Strain identifier

BacDive ID: 24051

Type strain: Yes

Species: Sinomicrobium oceani

Strain history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 03483

NCBI tax ID(s): 1150368 (species)

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

@ref: 21245

BacDive-ID: 24051

DSM-Number: 25598

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

description: Sinomicrobium oceani DSM 25598 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 1150368
  • Matching level: species

strain history

  • @ref: 21245
  • history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 03483

doi: 10.13145/bacdive24051.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Sinomicrobium
  • species: Sinomicrobium oceani
  • full scientific name: Sinomicrobium oceani Xu et al. 2013

@ref: 21245

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Sinomicrobium

species: Sinomicrobium oceani

full scientific name: Sinomicrobium oceani Xu et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30680negative4.3 µm0.6 µmrod-shapedyes
69480negative99.979

pigmentation

  • @ref: 30680
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21245
  • 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
21245positivegrowth28mesophilic
30680positivegrowth10-45
30680positiveoptimum32.5mesophilic

culture pH

@refabilitytypepH
30680positivegrowth06-08
30680positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30680
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30680no
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30680NaClpositivegrowth0-10 %
30680NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3068028757fructose+carbon source
3068017234glucose+carbon source
3068017754glycerol+carbon source
3068017716lactose+carbon source
3068037684mannose+carbon source
3068026546rhamnose+carbon source
3068018222xylose+carbon source
3068017632nitrate+reduction

enzymes

@refvalueactivityec
30680catalase+1.11.1.6
30680gelatinase+

Isolation, sampling and environmental information

isolation

  • @ref: 21245
  • sample type: deep-sea sediment
  • geographic location: South China Sea, Nansha Islands sea area (6° 0.733' N 113° 28.842' E) at a depth of 2548 m
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 6.0122
  • longitude: 113.481

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4663.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_230;96_2318;97_2816;98_3498;99_4663&stattab=map
  • Last taxonomy: Sinomicrobium
  • 16S sequence: JQ352762
  • Sequence Identity:
  • Total samples: 1411
  • soil counts: 159
  • aquatic counts: 649
  • animal counts: 575
  • plant counts: 28

Safety information

risk assessment

  • @ref: 21245
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21245
  • description: Sinomicrobium oceani strain SCSIO 03483 16S ribosomal RNA gene, partial sequence
  • accession: JQ352762
  • length: 1371
  • database: ena
  • NCBI tax ID: 1150368

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinomicrobium oceani CGMCC 1.12145GCA_900119185scaffoldncbi1150368
66792Sinomicrobium oceani strain CGMCC 1.121451150368.4wgspatric1150368
66792Sinomicrobium oceani CGMCC 1.121452596583572draftimg1150368

GC content

@refGC-contentmethod
2124538.4high performance liquid chromatography (HPLC)
3068038.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.118yes
flagellatedno96.273no
gram-positiveno97.699no
anaerobicno99.345yes
aerobicyes86.844yes
halophileno75.472no
spore-formingno96.624yes
glucose-fermentno83.425no
thermophileno98.609no
glucose-utilyes92.055yes

External links

@ref: 21245

culture collection no.: DSM 25598, CGMCC 1.12145, KCTC 23994, SCSIO 03483

straininfo link

  • @ref: 88022
  • straininfo: 399374

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22707529Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment.Xu Y, Tian XP, Liu YJ, Li J, Kim CJ, Yin H, Li WJ, Zhang SInt J Syst Evol Microbiol10.1099/ijs.0.041889-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23416571Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel.Wang G, Zhou D, Dai S, Tian X, Li J, Chen W, Xiang W, Li XInt J Syst Evol Microbiol10.1099/ijs.0.048413-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water MicrobiologyGenetics
Phylogeny24912822Sinomicrobium pectinilyticum sp. nov., a pectinase-producing bacterium isolated from alkaline and saline soil, and emended description of the genus Sinomicrobium.Cheng B, Li C, Lai Q, Du M, Shao Z, Xu P, Yang CInt J Syst Evol Microbiol10.1099/ijs.0.061671-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Polygalacturonase/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, alpha-Amylases/metabolismGenetics
Phylogeny35442876Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil.Wu P, Ren H, Zhu Q, Mei Y, Liang Y, Chen ZInt J Syst Evol Microbiol10.1099/ijsem.0.0052822022*Alkalies, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Vitamin K 2/chemistryTranscriptome

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
21245Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25598Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25598)
30680Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172701128776041
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
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
88022Reimer, 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-ID399374.1