Strain identifier

BacDive ID: 133078

Type strain: Yes

Species: Novosphingobium guangzhouense

Strain Designation: SA925

Strain history: <- Sha Sha, School of Life Sciences, Sun Yat-sen Univ., Guangzhou, People's Republic of China; SA925 <-

NCBI tax ID(s): 1850347 (species)

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General

@ref: 24866

BacDive-ID: 133078

DSM-Number: 32207

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

description: Novosphingobium guangzhouense SA925 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and has a yellow pigmentation.

NCBI tax id

  • NCBI tax id: 1850347
  • Matching level: species

strain history

  • @ref: 24866
  • history: <- Sha Sha, School of Life Sciences, Sun Yat-sen Univ., Guangzhou, People's Republic of China; SA925 <-

doi: 10.13145/bacdive133078.20230509.8.1

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 guangzhouense
  • full scientific name: Novosphingobium guangzhouense Sha et al. 2017

@ref: 24866

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium guangzhouense

full scientific name: Novosphingobium guangzhouense Sha et al. 2017

strain designation: SA925

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25198negative2 µm0.8 µmrod-shapedyes
69480negative99.995

colony morphology

  • @ref: 25198
  • colony color: yellow
  • colony shape: circular
  • medium used: LB agar

pigmentation

  • @ref: 25198
  • production: yes
  • color: yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25198LB (Luria-Bertani) MEDIUMyes
25198Trypticase Soy Agar (TSA)yes
24866LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25198positivegrowth10-35
24866positivegrowth28mesophilic

culture pH

  • @ref: 25198
  • ability: positive
  • type: growth
  • pH: 6.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25198
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.965

halophily

  • @ref: 25198
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2519817521(-)-quinic acid-assimilation
2519815588D-malate-assimilation
2519815589L-malate-assimilation
25198309162-oxoglutarate-assimilation
25198739183-O-methyl-D-glucose-assimilation
25198181014-hydroxyphenylacetic acid-assimilation
2519836219alpha-lactose-assimilation
2519873706bromosuccinate-assimilation
2519818333D-arabitol-assimilation
2519829990D-aspartate-assimilation
2519878697D-fructose 6-phosphate-assimilation
2519828847D-fucose-assimilation
2519830612D-glucarate-assimilation
251988391D-gluconate-assimilation
2519814314D-glucose 6-phosphate-assimilation
2519816899D-mannitol-assimilation
2519816523D-serine-assimilation
2519817924D-sorbitol-assimilation
2519815740formate-assimilation
2519816537galactarate-assimilation
2519816865gamma-aminobutyric acid-assimilation
251985291gelatin-assimilation
2519832323glucuronamide-assimilation
2519817596inosine-assimilation
2519817268myo-inositol-assimilation
2519816467L-arginine-assimilation
2519818183L-pyroglutamic acid-assimilation
2519862345L-rhamnose-assimilation
2519817115L-serine-assimilation
2519828053melibiose-assimilation
2519874611methyl (R)-lactate-assimilation
2519837657methyl D-glucoside-assimilation
2519863154N-acetyl-beta-D-mannosamine-assimilation
2519828037N-acetylgalactosamine-assimilation
2519835418n-acetylneuraminate-assimilation
2519817309pectin-assimilation
2519816634raffinose-assimilation
2519817164stachyose-assimilation
2519817992sucrose-assimilation
2519832528turanose-assimilation
2519816651(S)-lactate+assimilation
25198358601-methylphenanthrene+carbon source
25198645522-hydroxybutyrate+assimilation
25198286442-oxopentanoate+assimilation
25198370543-hydroxybutyrate+carbon source
2519830089acetate+assimilation
2519813705acetoacetate+assimilation
2519817925alpha-D-glucose+assimilation
251988295beta-hydroxybutyrate+assimilation
2519817057cellobiose+assimilation
2519816947citrate+assimilation
2519815824D-fructose+assimilation
2519812936D-galactose+assimilation
2519818024D-galacturonic acid+assimilation
2519815748D-glucuronate+assimilation
2519816024D-mannose+assimilation
2519823652dextrin+assimilation
2519828066gentiobiose+assimilation
2519817754glycerol+assimilation
2519870744glycine-proline+assimilation
2519829991L-aspartate+assimilation
2519818287L-fucose+assimilation
2519817464L-galactonic acid gamma-lactone+assimilation
2519829985L-glutamate+assimilation
2519815971L-histidine+assimilation
2519817306maltose+assimilation
2519851850methyl pyruvate+assimilation
25198506227N-acetylglucosamine+assimilation
2519817272propionate+assimilation
2519817814salicin+assimilation
2519827082trehalose+assimilation
2519816977L-alanine+/-assimilation
2519853423tween 40+/-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
2519828971ampicillinyesyes10 µg (disc)
251983508ceftazidimeyesyes30 µg (disc)
25198100241ciprofloxacinyesyes5 µg (disc)
2519863611moxifloxacinyesyes5 µg
2519863598levofloxacinyesyes5 µg
2519829007ceftriaxoneyesyes30 µg
25198204928cefotaximeyesyes30 µg (disc)
251983745clindamycinyesyes2 µg
25198478164cefepimeyesyes30 µg (disc)
25198209807cefoxitinyesyes30 µg
2519863607linezolidyesyes30 µg
2519843968meropenemyesyes10 µg
2519817334penicillinyesyes10 Unit
2519828077rifampicinyesyes5 µg
2519829687teicoplaninyesyes30 µg
251988232piperacillinyesyes100 µg (disc)16
251989421tazobactamyesyes10 µg (disc)16
2519828001vancomycinyesyes30 µg
2519827902tetracyclineyesyes30 µg (disc)
251982676amoxicillinyesyes20 µg (disc)10
2519848947clavulanic acidyesyes10 µg (disc)10
2519848923erythromycinyesyes15 µg (disc)
25198471744imipenemyesyes10 µg (disc)
251989587ticarcillinyesyes75 µg (disc)
2519845924trimethoprimyesyes1.2526
251989332sulfamethoxazoleyesyes23.7526

enzymes

@refvalueactivityec
25198acid phosphatase+3.1.3.2
25198alkaline phosphatase+3.1.3.1
25198alpha-chymotrypsin-3.4.21.1
25198alpha-galactosidase-3.2.1.22
25198alpha-glucosidase+3.2.1.20
25198alpha-mannosidase-3.2.1.24
25198beta-D-fucosidase-3.2.1.38
25198beta-galactosidase+3.2.1.23
25198beta-glucosidase+3.2.1.21
25198beta-glucuronidase-3.2.1.31
25198catalase-1.11.1.6
25198cystine arylamidase+3.4.11.3
25198cystine arylamidase+/-3.4.11.3
25198cytochrome oxidase-1.9.3.1
25198esterase (C 4)-
25198esterase Lipase (C 8)-
25198leucine arylamidase+3.4.11.1
25198lipase (C 14)-
25198N-acetyl-beta-glucosaminidase-3.2.1.52
25198naphthol-AS-BI-phosphohydrolase+
25198trypsin-3.4.21.4
25198valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2519811-Methyl C18:1ω7c1.3
    25198C12:00.1
    25198C14:00.7
    25198C14:0 2OH5.8
    25198C15:0 2OH0.2
    25198C16:011.9
    25198C16:0 2OH3.4
    25198C16:1ω5c2.9
    25198C16:1ω7c / C16:1ω6c10.7
    25198C17:1ω6c1
    25198C17:1ω8c0.1
    25198C18:00.5
    25198C18:1ω5c0.7
    25198C18:1ω7c59.7
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 24866
  • sample type: oil-polluted soil from a refinery
  • geographic location: Guangdong Province, Guangzhou
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 23.123
  • longitude: 113.478

isolation source categories

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

Safety information

risk assessment

  • @ref: 24866
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24866
  • description: Novosphingobium guangzhouense strain SA925 16S ribosomal RNA gene, partial sequence
  • accession: KX215153
  • length: 1484
  • database: ena
  • NCBI tax ID: 1850347

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium guangzhouense SA925GCA_002896965contigncbi1850347
66792Novosphingobium guangzhouense strain SA9251850347.3wgspatric1850347

GC content

  • @ref: 24866
  • GC-content: 60.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes68.158yes
gram-positiveno97.181yes
anaerobicno98.953yes
aerobicyes92.877yes
halophileno95.765no
spore-formingno92.859no
glucose-utilyes90.196no
flagellatedno86.168no
thermophileno98.944no
glucose-fermentno92.771no

External links

@ref: 24866

culture collection no.: DSM 32207, GDMCC 1.1110

straininfo link

  • @ref: 91343
  • straininfo: 406876

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902280
  • title: Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene.
  • authors: Sha S, Zhong J, Chen B, Lin L, Luan T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001669
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phenanthrenes/*metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24866Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-32207Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 32207)
25198S. Z. Sha, J.,Chen, B.,Lin, L.,Luan, T.Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene10.1099/ijsem.0.001669IJSEM 67: 489-497 201727902280
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
91343Reimer, 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-ID406876.1