Strain identifier

BacDive ID: 158174

Type strain: Yes

Species: Zhongshania aliphaticivorans

Strain Designation: SM-2

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; SM-2.

NCBI tax ID(s): 1470434 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 64767

BacDive-ID: 158174

DSM-Number: 107354

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Zhongshania aliphaticivorans SM-2 is a mesophilic, motile bacterium that was isolated from tidal flat.

NCBI tax id

  • NCBI tax id: 1470434
  • Matching level: species

strain history

@refhistory
64767<- JCM <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea
67770C. O. Jeon; Chung-Ang Univ., South Korea; SM-2.

doi: 10.13145/bacdive158174.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Spongiibacteraceae
  • genus: Zhongshania
  • species: Zhongshania aliphaticivorans
  • full scientific name: Zhongshania aliphaticivorans Lo et al. 2014

@ref: 64767

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Spongiibacteraceae

genus: Zhongshania

species: Zhongshania aliphaticivorans

full scientific name: Zhongshania aliphaticivorans Lo et al. 2014

strain designation: SM-2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.151
6948099.998negative

Culture and growth conditions

culture medium

  • @ref: 64767
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
64767positivegrowth28mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no99.998
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
64767+----------+--------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
64767tidal flatDanjin BayRepublic of KoreaKORAsia
67770Sea-tidal flat of Danjin bay in South Korea

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_3871.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_305;96_1986;97_2387;98_2948;99_3871&stattab=map
  • Last taxonomy: Zhongshania
  • 16S sequence: KF982857
  • Sequence Identity:
  • Total samples: 4397
  • soil counts: 107
  • aquatic counts: 3986
  • animal counts: 283
  • plant counts: 21

Safety information

risk assessment

  • @ref: 64767
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64767
  • description: Zhongshania aliphaticivorans strain SM-2 16S ribosomal RNA gene, partial sequence
  • accession: KF982857
  • length: 1403
  • database: ena
  • NCBI tax ID: 1470434

Genome sequences

  • @ref: 66792
  • description: Zhongshania aliphaticivorans SM-2
  • accession: GCA_001586255
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1470434

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes69.43no
gram-positiveno98.476no
anaerobicno98.506no
aerobicyes95.618no
halophileyes80.442no
spore-formingno94.834no
glucose-utilno58.291yes
motileyes79.324no
thermophileno99.176yes
glucose-fermentno91.093yes

External links

@ref: 64767

culture collection no.: DSM 107354, JCM 30138, KACC 18120

straininfo link

  • @ref: 111005
  • straininfo: 403472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25122615Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov.Lo N, Kang HJ, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.068593-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Hydrocarbons/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Genetics27034022Complete genome of Zhongshania aliphaticivorans SM-2(T), an aliphatic hydrocarbon-degrading bacterium isolated from tidal flat sediment.Jia B, Jeong HI, Kim KH, Jeon COJ Biotechnol10.1016/j.jbiotec.2016.03.0392016Bacteria/*genetics/*isolation & purification, Biodegradation, Environmental, *Genome, Bacterial, Geologic Sediments/*microbiology, Hydrocarbons/*metabolismEnzymology
Phylogeny30570482Zhongshania marina sp. nov., isolated from deep-sea water.On YG, Oh JS, Roh DHInt J Syst Evol Microbiol10.1099/ijsem.0.0031952018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny35982281Zhongshania aquimaris sp. nov., isolated from seawater.Weerawongwiwat V, Kim JH, Lee JS, Yoon JH, Sukhoom A, Kim WArch Microbiol10.1007/s00203-022-03184-22022Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
64767Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107354Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107354)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
111005Reimer, 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-ID403472.1