Strain identifier

BacDive ID: 131262

Type strain: Yes

Species: Sagittula marina

Strain Designation: F028-2

Strain history: S. J. Cho F028-2.

NCBI tax ID(s): 943940 (species)

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General

@ref: 22489

BacDive-ID: 131262

DSM-Number: 102235

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

description: Sagittula marina F028-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater sample.

NCBI tax id

  • NCBI tax id: 943940
  • Matching level: species

strain history

@refhistory
22489<- KCTC <- S.-B. Lee, Pohang University of Science and Technology, Republic of Korea; F028-2
67770S. J. Cho F028-2.

doi: 10.13145/bacdive131262.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Sagittula
  • species: Sagittula marina
  • full scientific name: Sagittula marina Lee et al. 2013

@ref: 22489

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sagittula

species: Sagittula marina

full scientific name: Sagittula marina Lee et al. 2013

strain designation: F028-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30634negative1 µm0.5 µmrod-shapedno
69480negative99.999

colony morphology

  • @ref: 22489
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 22489
  • 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
22489positivegrowth25mesophilic
30634positivegrowth04-30
30634positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30634positivegrowth6.5-9.0alkaliphile
30634positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30634
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30634NaClpositivegrowth01-07 %
30634NaClpositiveoptimum3 %

observation

  • @ref: 30634
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30634620642,3-butanediol+carbon source
3063430089acetate+carbon source
3063415963ribitol+carbon source
3063421217L-alaninamide+carbon source
3063416449alanine+carbon source
3063422599arabinose+carbon source
3063418403L-arabitol+carbon source
3063416947citrate+carbon source
3063417234glucose+carbon source
3063429987glutamate+carbon source
3063415428glycine+carbon source
3063428087glycogen+carbon source
3063417596inosine+carbon source
3063424996lactate+carbon source
3063425115malate+carbon source
3063429864mannitol+carbon source
3063437684mannose+carbon source
3063426271proline+carbon source
3063417272propionate+carbon source
3063451850methyl pyruvate+carbon source
3063430911sorbitol+carbon source
3063430031succinate+carbon source
3063417748thymidine+carbon source
6836925115malate+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
22489catalase+1.11.1.6
22489cytochrome-c oxidase+1.9.3.1
30634acid phosphatase+3.1.3.2
30634alkaline phosphatase+3.1.3.1
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
22489----++-+/-++++-+--+/-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
22489seawater sampleDamupo beach, PohangRepublic of KoreaKORAsia36.0475129.586
67770Seawater at Damupo beach in PohangRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_14122.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_7291;97_8740;98_10714;99_14122&stattab=map
  • Last taxonomy: Sagittula marina subclade
  • 16S sequence: HQ336489
  • Sequence Identity:
  • Total samples: 649
  • soil counts: 14
  • aquatic counts: 545
  • animal counts: 80
  • plant counts: 10

Safety information

risk assessment

  • @ref: 22489
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22489
  • description: Sagittula marina strain F028-2 16S ribosomal RNA gene, partial sequence
  • accession: HQ336489
  • length: 1376
  • database: ena
  • NCBI tax ID: 943940

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sagittula marina DSM 102235GCA_014196795scaffoldncbi943940
66792Sagittula marina strain DSM 102235943940.3wgspatric943940
66792Sagittula marina DSM 1022352829988960draftimg943940

GC content

@refGC-contentmethod
3063461.6
2248961.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno80.556no
gram-positiveno98.9yes
anaerobicno96.543yes
aerobicyes92.352yes
halophileyes74.123no
spore-formingno95.947no
glucose-utilyes92.538no
thermophileno99.205no
motileyes59.283no
glucose-fermentno91.301yes

External links

@ref: 22489

culture collection no.: DSM 102235, JCM 17627, KCTC 23543

straininfo link

  • @ref: 89706
  • straininfo: 401768

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23087166Sagittula marina sp. nov., isolated from seawater and emended description of the genus Sagittula.Lee DH, Cho SJ, Kim SM, Lee SBInt J Syst Evol Microbiol10.1099/ijs.0.040766-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny35258448Sagittula salina sp. nov., isolated from marine waste.Satari L, Molina-Menor E, Vidal-Verdu A, Pascual J, Pereto J, Porcar MInt J Syst Evol Microbiol10.1099/ijsem.0.0052402022Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Mediterranean Sea, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water PollutantsTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
22489Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102235Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102235)
30634Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172696528776041
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
89706Reimer, 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-ID401768.1