Strain identifier
BacDive ID: 12681
Type strain:
Species: Pseudoalteromonas rubra
Strain Designation: Cerbom 18
Strain history: CIP <- 1994, NCIMB <- M. Aubert, Nice, France
NCBI tax ID(s): 1117318 (strain), 43658 (species)
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 id | Matching level |
---|---|
1117318 | strain |
43658 | species |
strain history
@ref | history |
---|---|
2850 | <- LMG <- M.J. Gauthier, Cerbom 18 |
122286 | CIP <- 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
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
2850 | https://www.dsmz.de/microorganisms/photos/DSM_6842.jpg | Micrograph of DSM 6842. | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH |
2850 | https://www.dsmz.de/microorganisms/photos/DSM_6842-1.jpg | DSM 6842 grown on DSMZ medium 514. | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2850 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
42026 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
122286 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2850 | positive | growth | 25 | mesophilic |
42026 | positive | growth | 22 | psychrophilic |
122286 | positive | growth | 22-30 | |
122286 | no | growth | 5 | psychrophilic |
122286 | no | growth | 10 | psychrophilic |
122286 | no | growth | 41 | thermophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122286 | 4853 | esculin | - | hydrolysis |
122286 | 17632 | nitrate | - | reduction |
122286 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 122286
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
122286 | 15688 | acetoin | - | |
122286 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
122286 | oxidase | + | |
122286 | beta-galactosidase | - | 3.2.1.23 |
122286 | alcohol dehydrogenase | - | 1.1.1.1 |
122286 | gelatinase | + | |
122286 | caseinase | + | 3.4.21.50 |
122286 | catalase | + | 1.11.1.6 |
122286 | lecithinase | - | |
122286 | lysine decarboxylase | - | 4.1.1.18 |
122286 | ornithine decarboxylase | - | 4.1.1.17 |
122286 | tryptophan deaminase | - | |
122286 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2850 | surface seawater | Mediterranean Sea near Nice | France | FRA | Europe |
122286 | Environment, Seawater | Nice | France | FRA | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
2850 | 1 | Risk group (German classification) |
122286 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoalteromonas rubra DSM 6842 | GCA_000238295 | chromosome | ncbi | 43658 |
66792 | Pseudoalteromonas rubra ATCC 29570 | 1117318.14 | wgs | patric | 1117318 |
66792 | Pseudoalteromonas rubra ATCC 29570 | 2541047006 | draft | img | 1117318 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.926 | no |
motile | yes | 89.926 | no |
flagellated | yes | 90.39 | no |
flagellated | yes | 90.39 | no |
gram-positive | no | 98.945 | no |
gram-positive | no | 98.945 | no |
anaerobic | no | 94.647 | no |
anaerobic | no | 94.647 | no |
aerobic | yes | 78.27 | no |
aerobic | yes | 78.27 | no |
halophile | no | 55.27 | no |
halophile | no | 55.27 | no |
spore-forming | no | 92.679 | no |
spore-forming | no | 92.679 | no |
thermophile | no | 99.596 | no |
glucose-util | yes | 89.962 | no |
glucose-util | yes | 89.962 | no |
thermophile | no | 99.596 | no |
glucose-ferment | no | 72.304 | no |
glucose-ferment | no | 72.304 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9734030 | Pseudoalteromonas 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 R | Int J Syst Bacteriol | 10.1099/00207713-48-3-769 | 1998 | Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/chemistry, Gram-Negative Aerobic Bacteria/*classification/genetics/metabolism, Laminaria/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Water Microbiology | Genetics |
Genetics | 16126182 | The 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 AV | Carbohydr Res | 10.1016/j.carres.2005.07.007 | 2005 | Carbohydrate Sequence, Carbon Isotopes, Hydrogen, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, O Antigens/*chemistry, Pseudoalteromonas/*chemistry | |
Genetics | 19695563 | Structure 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 JM | Carbohydr Res | 10.1016/j.carres.2009.06.035 | 2009 | Carbohydrate Sequence, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Malates/chemistry, Molecular Sequence Data, Molecular Structure, Polysaccharides, Bacterial/*chemistry, Pseudoalteromonas/*metabolism, Spectrometry, Mass, Electrospray Ionization, Vibrio vulnificus/*metabolism | Metabolism |
Genetics | 22374963 | Genome 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 YZ | J Bacteriol | 10.1128/JB.06822-11 | 2012 | Biosynthetic Pathways/genetics, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Indoles/metabolism, Molecular Sequence Data, Multigene Family, Pseudoalteromonas/*genetics/metabolism, Pyrroles/metabolism, Sequence Analysis, DNA | Metabolism |
Enzymology | 35578070 | Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842. | Chen R, Liao YT, Gao TT, Zhang YM, Lu LH, Wang CH | Mol Biotechnol | 10.1007/s12033-022-00505-0 | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2850 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6842) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6842 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
42026 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15983 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João 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 | |||
81892 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92114.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122286 | Curators of the CIP | Collection of Institut Pasteur (CIP 104110) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104110 |