Strain identifier

BacDive ID: 13787

Type strain: Yes

Species: Epibacterium scottomollicae

Strain Designation: R-28751

Strain history: <- CCUG <- I. Vandecandelaere, LMG; R-28751

NCBI tax ID(s): 483013 (species)

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General

@ref: 18003

BacDive-ID: 13787

DSM-Number: 25328

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

description: Epibacterium scottomollicae R-28751 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine biofilm on stainless steel electrode.

NCBI tax id

  • NCBI tax id: 483013
  • Matching level: species

strain history

  • @ref: 18003
  • history: <- CCUG <- I. Vandecandelaere, LMG; R-28751

doi: 10.13145/bacdive13787.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Epibacterium
  • species: Epibacterium scottomollicae
  • full scientific name: Epibacterium scottomollicae (Vandecandelaere et al. 2008) Wirth and Whitman 2018

  • synonyms

    @refsynonym
    20215Tritonibacter scottomollicae
    20215Ruegeria scottomollicae

@ref: 18003

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tritonibacter

species: Tritonibacter scottomollicae

full scientific name: Tritonibacter scottomollicae (Vandecandelaere et al. 2008) Hördt et al. 2020

strain designation: R-28751

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32649negative1.3 µm1 µmovoid-shapedyes
69480negative99.993

colony morphology

@refincubation period
180031-2 days
607622-3 days

pigmentation

  • @ref: 32649
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18003
  • 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
18003positivegrowth20psychrophilic
32649positivegrowth04-40
32649positiveoptimum30mesophilic
60762positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
32649positivegrowth05-09alkaliphile
32649positiveoptimum6.5-8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32649aerobe
60762aerobe

spore formation

@refspore formationconfidence
32649no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
32649NaClpositivegrowth01-15 %
32649NaClpositiveoptimum01-15 %

observation

  • @ref: 32649
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
326494853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+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

@refChebi-IDmetaboliteproduction
3264935581indoleyes
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
3264935581indole+
6836935581indole-

enzymes

@refvalueactivityec
18003catalase+1.11.1.6
18003cytochrome-c oxidase+1.9.3.1
32649alkaline phosphatase+3.1.3.1
32649alpha-galactosidase+3.2.1.22
32649catalase+1.11.1.6
32649cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18003-----+/--+/----+/-++---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
18003marine biofilm on stainless steel electrodeGenuaItalyITAEurope
60762Marine biofilm on stainless steel electrodeGenoa,the harbourItalyITAEurope2004-10-01

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Environmental#Aquatic#Marine
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_10156.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_566;98_1495;99_10156&stattab=map
  • Last taxonomy: Epibacterium scottomollicae
  • 16S sequence: AM905330
  • Sequence Identity:
  • Total samples: 75
  • soil counts: 1
  • aquatic counts: 72
  • animal counts: 2

Safety information

risk assessment

  • @ref: 18003
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18003
  • description: Ruegeria scottomollicae partial 16S rRNA gene, type strain LMG 24367T
  • accession: AM905330
  • length: 1398
  • database: ena
  • NCBI tax ID: 483013

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tritonibacter scottomollicae DSM 25328GCA_003003215scaffoldncbi483013
66792Ruegeria scottomollicae strain DSM 25328483013.3wgspatric483013
66792Epibacterium scottomollicae DSM 253282728369517draftimg483013

GC content

  • @ref: 32649
  • GC-content: 60.6-61.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno69.478no
gram-positiveno98.744yes
anaerobicno98.76no
aerobicyes89.178yes
halophileyes84.685no
spore-formingno94.645yes
glucose-utilyes83.175yes
thermophileno96.866yes
motileyes79.999yes
glucose-fermentno88.47yes

External links

@ref: 18003

culture collection no.: DSM 25328, CCUG 55858, LMG 24367

straininfo link

  • @ref: 82965
  • straininfo: 343775

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060048Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Faimali M, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.65843-02008Alphaproteobacteria/chemistry/*classification/genetics/*physiology/ultrastructure, *Biofilms, *Electricity, Electrodes/*microbiology, Fatty Acids/analysis, Marine Biology, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny25180090Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.066142-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18003Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25328)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25328
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
32649Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2886028776041
60762Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55858)https://www.ccug.se/strain?id=55858
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
82965Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343775.1StrainInfo: A central database for resolving microbial strain identifiers