+builds acid from
4363553424tween 20+hydrolysis
4363553426tween 80+hydrolysis
4363517632nitrate+reduction
4363517128adipate+/-assimilation
4363516947citrate+/-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
436353534cephalexinyesyes30 µg (disc)
4363518208penicillin gyesyes10 µg (disc)
4363517076streptomycinyesyes10 µg (disc)
436352676amoxicillinyesyes20 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4363515688acetoinno
4363516136hydrogen sulfideno
4363535581indoleyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4363517234glucose-
4363515688acetoin-

enzymes

@refvalueactivityec
43635catalase+1.11.1.6
43635cytochrome oxidase+1.9.3.1
43635alkaline phosphatase+3.1.3.1
43635esterase (C 4)+
43635acid phosphatase+3.1.3.2
43635leucine arylamidase+3.4.11.1
43635naphthol-AS-BI-phosphohydrolase+/-
43635valine arylamidase+/-
43635cystine arylamidase+/-3.4.11.3
43635lipase (C 14)-
43635trypsin-3.4.21.4
43635alpha-chymotrypsin-3.4.21.1
43635alpha-galactosidase-3.2.1.22
43635beta-galactosidase-3.2.1.23
43635beta-glucuronidase-3.2.1.31
43635beta-glucosidase-3.2.1.21
43635N-acetyl-beta-glucosaminidase-3.2.1.52
43635alpha-mannosidase-3.2.1.24
43635alpha-fucosidase-3.2.1.51
43635arginine dihydrolase-3.5.3.6
43635urease-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 43635
  • sample type: sludge collected from the vicinity of a pesticide manufacturer
  • geographic location: Nantong, Jiangsu Province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1912.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_534;99_1912&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: KU168038
  • Sequence Identity:
  • Total samples: 2331
  • soil counts: 1401
  • aquatic counts: 297
  • animal counts: 341
  • plant counts: 292

Sequence information

16S sequences

  • @ref: 43635
  • description: 16S rRNA gene sequence
  • accession: KU168038
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus nantongensis X1GCA_001598055chromosomencbi1796606
66792Cupriavidus nantongensis strain X11796606.3completepatric1796606
66792Cupriavidus nantongensis strain X11796606.6plasmidpatric1796606
66792Cupriavidus nantongensis X12687453284completeimg1796606

GC content

  • @ref: 43635
  • GC-content: 66.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes86.194no
gram-positiveno98.287yes
anaerobicno98.996no
aerobicyes93.046no
halophileno96.471no
spore-formingno93.928no
glucose-utilno70.614yes
flagellatedno63.903yes
thermophileno98.141yes
glucose-fermentno91.187no

External links

@ref: 43635

culture collection no.: KCTC 42909, LMG 29218

literature

  • topic: Phylogeny
  • Pubmed-ID: 27001671
  • title: Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.
  • authors: Sun LN, Wang DS, Yang ED, Fang LC, Chen YF, Tang XY, Hua RM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001034
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, Chlorpyrifos/*metabolism, Cupriavidus/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry
  • topic2: Transcriptome

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
43635Le-Ni Sun, Dao-Sheng Wang, En-Dong Yang, Lian-Cheng Fang, Yi-Fei Chen, Xin-Yun Tang, Ri-Mao HuaCupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge10.1099/ijsem.0.001034IJSEM 66: 2335-2341 201627001671
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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