Strain identifier

BacDive ID: 130625

Type strain: Yes

Species: Aliiroseovarius sediminilitoris

Strain Designation: M-M10

Strain history: <- JH Yoon, Sungkyunkwan Univ.

NCBI tax ID(s): 1173584 (species)

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

@ref: 21770

BacDive-ID: 130625

DSM-Number: 29439

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

description: Aliiroseovarius sediminilitoris M-M10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seashore sediment.

NCBI tax id

  • NCBI tax id: 1173584
  • Matching level: species

strain history

@refhistory
21770<- KCTC <- J.-H. Yoon, KRIBB; M-M10
67771<- JH Yoon, Sungkyunkwan Univ.

doi: 10.13145/bacdive130625.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Aliiroseovarius
  • species: Aliiroseovarius sediminilitoris
  • full scientific name: Aliiroseovarius sediminilitoris (Park and Yoon 2013) Park et al. 2015
  • synonyms

    @refsynonym
    20215Pseudoroseovarius sediminilitoris
    20215Roseovarius sediminilitoris

@ref: 21770

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Aliiroseovarius

species: Aliiroseovarius sediminilitoris

full scientific name: Aliiroseovarius sediminilitoris (Park and Yoon 2013) Park et al. 2015

strain designation: M-M10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30758negative1.8 µm0.35 µmovoid-shapedyes
67771negative
69480negative99.999

colony morphology

  • @ref: 21770
  • incubation period: 1-2 days

pigmentation

  • @ref: 30758
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21770
  • 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
21770positivegrowth30mesophilic
30758positivegrowth04-37
30758positiveoptimum30mesophilic
62829positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
30758positivegrowth5.5-8
30758positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30758aerobe
62829aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.993

halophily

  • @ref: 30758
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 2 %

observation

  • @ref: 30758
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3075830089acetate+carbon source
3075816947citrate+carbon source
3075828757fructose+carbon source
3075825115malate+carbon source
3075815361pyruvate+carbon source
3075830031succinate+carbon source
307584853esculin+hydrolysis
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
21770catalase+1.11.1.6
21770cytochrome-c oxidase+1.9.3.1
30758alkaline phosphatase+3.1.3.1
30758catalase+1.11.1.6
30758cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21770-----+-++-++++---++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21770seashore sedimentSouth Sea, Geoje islandRepublic of KoreaKORAsia
62829Seashore sedimentGeoje IslandRepublic of KoreaKORAsia
67771From tidal flatSouth SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_64167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_46;97_48;98_44338;99_64167&stattab=map
  • Last taxonomy: Aliiroseovarius sediminilitoris subclade
  • 16S sequence: JQ739459
  • Sequence Identity:
  • Total samples: 459
  • soil counts: 16
  • aquatic counts: 428
  • animal counts: 10
  • plant counts: 5

Safety information

risk assessment

  • @ref: 21770
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21770
  • description: Roseovarius sediminilitoris strain M-M10 16S ribosomal RNA gene, partial sequence
  • accession: JQ739459
  • length: 1391
  • database: ena
  • NCBI tax ID: 1173584

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aliiroseovarius sediminilitoris DSM 29439GCA_900109955contigncbi1173584
66792Aliiroseovarius sediminilitoris strain DSM 294391173584.3wgspatric1173584
66792Aliiroseovarius sediminilitoris DSM 294392687453744draftimg1173584

GC content

@refGC-contentmethod
3075863
2177063.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno62.169no
gram-positiveno98.563no
anaerobicno98.265yes
halophileyes68.401no
spore-formingno97.818no
flagellatedno84.931no
thermophileno93.789yes
glucose-utilyes72.191no
aerobicyes88.893no
glucose-fermentno91.582no

External links

@ref: 21770

culture collection no.: DSM 29439, CCUG 62413, KCTC 23959

straininfo link

  • @ref: 89139
  • straininfo: 401555

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22941298Roseovarius sediminilitoris sp. nov., isolated from seashore sediment.Park S, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.043737-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny25964517Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitoris comb. nov.Park S, Park JM, Kang CH, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.0003152015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny26066711Pseudoroseovarius zhejiangensis gen. nov., sp. nov., a novel alpha-proteobacterium isolated from the chemical wastewater, and reclassification of Roseovarius crassostreae as Pseudoroseovarius crassostreae comb. nov., Roseovarius sediminilitoris as Pseudoroseovarius sediminilitoris comb. nov. and Roseovarius halocynthiae as Pseudoroseovarius halocynthiae comb. nov.Sun C, Pan J, Zhang XQ, Su Y, Wu MAntonie Van Leeuwenhoek10.1007/s10482-015-0480-92015Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Waste Water/*microbiologyGenetics

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
21770Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29439Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29439)
30758Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172708928776041
62829Curators of the CCUGhttps://www.ccug.se/strain?id=62413Culture Collection University of Gothenburg (CCUG) (CCUG 62413)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
89139Reimer, 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-ID401555.1