Strain identifier

BacDive ID: 131261

Type strain: Yes

Species: Extensimonas vulgaris

Strain Designation: S4

Strain history: W.-Y. Zhang S4.

NCBI tax ID(s): 1031594 (species)

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General

@ref: 22488

BacDive-ID: 131261

DSM-Number: 100911

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

description: Extensimonas vulgaris S4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from industrial wastewater.

NCBI tax id

  • NCBI tax id: 1031594
  • Matching level: species

strain history

@refhistory
22488<- JCM <- W.-Y. Zhang, College of Life Sciences, Zhejiang University, Hangzhou, PR China; S4
67770W.-Y. Zhang S4.

doi: 10.13145/bacdive131261.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Extensimonas
  • species: Extensimonas vulgaris
  • full scientific name: Extensimonas vulgaris Zhang et al. 2013

@ref: 22488

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Extensimonas

species: Extensimonas vulgaris

full scientific name: Extensimonas vulgaris Zhang et al. 2013

strain designation: S4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30530negative1.6 µm0.85 µmrod-shapedyes
69480yes95.878
69480negative100

colony morphology

  • @ref: 22488
  • incubation period: 2-3 days

pigmentation

  • @ref: 30530
  • production: no

Culture and growth conditions

culture medium

  • @ref: 22488
  • name: CM-MEDIUM (DSMZ Medium 1595)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1595
  • composition: Name: CM MEDIUM (DSMZ Medium 1595) Composition: Agar 14.0 g/l Peptone 1.0 g/l D-Glucose 1.0 g/l NaCl 0.5 g/l Yeast extract 0.5 g/l Beef extract 0.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22488positivegrowth37mesophilic
30530positivegrowth15-50
30530positiveoptimum48thermophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30530positivegrowth5.5-8.5alkaliphile
30530positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 30530
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30530no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
30530NaClpositivegrowth0-2 %
30530NaClpositiveoptimum0.5 %

observation

  • @ref: 30530
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3053016449alanine+carbon source
3053022653asparagine+carbon source
3053016947citrate+carbon source
3053029987glutamate+carbon source
3053015792malonate+carbon source
3053017814salicin+carbon source
3053030031succinate+carbon source
3053017632nitrate+reduction

enzymes

@refvalueactivityec
30530acid phosphatase+3.1.3.2
30530alkaline phosphatase+3.1.3.1
30530catalase+1.11.1.6
30530cytochrome oxidase+1.9.3.1
30530urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
22488industrial wastewaterXiaoshan, Zhejiang ProvinceChinaCHNAsia
67770Industrial wastewater from Xiaoshan, in December 2009Zhejiang ProvinceChinaCHNAsiaDecember 2009

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Industrial wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_124042.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_14871;97_18157;98_83420;99_124042&stattab=map
  • Last taxonomy: Extensimonas vulgaris subclade
  • 16S sequence: HQ596491
  • Sequence Identity:
  • Total samples: 147
  • soil counts: 15
  • aquatic counts: 111
  • animal counts: 18
  • plant counts: 3

Safety information

risk assessment

  • @ref: 22488
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22488
  • description: Extensimonas vulgaris strain S4 16S ribosomal RNA gene, partial sequence
  • accession: HQ596491
  • length: 1454
  • database: ena
  • NCBI tax ID: 1031594

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Extensimonas vulgaris S4GCA_007996985scaffoldncbi1031594
66792Extensimonas vulgaris CGMCC 1.10977GCA_007830535scaffoldncbi1031594
66792Extensimonas vulgaris strain CGMCC 1.109771031594.4wgspatric1031594
66792Extensimonas vulgaris strain DSM 1009111031594.3wgspatric1031594
66792Extensimonas vulgaris CGMCC 1.109772596583579draftimg1031594
66792Extensimonas vulgaris DSM 1009112770939495draftimg1031594
67770Extensimonas vulgaris DSM 100911GCA_003337425scaffoldncbi1031594

GC content

@refGC-contentmethod
3053068.8
2248868.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.782yes
flagellatedyes58.52no
gram-positiveno98.438yes
anaerobicno95.756yes
aerobicyes84.302no
halophileno96.236no
spore-formingno94.575yes
glucose-utilno74.551no
thermophileno66.634no
glucose-fermentno87.176no

External links

@ref: 22488

culture collection no.: DSM 100911, CGMCC 1.10977, JCM 17803

straininfo link

  • @ref: 89705
  • straininfo: 406481

literature

  • topic: Phylogeny
  • Pubmed-ID: 23064351
  • title: Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae.
  • authors: Zhang WY, Fang MX, Zhang WW, Xiao C, Zhang XQ, Yu ZP, Zhu XF, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038158-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, China, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis, Waste Water/*microbiology, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
22488Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100911Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100911)
30530Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172686228776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
89705Reimer, 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-ID406481.1