Strain identifier

BacDive ID: 132261

Type strain: Yes

Species: Sinimarinibacterium flocculans

Strain Designation: NH6-24

Strain history: S.-Q. Zhang NH6-24.

NCBI tax ID(s): 985250 (species)

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General

@ref: 24050

BacDive-ID: 132261

DSM-Number: 104150

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

description: Sinimarinibacterium flocculans NH6-24 is a mesophilic, motile bacterium that was isolated from Surface seawater.

NCBI tax id

  • NCBI tax id: 985250
  • Matching level: species

strain history

@refhistory
24050<- X. Zhang; Zhejiang University, Hangzhou, P.R. CHINA; NH6-24<-X.-Q. Zhang
67770S.-Q. Zhang NH6-24.

doi: 10.13145/bacdive132261.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Nevskiales
  • family: Nevskiaceae
  • genus: Sinimarinibacterium
  • species: Sinimarinibacterium flocculans
  • full scientific name: Sinimarinibacterium flocculans Zhang et al. 2015

@ref: 24050

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Nevskiales

family: Nevskiaceae

genus: Sinimarinibacterium

species: Sinimarinibacterium flocculans

full scientific name: Sinimarinibacterium flocculans Zhang et al. 2015

strain designation: NH6-24

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94.173
6948099.991negative

Culture and growth conditions

culture medium

  • @ref: 24050
  • 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
24050positivegrowth37mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.987

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
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+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24050------+-------------+
24050-----++-------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24050Surface seawaterSouth China SeaChinaCHNAsia18.1156110.761
67770Surface seawater of the South China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_42346.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_15042;97_18367;98_30770;99_42346&stattab=map
  • Last taxonomy: Sinimarinibacterium flocculans subclade
  • 16S sequence: HQ875491
  • Sequence Identity:
  • Total samples: 764
  • soil counts: 166
  • aquatic counts: 495
  • animal counts: 57
  • plant counts: 46

Safety information

risk assessment

  • @ref: 24050
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24050
  • description: Sinimarinibacterium flocculans strain NH6-24 16S ribosomal RNA gene, partial sequence
  • accession: HQ875491
  • length: 1493
  • database: ena
  • NCBI tax ID: 985250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinimarinibacterium flocculans strain DSM 104150985250.3wgspatric985250
66792Sinimarinibacterium flocculans DSM 1041502756170279draftimg985250
67770Sinimarinibacterium flocculans DSM 104150GCA_003201205scaffoldncbi985250

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.845no
flagellatedno57.155no
gram-positiveno98.873no
anaerobicno97.334no
halophileno81.888no
spore-formingno95.579no
thermophileno93.91yes
glucose-utilno65.907yes
aerobicyes92.73no
glucose-fermentno92.694no

External links

@ref: 24050

culture collection no.: DSM 104150, CGMCC 1.10815, JCM 17607

straininfo link

  • @ref: 90610
  • straininfo: 398552

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26297652Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater.Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X, Wu YH, Xu XW, Wu MInt J Syst Evol Microbiol10.1099/ijsem.0.0004522015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny32589213Polyphasic taxonomic analysis of Sinimarinibacterium arenosum sp. nov., a halophilic bacterium isolated from marine sediment.Kim JH, Baek J, Yoon JH, Sukhoom A, Kim WFEMS Microbiol Lett10.1093/femsle/fnaa1052020Base Composition, Fatty Acids, Gammaproteobacteria/genetics, Geologic Sediments/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/*genetics, Seawater
Phylogeny34739364Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum.Jiang Y, Jiang L, Peng Y, Kim KH, Shin HH, Kim YM, Lee J, Li ZInt J Syst Evol Microbiol10.1099/ijsem.0.0050842021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Dinoflagellida/microbiology, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

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
24050Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104150Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104150)
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
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
90610Reimer, 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-ID398552.1