Strain identifier

BacDive ID: 12681

Type strain: Yes

Species: Pseudoalteromonas rubra

Strain Designation: Cerbom 18

Strain history: CIP <- 1994, NCIMB <- M. Aubert, Nice, France

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General

@ref: 2850

BacDive-ID: 12681

DSM-Number: 6842

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

description: Pseudoalteromonas rubra Cerbom 18 is a mesophilic, Gram-negative, motile bacterium that was isolated from surface seawater.

NCBI tax id

NCBI tax idMatching level
1117318strain
43658species

strain history

@refhistory
2850<- LMG <- M.J. Gauthier, Cerbom 18
122286CIP <- 1994, NCIMB <- M. Aubert, Nice, France

doi: 10.13145/bacdive12681.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Pseudoalteromonadaceae
  • genus: Pseudoalteromonas
  • species: Pseudoalteromonas rubra
  • full scientific name: Pseudoalteromonas rubra (Gauthier 1976) Gauthier et al. 1995
  • synonyms

    • @ref: 20215
    • synonym: Alteromonas rubra

@ref: 2850

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Pseudoalteromonadaceae

genus: Pseudoalteromonas

species: Pseudoalteromonas rubra

full scientific name: Pseudoalteromonas rubra (Gauthier 1976) Gauthier et al. 1995

strain designation: Cerbom 18

type strain: yes

Morphology

cell morphology

  • @ref: 122286
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
2850https://www.dsmz.de/microorganisms/photos/DSM_6842.jpgMicrograph of DSM 6842.Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
2850https://www.dsmz.de/microorganisms/photos/DSM_6842-1.jpgDSM 6842 grown on DSMZ medium 514.Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2850BACTO 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
42026Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122286CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2850positivegrowth25mesophilic
42026positivegrowth22psychrophilic
122286positivegrowth22-30
122286nogrowth5psychrophilic
122286nogrowth10psychrophilic
122286nogrowth41thermophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1222864853esculin-hydrolysis
12228617632nitrate-reduction
12228616301nitrite-reduction

metabolite production

  • @ref: 122286
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12228615688acetoin-
12228617234glucose-

enzymes

@refvalueactivityec
122286oxidase+
122286beta-galactosidase-3.2.1.23
122286alcohol dehydrogenase-1.1.1.1
122286gelatinase+
122286caseinase+3.4.21.50
122286catalase+1.11.1.6
122286lecithinase-
122286lysine decarboxylase-4.1.1.18
122286ornithine decarboxylase-4.1.1.17
122286tryptophan deaminase-
122286urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2850surface seawaterMediterranean Sea near NiceFranceFRAEurope
122286Environment, SeawaterNiceFranceFRAEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_733.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_57;96_353;97_393;98_450;99_733&stattab=map
  • Last taxonomy: Pseudoalteromonas
  • 16S sequence: X82147
  • Sequence Identity:
  • Total samples: 3178
  • soil counts: 55
  • aquatic counts: 2485
  • animal counts: 574
  • plant counts: 64

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28501Risk group (German classification)
1222861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 2850
  • description: A.rubra 16S rRNA gene (ATCC 29570T)
  • accession: X82147
  • length: 1426
  • database: ena
  • NCBI tax ID: 1117318

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoalteromonas rubra DSM 6842GCA_000238295chromosomencbi43658
66792Pseudoalteromonas rubra ATCC 295701117318.14wgspatric1117318
66792Pseudoalteromonas rubra ATCC 295702541047006draftimg1117318

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.926no
motileyes89.926no
flagellatedyes90.39no
flagellatedyes90.39no
gram-positiveno98.945no
gram-positiveno98.945no
anaerobicno94.647no
anaerobicno94.647no
aerobicyes78.27no
aerobicyes78.27no
halophileno55.27no
halophileno55.27no
spore-formingno92.679no
spore-formingno92.679no
thermophileno99.596no
glucose-utilyes89.962no
glucose-utilyes89.962no
thermophileno99.596no
glucose-fermentno72.304no
glucose-fermentno72.304no

External links

@ref: 2850

culture collection no.: DSM 6842, ATCC 29570, LMG 2876, NCIMB 1890, CIP 104110, DSM 6064

straininfo link

  • @ref: 81892
  • straininfo: 92114

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734030Pseudoalteromonas bacteriolytica sp. nov., a marine bacterium that is the causative agent of red spot disease of Laminaria japonica.Sawabe T, Makino H, Tatsumi M, Nakano K, Tajima K, Iqbal MM, Yumoto I, Ezura Y, Christen RInt J Syst Bacteriol10.1099/00207713-48-3-7691998Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/chemistry, Gram-Negative Aerobic Bacteria/*classification/genetics/metabolism, Laminaria/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyGenetics
Genetics16126182The structure of the O-polysaccharide of the Pseudoalteromonas rubra ATCC 29570T lipopolysaccharide containing a keto sugar.Kilcoyne M, Shashkov AS, Knirel YA, Gorshkova RP, Nazarenko EL, Ivanova EP, Gorshkova NM, Senchenkova SN, Savage AVCarbohydr Res10.1016/j.carres.2005.07.0072005Carbohydrate Sequence, Carbon Isotopes, Hydrogen, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, O Antigens/*chemistry, Pseudoalteromonas/*chemistry
Genetics19695563Structure of a polysaccharide from the lipopolysaccharides of Vibrio vulnificus strains CECT 5198 and S3-I2-36, which is remarkably similar to the O-polysaccharide of Pseudoalteromonas rubra ATCC 29570.Shashkov AS, Senchenkova SN, Chizhov AO, Knirel YA, Esteve C, Alcaide E, Merino S, Tomas JMCarbohydr Res10.1016/j.carres.2009.06.0352009Carbohydrate Sequence, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Malates/chemistry, Molecular Sequence Data, Molecular Structure, Polysaccharides, Bacterial/*chemistry, Pseudoalteromonas/*metabolism, Spectrometry, Mass, Electrospray Ionization, Vibrio vulnificus/*metabolismMetabolism
Genetics22374963Genome sequence of the cycloprodigiosin-producing bacterial strain Pseudoalteromonas rubra ATCC 29570(T).Xie BB, Shu YL, Qin QL, Rong JC, Zhang XY, Chen XL, Zhou BC, Zhang YZJ Bacteriol10.1128/JB.06822-112012Biosynthetic Pathways/genetics, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Indoles/metabolism, Molecular Sequence Data, Multigene Family, Pseudoalteromonas/*genetics/metabolism, Pyrroles/metabolism, Sequence Analysis, DNAMetabolism
Enzymology35578070Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842.Chen R, Liao YT, Gao TT, Zhang YM, Lu LH, Wang CHMol Biotechnol10.1007/s12033-022-00505-02022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2850Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6842)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6842
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
42026Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15983
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
81892Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92114.1StrainInfo: A central database for resolving microbial strain identifiers
122286Curators of the CIPCollection of Institut Pasteur (CIP 104110)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104110