Strain identifier
BacDive ID: 6002
Type strain:
Species: Cobetia marina
Strain history: CIP <- 1996, NCIMB <- G.E. Jones, Arthrobacter marinus
NCBI tax ID(s): 28258 (species)
General
@ref: 1747
BacDive-ID: 6002
DSM-Number: 4741
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile
description: Cobetia marina DSM 4741 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 28258
- Matching level: species
strain history
@ref | history |
---|---|
1747 | <- ATCC <- A.B. Cobet <- G. Jones <- C. Wirsen |
67770 | IAM 14107 <-- ATCC 25374 <-- A. B. Cobet ("Arthrobacter marinus") <-- G. Jones <-- C. Wirsen. |
120797 | CIP <- 1996, NCIMB <- G.E. Jones, Arthrobacter marinus |
doi: 10.13145/bacdive6002.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Halomonadaceae
- genus: Cobetia
- species: Cobetia marina
- full scientific name: Cobetia marina (Cobet et al. 1970) Arahal et al. 2002
synonyms
@ref synonym 20215 Pseudomonas marina 20215 Halomonas marina 20215 Arthrobacter marinus 20215 Halomonas halodurans 20215 Deleya marina
@ref: 1747
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Cobetia
species: Cobetia marina
full scientific name: Cobetia marina (Cobet et al. 1970) Arahal et al. 2002 emend. Romanenko et al. 2013
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.519 | |
69480 | 99.988 | negative | |
120797 | yes | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1747 | 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 |
39090 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
120797 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1747 | positive | growth | 26 | mesophilic |
39090 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
120797 | positive | growth | 5-41 | |
120797 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120797
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120797 | NaCl | positive | growth | 2-10 % |
120797 | NaCl | no | growth | 0 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | + | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
120797 | esculin | - | hydrolysis | 4853 |
120797 | hippurate | - | hydrolysis | 606565 |
120797 | nitrate | - | reduction | 17632 |
120797 | nitrite | - | reduction | 16301 |
120797 | phenol | - | degradation | 15882 |
120797 | malonate | + | assimilation | 15792 |
120797 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 120797
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 120797
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
120797 | oxidase | - | |
120797 | beta-galactosidase | - | 3.2.1.23 |
120797 | alcohol dehydrogenase | - | 1.1.1.1 |
120797 | gelatinase | - | |
120797 | DNase | - | |
120797 | caseinase | - | 3.4.21.50 |
120797 | catalase | + | 1.11.1.6 |
120797 | gamma-glutamyltransferase | + | 2.3.2.2 |
120797 | lecithinase | - | |
120797 | lipase | - | |
120797 | lysine decarboxylase | - | 4.1.1.18 |
120797 | ornithine decarboxylase | - | 4.1.1.17 |
120797 | protease | - | |
120797 | tryptophan deaminase | - | |
120797 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120797 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120797 | - | - | - | - | - | - | - | - | - | + | + | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | +/- | - | - | +/- | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120797 | + | + | + | + | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | + | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + | + | - | - | + | + | - | - | - | - | - | - | - | + | + | + | + | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1747 | seawater | ||||
67770 | Littoral water sample at Woods Hole | MA | USA | USA | North America |
120797 | Environment, Littoral seawater sample | Woods Hole, Massachusetts | United States of America | USA | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_895.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_532;97_613;98_707;99_895&stattab=map
- Last taxonomy: Cobetia
- 16S sequence: NR_042065
- Sequence Identity:
- Total samples: 19571
- soil counts: 974
- aquatic counts: 12909
- animal counts: 5462
- plant counts: 226
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1747 | 1 | Risk group (German classification) |
120797 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Deleya marina (ATCC 25374) 16S ribosomal RNA (16S rRNA) gene | M93354 | 1483 | ena | 28258 |
1747 | Halomonas marina partial 16S rRNA gene, strain DSM 4741 | AJ306890 | 1536 | ena | 28258 |
1747 | Cobetia marina strain DSM 4741 16S ribosomal RNA, partial sequence | NR_042065 | 1536 | nuccore | 28258 |
67770 | Cobetia marina gene for 16S rRNA, partial sequence, strain: NBRC 102605 | AB681880 | 1466 | ena | 28258 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cobetia marina JCM 21022 | GCA_001720485 | complete | ncbi | 28258 |
66792 | Cobetia marina strain JCM 21022 | 28258.9 | complete | patric | 28258 |
66792 | Cobetia sp. MM1IDA2H-1 strain MM1IDA2H-1AD | 1268241.8 | wgs | patric | 1268241 |
66792 | Cobetia marina JCM 21022 | 2751185720 | complete | img | 28258 |
GC content
- @ref: 67770
- GC-content: 63.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 76.505 | no |
gram-positive | no | 98.755 | no |
anaerobic | no | 98.908 | no |
aerobic | yes | 93.874 | no |
halophile | yes | 91.838 | no |
spore-forming | no | 97.022 | no |
glucose-util | yes | 92.69 | no |
thermophile | no | 99.048 | yes |
motile | yes | 92.18 | no |
glucose-ferment | no | 76.069 | no |
External links
@ref: 1747
culture collection no.: DSM 4741, ATCC 25374, JCM 21022, CCUG 49558, CECT 4278, CIP 104765, IAM 14107, LMG 2217, NBRC 102605, NCIMB 1877
straininfo link
- @ref: 75491
- straininfo: 2165
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phenotype | 1781675 | Comparison of the adhesion properties of Deleya marina and the exopolysaccharide-defective mutant strain DMR. | Shea C, Nunley JW, Williamson JC, Smith-Somerville HE | Appl Environ Microbiol | 10.1128/aem.57.11.3107-3113.1991 | 1991 | Bacteria/genetics/ultrastructure, *Bacterial Adhesion, *Bacterial Physiological Phenomena, Colony Count, Microbial, Microscopy, Electron, Scanning, *Mutation, Phenotype, Polysaccharides, Bacterial/genetics/*physiology/ultrastructure | |
Metabolism | 9271247 | N-acyl amino acid biosynthesis in marine bacterium, Deleya marina. | Yagi H, Corzo G, Nakahara T | Biochim Biophys Acta | 10.1016/s0304-4165(97)00009-3 | 1997 | Bacteria/*metabolism, Marine Biology, Ornithine/analogs & derivatives/*biosynthesis/chemistry, Protein Conformation, Seawater | |
Enzymology | 9714788 | Novel diglycosyldiacylglycerol from the gram-negative bacterium Deleya marina. | Yagi H, Maruyama A | Biochim Biophys Acta | 10.1016/s0005-2760(98)00070-8 | 1998 | Glycolipids/chemistry/*isolation & purification, Gram-Negative Bacteria/*metabolism, Magnetic Resonance Spectroscopy/methods, *Water Microbiology | Phylogeny |
Phylogeny | 12353874 | Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina. | Arahal DR, Castillo AM, Ludwig W, Schleifer KH, Ventosa A | Syst Appl Microbiol | 10.1078/0723-2020-00113 | 2002 | Base Sequence, Gammaproteobacteria/*classification, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Pathogenicity | 17453727 | Combinatorial materials research applied to the development of new surface coatings III. Utilisation of a high-throughput multiwell plate screening method to rapidly assess bacterial biofilm retention on antifouling surfaces. | Stafslien S, Daniels J, Chisholm B, Christianson D | Biofouling | 10.1080/08927010601127311 | 2007 | Bacteria/drug effects/*isolation & purification, Bacterial Adhesion, Biofilms/drug effects/*growth & development, Coated Materials, Biocompatible, Disinfectants/pharmacology, Marine Biology, Materials Testing/methods, Polymethyl Methacrylate, Ships, Water Microbiology | Enzymology |
Phylogeny | 19654339 | Cobetia crustatorum sp. nov., a novel slightly halophilic bacterium isolated from traditional fermented seafood in Korea. | Kim MS, Roh SW, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.008847-0 | 2009 | Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Fermentation, Halomonadaceae/*classification/genetics/*isolation & purification/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/*metabolism | Metabolism |
Phylogeny | 22427450 | Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina. | Romanenko LA, Tanaka N, Svetashev VI, Falsen E | Int J Syst Evol Microbiol | 10.1099/ijs.0.036863-0 | 2012 | Alaska, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Halomonadaceae/*classification/genetics/isolation & purification, Halomonas/classification/genetics/isolation & purification, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Water Microbiology | Enzymology |
24192832 | Inhibition of larval barnacle attachment to bacterial films: An investigation of physical properties. | Maki JS, Rittschof D, Mitchell R | Microb Ecol | 10.1007/BF00165910 | 1992 | |||
Metabolism | 34930259 | High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741(T) and in silico analyses of the genus specific PhaC2 polymerase variant. | Christensen M, Jablonski P, Altermark B, Irgum K, Hansen H | Microb Cell Fact | 10.1186/s12934-021-01713-0 | 2021 | Acetates/metabolism, Bacterial Proteins/metabolism, Halomonadaceae/*genetics/*metabolism, Metabolic Engineering/*methods, Phylogeny, Polyhydroxyalkanoates/analysis/*biosynthesis | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1747 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4741) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4741 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39090 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16709 | ||||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75491 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2165.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120797 | Curators of the CIP | Collection of Institut Pasteur (CIP 104765) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104765 |