Strain identifier

BacDive ID: 481

Type strain: Yes

Species: Marinobacter flavimaris

Strain Designation: SW145

Strain history: CIP <- 2005, KCTC <- J. H. Yoon, Korea: strain SW145

NCBI tax ID(s): 262076 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6256

BacDive-ID: 481

DSM-Number: 16070

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

description: Marinobacter flavimaris SW145 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sea water of tidal flat.

NCBI tax id

  • NCBI tax id: 262076
  • Matching level: species

strain history

@refhistory
6256<- J.-H. Yoon; SW145
67770J.-H. Yoon SW-145.
119378CIP <- 2005, KCTC <- J. H. Yoon, Korea: strain SW145

doi: 10.13145/bacdive481.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacter
  • species: Marinobacter flavimaris
  • full scientific name: Marinobacter flavimaris Yoon et al. 2004

@ref: 6256

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter flavimaris

full scientific name: Marinobacter flavimaris Yoon et al. 2004

strain designation: SW145

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23298negative1.5-3.0 µm0.6-0.9 µmrod-shapedyesmonotrichous, polar
119378negativerod-shapedyes

colony morphology

  • @ref: 23298
  • colony size: 1-2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6256BACTO 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
23298Marine agar (MA)yes
37266Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119378CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6256positivegrowth30mesophilic
23298positivegrowth4psychrophilic
23298positivemaximum45thermophilic
23298positiveoptimum37mesophilic
37266positivegrowth30mesophilic
67770positivegrowth30mesophilic
119378positivegrowth5-41

culture pH

@refabilitytypepH
23298positiveoptimum7.0-8.0
23298positivegrowth5.5
23298nogrowth5.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23298anaerobe
119378obligate aerobe

spore formation

  • @ref: 23298
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
23298NaClpositiveoptimum2-6 %
23298NaClpositivegrowth20 %
23298NaClnogrowth>21 %
23298slightly halophilic
23298NaClnogrowth0 %
119378NaClpositivegrowth2-10 %
119378NaClnogrowth0 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329835391aspartate-assimilation
2329817634D-glucose-assimilation
2329816899D-mannitol-assimilation
2329816449dl-alanine-assimilation
2329816467L-arginine-assimilation
2329829985L-glutamate-assimilation
2329815963ribitol-builds acid from
2329817057cellobiose-builds acid from
2329812936D-galactose-builds acid from
2329817634D-glucose-builds acid from
2329816899D-mannitol-builds acid from
2329816024D-mannose-builds acid from
232986731melezitose-builds acid from
2329816634raffinose-builds acid from
2329816988D-ribose-builds acid from
2329817924D-sorbitol-builds acid from
2329816551D-trehalose-builds acid from
2329865327D-xylose-builds acid from
2329830849L-arabinose-builds acid from
2329862345L-rhamnose-builds acid from
2329817716lactose-builds acid from
2329817306maltose-builds acid from
2329828053melibiose-builds acid from
2329817268myo-inositol-builds acid from
2329817992sucrose-builds acid from
2329817754glycerol-carbon source
2329845296hexadecane-carbon source
2329817115L-serine-carbon source
2329817754glycerol-energy source
2329845296hexadecane-energy source
2329817115L-serine-energy source
23298casein-hydrolysis
232984853esculin-hydrolysis
232985291gelatin-hydrolysis
2329817368hypoxanthine-hydrolysis
2329828017starch-hydrolysis
2329818186tyrosine-hydrolysis
2329815318xanthine-hydrolysis
2329816301nitrite-reduction
2329815824D-fructose+assimilation
232988391D-gluconate+assimilation
2329830031succinate+assimilation
2329815824D-fructose+builds acid from
2329853424tween 20+hydrolysis
2329853423tween 40+hydrolysis
2329853425tween 60+hydrolysis
2329853426tween 80+hydrolysis
2329817632nitrate+reduction
1193784853esculin-hydrolysis
11937817632nitrate-builds gas from
11937817632nitrate+reduction
11937816301nitrite-builds gas from
11937816301nitrite-reduction
11937817632nitrate-respiration

metabolite production

  • @ref: 119378
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23298lipase (C 14)-
23298urease-3.5.1.5
23298valine arylamidase-
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
119378oxidase+
119378beta-galactosidase-3.2.1.23
119378alcohol dehydrogenase-1.1.1.1
119378gelatinase-
119378amylase-
119378caseinase-3.4.21.50
119378catalase+1.11.1.6
119378tween esterase+
119378gamma-glutamyltransferase+2.3.2.2
119378lecithinase+
119378lipase-
119378lysine decarboxylase-4.1.1.18
119378ornithine decarboxylase-4.1.1.17
119378phenylalanine ammonia-lyase+4.3.1.24
119378protease-
119378tryptophan deaminase-
119378urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119378-+-+-+----++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6256sea water of tidal flatDaepo Beach of Yellow SeaRepublic of KoreaKORAsia
67770Seawater of the Yellow SeaRepublic of KoreaKORAsia
119378Environment, Sea water of tidal flatYellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_2437.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_1317;97_1564;98_1903;99_2437&stattab=map
  • Last taxonomy: Marinobacter
  • 16S sequence: AY517632
  • Sequence Identity:
  • Total samples: 3438
  • soil counts: 149
  • aquatic counts: 3127
  • animal counts: 133
  • plant counts: 29

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62561Risk group (German classification)
1193781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23298
  • description: Marinobacter flavimaris strain SW-145 16S ribosomal RNA gene, partial sequence
  • accession: AY517632
  • length: 1495
  • database: nuccore
  • NCBI tax ID: 262076

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter flavimaris KCTC 12185GCA_003363485contigncbi262076
66792Marinobacter flavimaris strain KCTC 12185262076.4wgspatric262076

GC content

@refGC-contentmethod
2329858.00high performance liquid chromatography (HPLC)
6777058high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.09yes
gram-positiveno98.695yes
anaerobicno97.459yes
aerobicyes82.447yes
halophileyes91.543yes
spore-formingno95.959yes
glucose-utilno54.491yes
flagellatedyes85.663no
thermophileno98.777no
glucose-fermentno90.706no

External links

@ref: 6256

culture collection no.: DSM 16070, JCM 12323, CGMCC 1.8487, KCTC 12185, CIP 108615

straininfo link

  • @ref: 70160
  • straininfo: 134296

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388746Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.Yoon JH, Yeo SH, Kim IG, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63151-02004Alteromonadaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA/genetics, Gram-Negative Bacteria/classification/cytology/isolation & purification/physiology, Growth Inhibitors/pharmacology, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Seawater/*microbiology, Sequence Analysis, DNA, Spores, Bacterial, Temperature, Ubiquinone/analysis, Water MicrobiologyEnzymology
Phylogeny16514021Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxin-producing dinoflagellates.Green DH, Bowman JP, Smith EA, Gutierrez T, Bolch CJSInt J Syst Evol Microbiol10.1099/ijs.0.63447-02006Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Animals, DNA, Ribosomal/chemistry, Dinoflagellida/*microbiology/pathogenicity, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6256Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16070)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16070
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
23298Jung-Hoon Yoon, Soo-Hwan Yeo, In-Gi Kim, Tae-Kwang Oh10.1099/ijs.0.63151-0Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in KoreaIJSEM 54: 1799-1803 200415388746
37266Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6264
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
70160Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134296.1StrainInfo: A central database for resolving microbial strain identifiers
119378Curators of the CIPCollection of Institut Pasteur (CIP 108615)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108615