Strain identifier

BacDive ID: 141008

Type strain: Yes

Species: Novosphingobium clariflavum

Strain Designation: 164

Strain history: <- Y. Ge, Chinese Center for Industrial Culture Collection, Beijing (CICC), China; CICC 11035s <- Z. Lei; 164

NCBI tax ID(s): 2029884 (species)

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General

@ref: 43903

BacDive-ID: 141008

DSM-Number: 103351

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

description: Novosphingobium clariflavum 164 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from used sponge for equipment cleaning at a household product plant, China.

NCBI tax id

  • NCBI tax id: 2029884
  • Matching level: species

strain history

  • @ref: 69014
  • history: <- Y. Ge, Chinese Center for Industrial Culture Collection, Beijing (CICC), China; CICC 11035s <- Z. Lei; 164

doi: 10.13145/bacdive141008.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium clariflavum
  • full scientific name: Novosphingobium clariflavum Zhang et al. 2017

@ref: 43903

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium clariflavum

full scientific name: Novosphingobium clariflavum Zhang et al. 2017

strain designation: 164

type strain: yes

Morphology

cell morphology

  • @ref: 43903
  • gram stain: negative
  • cell length: 0.8-1.5 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 43903
  • colony color: bright-yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Trypticase soy agar

Culture and growth conditions

culture medium

@refnamegrowthlink
69014TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
43903Trypticase soy agaryes

culture temp

@refgrowthtypetemperaturerange
43903positiveoptimum28mesophilic
43903positivegrowth15-35
69014positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43903positivegrowth4.0-8.0acidophile
43903positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43903
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43903NaClpositiveoptimum0 %(w/v)
43903NaClpositivegrowth0-2 %(w/v)

observation

  • @ref: 43903
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43903506227N-acetylglucosamine-assimilation
4390317632nitrate-assimilation
43903168082-dehydro-D-gluconate-builds acid from
43903581435-dehydro-D-gluconate-builds acid from
4390315963ribitol-builds acid from
4390317108D-arabinose-builds acid from
4390318333D-arabitol-builds acid from
4390316988D-ribose-builds acid from
4390316443D-tagatose-builds acid from
4390316813galactitol-builds acid from
439035291gelatin-builds acid from
4390317754glycerol-builds acid from
4390328087glycogen-builds acid from
4390315443inulin-builds acid from
4390330849L-arabinose-builds acid from
4390318403L-arabitol-builds acid from
4390325097lyxose-builds acid from
4390329864mannitol-builds acid from
439036731melezitose-builds acid from
4390374863methyl beta-D-xylopyranoside-builds acid from
43903506227N-acetylglucosamine-builds acid from
4390330911sorbitol-builds acid from
4390328017starch-builds acid from
4390317151xylitol-builds acid from
4390318222xylose-builds acid from
4390362318D-lyxose-carbon source
4390328066gentiobiose-carbon source
4390315978glycerol 3-phosphate-carbon source
4390318287L-fucose-carbon source
439036731melezitose-carbon source
4390316634raffinose-carbon source
4390328017starch-carbon source
4390328017starch-hydrolysis
4390353426tween 80-hydrolysis
4390318186tyrosine-hydrolysis
4390322599arabinose+assimilation
4390316024D-mannose+assimilation
4390325115malate+assimilation
4390317306maltose+assimilation
4390317057cellobiose+builds acid from
4390328757fructose+builds acid from
4390333984fucose+builds acid from
4390328260galactose+builds acid from
4390317234glucose+builds acid from
4390317716lactose+builds acid from
43903maltose hydrate+builds acid from
4390326546rhamnose+builds acid from
4390327613amygdalin+carbon source
4390317057cellobiose+carbon source
4390315824D-fructose+carbon source
4390328847D-fucose+carbon source
4390312936D-galactose+carbon source
4390317634D-glucose+carbon source
4390316024D-mannose+carbon source
439034853esculin+carbon source
4390317234glucose+carbon source
4390330849L-arabinose+carbon source
4390362345L-rhamnose+carbon source
4390317716lactose+carbon source
4390317306maltose+carbon source
4390327082trehalose+carbon source
439034853esculin+hydrolysis
4390353424tween 20+hydrolysis
4390318305arbutin+/-carbon source
4390328053melibiose+/-carbon source
43903320061methyl alpha-D-glucopyranoside+/-carbon source
4390317814salicin+/-carbon source
4390317992sucrose+/-carbon source
4390332528turanose+/-carbon source
6837217754glycerol-assimilation
6837217113erythritol-assimilation
6837217108D-arabinose-assimilation
6837230849L-arabinose+assimilation
6837216988D-ribose-assimilation
6837265327D-xylose+assimilation
6837265328L-xylose-assimilation
6837215963ribitol-assimilation
6837274863methyl beta-D-xylopyranoside-assimilation
6837212936D-galactose+assimilation
6837217634D-glucose+assimilation
6837215824D-fructose+assimilation
6837216024D-mannose+assimilation
6837217266L-sorbose-assimilation
6837262345L-rhamnose+assimilation
6837216813galactitol-assimilation
6837217268myo-inositol-assimilation
6837216899D-mannitol-assimilation
6837230911sorbitol-assimilation
6837243943methyl alpha-D-mannoside-assimilation
68372320061methyl alpha-D-glucopyranoside-assimilation
6837259640N-acetylglucosamine-assimilation
6837227613amygdalin-assimilation
6837218305arbutin+assimilation
683724853esculin+assimilation
6837217814salicin+assimilation
6837217057cellobiose+assimilation
6837217306maltose+assimilation
6837217716lactose+assimilation
6837228053melibiose+assimilation
6837217992sucrose+assimilation
6837227082trehalose+assimilation
6837215443inulin-assimilation
683726731melezitose-assimilation
6837216634raffinose-assimilation
6837228017starch+assimilation
6837228087glycogen-assimilation
6837217151xylitol-assimilation
6837228066gentiobiose+assimilation
6837232528turanose+assimilation
6837262318D-lyxose-assimilation
6837216443D-tagatose-assimilation
6837228847D-fucose+assimilation
6837218287L-fucose-assimilation
6837218333D-arabitol-assimilation
6837218403L-arabitol-assimilation
6837224265gluconate-assimilation
68372Potassium 2-ketogluconate-assimilation
68372Potassium 5-ketogluconate-assimilation

metabolite production

  • @ref: 43903
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

  • @ref: 43903
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
43903catalase+1.11.1.6
43903urease-3.5.1.5
43903cytochrome oxidase+/-1.9.3.1

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
43903----+-+---++++-+--------+++++++++---+--++--+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture temperaturegeographic location
43903used sponge for equipment cleaning at a household product plant, ChinaChinaCHNAsiaTrypticase soy agar28
69014air environment of a cosmetic factoryChinaCHNAsiaBeijing

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Environmental#Microbial community

Safety information

risk assessment

  • @ref: 69014
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 43903
  • description: 16S rRNA gene sequence
  • accession: KU530129
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Novosphingobium clariflavum 164
  • accession: GCA_026420865
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2029884

GC content

  • @ref: 69014
  • GC-content: 65.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes60.998no
flagellatedno83.333no
gram-positiveno97.12no
anaerobicno98.802no
aerobicyes90.852yes
halophileno96.477yes
spore-formingno93.461no
glucose-fermentno92.772no
thermophileno96.517yes
glucose-utilyes91.821yes

External links

@ref: 43903

culture collection no.: CICC 11035s, DSM 103351

straininfo link

  • @ref: 96827
  • straininfo: 397516

literature

  • topic: Phylogeny
  • Pubmed-ID: 28840813
  • title: Novosphingobium clariflavum sp. nov., isolated from a household product plant.
  • authors: Zhang X, Liu Y, Lin Y, Wang L, Yao S, Cao Y, Zhai L, Tang X, Zhang L, Zhang T, Ge Y, Ling K, Liu J, Cheng C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001803
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Household Products, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43903Xin Zhang, Yang Liu, Yafang Lin, Lijiang Wang, Su Yao, Yanhua Cao, Lei Zhai, Xiaoli Tang, Lu Zhang, Tianci Zhang, Yuanyuan Ge, Kong Ling, Jiquan Liu, Chi ChengNovosphingobium clariflavum sp. nov., isolated from a household product plant10.1099/ijsem.0.001803IJSEM 67: 3150-3155 201728840813
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
68372Automatically annotated from API 50CH assim
69014Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103351Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103351)
96827Reimer, 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-ID397516.1