Strain identifier

BacDive ID: 13759

Type strain: Yes

Species: Roseivivax isoporae

Strain Designation: sw-2

Variant: Isotype of BacDive ID 13760

Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen

NCBI tax ID(s): 1449351 (strain), 591206 (species)

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General

@ref: 16212

BacDive-ID: 13759

DSM-Number: 22223

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

description: Roseivivax isoporae sw-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from reef-building coral .

NCBI tax id

NCBI tax idMatching level
591206species
1449351strain

strain history

  • @ref: 16212
  • history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen

doi: 10.13145/bacdive13759.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseivivax
  • species: Roseivivax isoporae
  • full scientific name: Roseivivax isoporae Chen et al. 2012

@ref: 16212

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseivivax

species: Roseivivax isoporae

full scientific name: Roseivivax isoporae Chen et al. 2012

strain designation: sw-2

variant: Isotype of BacDive ID 13760

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30299negative1.5 µm0.85 µmrod-shapedyes
69480negative99.997

pigmentation

  • @ref: 30299
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16212
  • 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
16212positivegrowth25mesophilic
30299positivegrowth10-40
30299positiveoptimum37.5mesophilic

culture pH

@refabilitytypepHPH range
30299positivegrowth07-11alkaliphile
30299positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30299
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
30299NaClpositivegrowth0-15 %
30299NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3029930089acetate+carbon source
3029916449alanine+carbon source
3029922599arabinose+carbon source
3029929016arginine+carbon source
3029922653asparagine+carbon source
3029917057cellobiose+carbon source
3029928757fructose+carbon source
3029928260galactose+carbon source
3029917234glucose+carbon source
3029929987glutamate+carbon source
3029917754glycerol+carbon source
3029927570histidine+carbon source
3029925017leucine+carbon source
3029928044phenylalanine+carbon source
3029926271proline+carbon source
3029917822serine+carbon source
3029930031succinate+carbon source
3029917992sucrose+carbon source
3029926986threonine+carbon source
3029927082trehalose+carbon source
3029916296D-tryptophan+carbon source
3029916199urea+carbon source
302994853esculin+hydrolysis

enzymes

@refvalueactivityec
30299acid phosphatase+3.1.3.2
30299alkaline phosphatase+3.1.3.1
30299alpha-galactosidase+3.2.1.22
30299catalase+1.11.1.6
30299cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16212
  • sample type: reef-building coral (Isopora palifera)
  • host species: Isopora palifera
  • geographic location: Pingtung county, coast at Kenting (21°56'29'' N and 120°44'70'' E), 3–8 m below sea level
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia
  • latitude: 21.9414
  • longitude: 120.753

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Cnidaria (Corals)

Safety information

risk assessment

  • @ref: 16212
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16212
  • description: Roseivivax isoporae strain sw-2 16S ribosomal RNA gene, partial sequence
  • accession: FJ593905
  • length: 1402
  • database: ena
  • NCBI tax ID: 1449351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseivivax isoporae LMG 25204GCA_000521865contigncbi1449351
66792Roseivivax isoporae LMG 252041449351.3wgspatric1449351
66792Roseivivax isoporae LMG 252042609459988draftimg1449351

GC content

@refGC-contentmethod
1621268.8high performance liquid chromatography (HPLC)
3029968.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes63.21yes
gram-positiveno98.502yes
anaerobicno94.727yes
halophileyes65.633no
spore-formingno95.486no
thermophileno97.744no
glucose-utilyes92.406no
aerobicyes91.995yes
flagellatedno80.091no
glucose-fermentno89.611no

External links

@ref: 16212

culture collection no.: DSM 22223, BCRC 17966, LMG 25204

straininfo link

  • @ref: 82940
  • straininfo: 360701

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21764981Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax.Chen MH, Sheu SY, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.032961-02011Animals, Anthozoa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolismMetabolism
Phylogeny24567080Roseivivax atlanticus sp. nov., isolated from surface seawater of the Atlantic Ocean.Li G, Lai Q, Liu X, Sun F, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0140-52014Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny24812358Roseivivax marinus sp. nov., isolated from deep water.Dai X, Shi X, Gao X, Liu J, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.062760-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16212Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22223)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22223
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30299Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2664028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82940Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360701.1StrainInfo: A central database for resolving microbial strain identifiers