Strain identifier

BacDive ID: 13785

Type strain: No

Species: Epibacterium mobile

Strain history: CIP <- 2007, NBRC, Ruegeria pelagia <- Y.J. Choo, Inha Univ., Incheon, Korea: strain HTCC2662

NCBI tax ID(s): 379347 (species)

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General

@ref: 16844

BacDive-ID: 13785

DSM-Number: 23402

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

description: Epibacterium mobile DSM 23402 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 379347
  • Matching level: species

strain history

@refhistory
16844<- NBRC <- Y.-J. Choo, Inha University, Incheon, Korea; HTCC 2662
120989CIP <- 2007, NBRC, Ruegeria pelagia <- Y.J. Choo, Inha Univ., Incheon, Korea: strain HTCC2662

doi: 10.13145/bacdive13785.20230509.8.1

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 mobile
  • full scientific name: Epibacterium mobile (Muramatsu et al. 2007) Wirth and Whitman 2018

  • synonyms

    @refsynonym
    20215Tritonibacter mobilis
    20215Tritonibacter mobilis subsp. pelagius
    20215Ruegeria pelagia
    20215Ruegeria mobilis

@ref: 16844

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tritonibacter

species: Tritonibacter mobilis subsp. mobilis

full scientific name: Tritonibacter mobilis subsp. mobilis (Muramatsu et al. 2007) Hördt et al. 2020

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32143negative1.45 µm0.95 µmrod-shapedno
69480negative99.99
120989negativeoval-shapedno

pigmentation

  • @ref: 32143
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16844BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
34988Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120989CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16844positivegrowth28mesophilic
32143positivegrowth16-42
32143positiveoptimum33.5mesophilic
34988positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32143positivegrowth04-12alkaliphile
32143positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32143facultative aerobe
120989facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
32143NaClpositivegrowth0-10 %
32143NaClpositiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3214316000ethanolamine+carbon source
32143620642,3-butanediol+carbon source
3214330089acetate+carbon source
3214315963ribitol+carbon source
3214321217L-alaninamide+carbon source
3214316449alanine+carbon source
3214340585alpha-cyclodextrin+carbon source
32143286442-oxopentanoate+carbon source
3214322599arabinose+carbon source
3214318403L-arabitol+carbon source
3214322653asparagine+carbon source
3214335391aspartate+carbon source
3214317126DL-carnitine+carbon source
3214317057cellobiose+carbon source
3214316947citrate+carbon source
3214323652dextrin+carbon source
3214315740formate+carbon source
3214328757fructose+carbon source
3214328260galactose+carbon source
3214324175galacturonate+carbon source
3214316865gamma-aminobutyric acid+carbon source
3214317234glucose+carbon source
3214329987glutamate+carbon source
3214317754glycerol+carbon source
3214328087glycogen+carbon source
3214327570histidine+carbon source
32143182404-hydroxy-L-proline+carbon source
3214317596inosine+carbon source
3214324996lactate+carbon source
3214317716lactose+carbon source
3214325017leucine+carbon source
3214317306maltose+carbon source
3214329864mannitol+carbon source
3214328053melibiose+carbon source
3214317268myo-inositol+carbon source
32143506227N-acetylglucosamine+carbon source
3214318257ornithine+carbon source
3214328044phenylalanine+carbon source
3214326271proline+carbon source
3214317272propionate+carbon source
3214317148putrescine+carbon source
3214351850methyl pyruvate+carbon source
3214317822serine+carbon source
3214330911sorbitol+carbon source
3214330031succinate+carbon source
3214317992sucrose+carbon source
3214326986threonine+carbon source
3214317748thymidine+carbon source
3214327082trehalose+carbon source
3214353423tween 40+carbon source
3214353426tween 80+carbon source
3214316704uridine+carbon source
3214327248urocanic acid+carbon source
3214317151xylitol+carbon source
321434853esculin+hydrolysis
12098917632nitrate-reduction
12098916301nitrite-reduction

metabolite production

  • @ref: 120989
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32143acid phosphatase+3.1.3.2
32143alkaline phosphatase+3.1.3.1
32143catalase+1.11.1.6
32143cytochrome oxidase+1.9.3.1
120989oxidase+
120989catalase+1.11.1.6
120989urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120989-+++-++---++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16844seawaterAtlantic Ocean, Western Sargasso Sea, Atlantic Time Series StationBermudaBMUMiddle and South America
120989Environment, SeawaterSargasso SeaAtlantic Ocean2001

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1008.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_675;98_785;99_1008&stattab=map
  • Last taxonomy: Epibacterium mobile subclade
  • 16S sequence: AB681677
  • Sequence Identity:
  • Total samples: 19312
  • soil counts: 558
  • aquatic counts: 16540
  • animal counts: 2089
  • plant counts: 125

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
168441Risk group (German classification)
1209891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ruegeria mobilis gene for 16S rRNA, partial sequence, strain: NBRC 102038AB6816771387ena379347
20218Ruegeria pelagia strain NBRC 102038 16S ribosomal RNA gene, partial sequenceEU9771381425ena379347
16844Ruegeria pelagia strain HTCC2662 16S ribosomal RNA gene, partial sequenceDQ9161411425ena379347

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tritonibacter mobilis NBRC102038GCA_001681735contigncbi379347
66792Ruegeria mobilis strain NBRC102038379347.144wgspatric379347
66792Epibacterium mobile NBRC 1020382816332506draftimg379347

GC content

  • @ref: 16844
  • GC-content: 58.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.896yes
anaerobicno98.695no
halophileyes83.02no
spore-formingno96.37no
glucose-utilyes90.044yes
aerobicyes86.507yes
motileyes78.474yes
flagellatedno68.959no
thermophileno96.268yes
glucose-fermentno90.279no

External links

@ref: 16844

culture collection no.: DSM 23402, KCCM 42378, NBRC 102038, HTCC 2662, CIP 109709

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16844Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23402)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23402
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32143Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128387
34988Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7483
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)
68382Automatically annotated from API zym
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
120989Curators of the CIPCollection of Institut Pasteur (CIP 109709)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109709