Strain identifier

BacDive ID: 11297

Type strain: Yes

Species: Bermanella marisrubri

Strain Designation: RED65

Strain history: <- CECT <- J. Pinhassi, Dept. Biology and Environmental Sci., Univ. Kalmar, Sweden

NCBI tax ID(s): 207949 (species)

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General

@ref: 16761

BacDive-ID: 11297

DSM-Number: 23232

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

description: Bermanella marisrubri RED65 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-seawater sample.

NCBI tax id

  • NCBI tax id: 207949
  • Matching level: species

strain history

  • @ref: 16761
  • history: <- CECT <- J. Pinhassi, Dept. Biology and Environmental Sci., Univ. Kalmar, Sweden

doi: 10.13145/bacdive11297.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Bermanella
  • species: Bermanella marisrubri
  • full scientific name: Bermanella marisrubri Pinhassi et al. 2009

@ref: 16761

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Bermanella

species: Bermanella marisrubri

full scientific name: Bermanella marisrubri Pinhassi et al. 2009

strain designation: RED65

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28937negative3.15 µm0.45 µmspiral-shapedyes
69480yes95.504
69480negative99.999

Culture and growth conditions

culture medium

  • @ref: 16761
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
16761positivegrowth28mesophilic
28937positivegrowth15-42
28937positiveoptimum27.5mesophilic
59417positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28937aerobe
59417aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
28937NaClpositivegrowth01-12 %
28937NaClpositiveoptimum6.5 %

observation

  • @ref: 28937
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2893730089acetate+carbon source
2893729987glutamate+carbon source
2893725115malate+carbon source
2893751850methyl pyruvate+carbon source
2893730031succinate+carbon source
2893753423tween 40+carbon source
2893753426tween 80+carbon source

enzymes

@refvalueactivityec
28937catalase+1.11.1.6
28937cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16761surface-seawater samplenorthern Red Sea, Gulf of EilatIsraelISRAsia
59417Seawater surfaceRed Sea,Gulf of EilatIsraelISRAsia2000-09-24

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_174099.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_306;96_64804;97_84068;98_113982;99_174099&stattab=map
  • Last taxonomy: Bermanella marisrubri subclade
  • 16S sequence: AY136131
  • Sequence Identity:
  • Total samples: 5172
  • soil counts: 203
  • aquatic counts: 4489
  • animal counts: 405
  • plant counts: 75

Safety information

risk assessment

  • @ref: 16761
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16761
  • description: Bermanella marisrubri strain RED65 16S ribosomal RNA gene, complete sequence
  • accession: AY136131
  • length: 1533
  • database: ena
  • NCBI tax ID: 207949

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bermanella marisrubri RED65GCA_012295615completencbi207949
66792Bermanella marisrubri RED65GCA_000153565scaffoldncbi207949
66792Bermanella marisrubri RED65638341141draftimg207949

GC content

@refGC-content
1676144.0
2893744

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.215yes
flagellatedyes92.278no
gram-positiveno98.928yes
anaerobicno98.608yes
aerobicyes94.028no
halophileyes90.095yes
spore-formingno95.681no
glucose-utilyes60.268no
thermophileno99.277yes
glucose-fermentno87.437no

External links

@ref: 16761

culture collection no.: DSM 23232, CCUG 52064, CECT 7074

straininfo link

  • @ref: 80530
  • straininfo: 360707

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19196781Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea.Pinhassi J, Pujalte MJ, Pascual J, Gonzalez JM, Lekunberri I, Pedros-Alio C, Arahal DRInt J Syst Evol Microbiol10.1099/ijs.0.002113-02009*Genome, Bacterial, Indian Ocean, Molecular Sequence Data, Oceanospirillaceae/*classification/*genetics/ultrastructure, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, *Water MicrobiologyGenetics
Enzymology23824188A novel bacterial enzyme with D-glucuronyl C5-epimerase activity.Raedts J, Lundgren M, Kengen SW, Li JP, van der Oost JJ Biol Chem10.1074/jbc.M113.4764402013Animals, Aquatic Organisms/enzymology/genetics, Bacterial Proteins/*chemistry/*genetics, Carbohydrate Epimerases/*chemistry/*genetics, Escherichia coli/enzymology/genetics, Gammaproteobacteria/*enzymology/*genetics, Glycosaminoglycans/chemistry/genetics, Humans, Mice, Recombinant Proteins/chemistry/genetics, Sequence Alignment, Sequence Homology, Amino AcidPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16761Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23232)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23232
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
28937Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2537628776041
59417Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52064)https://www.ccug.se/strain?id=52064
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
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
80530Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360707.1StrainInfo: A central database for resolving microbial strain identifiers