Strain identifier

BacDive ID: 291

Type strain: Yes

Species: Oceanisphaera litoralis

Strain Designation: R5

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 225144 (species)

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General

@ref: 5796

BacDive-ID: 291

DSM-Number: 15406

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Oceanisphaera litoralis R5 is an obligate aerobe, mesophilic, motile bacterium that was isolated from bottom sediments.

NCBI tax id

  • NCBI tax id: 225144
  • Matching level: species

strain history

@refhistory
5796<- L. A. Romanenko; R5
364102005, DSMZ
120633CIP <- 2005, DSMZ

doi: 10.13145/bacdive291.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Oceanisphaera
  • species: Oceanisphaera litoralis
  • full scientific name: Oceanisphaera litoralis Romanenko et al. 2003

@ref: 5796

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Oceanisphaera

species: Oceanisphaera litoralis

full scientific name: Oceanisphaera litoralis Romanenko et al. 2003

strain designation: R5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.902
6948099.998negative
120633yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5796BACTO 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
36410Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120633CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5796positivegrowth28mesophilic
36410positivegrowth37mesophilic
120633positivegrowth5-37
120633nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120633
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
120633NaClpositivegrowth2-6 %
120633NaClnogrowth0 %
120633NaClnogrowth8 %
120633NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12063316947citrate-carbon source
1206334853esculin-hydrolysis
12063317632nitrate+reduction
12063316301nitrite-reduction
12063317632nitrate-respiration

metabolite production

  • @ref: 120633
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
120633oxidase+
120633beta-galactosidase+3.2.1.23
120633alcohol dehydrogenase-1.1.1.1
120633gelatinase-
120633amylase-
120633DNase-
120633caseinase-3.4.21.50
120633catalase+1.11.1.6
120633tween esterase-
120633lecithinase-
120633lipase-
120633lysine decarboxylase-4.1.1.18
120633ornithine decarboxylase-4.1.1.17
120633protease-
120633tryptophan deaminase-
120633urease+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
120633-++--+----++--+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120633------------------++-------+--------------------++----+-+-+--+++-----+-++-----+-+-------+-+-+++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5796bottom sedimentsSea of JapanRussiaRUSAsia
120633Environment, Marine bottom sand sample

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_177717.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_6771;97_8105;98_42659;99_177717&stattab=map
  • Last taxonomy: Oceanisphaera litoralis
  • 16S sequence: AJ550470
  • Sequence Identity:
  • Total samples: 7
  • aquatic counts: 3
  • animal counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57961Risk group (German classification)
1206331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5796
  • description: Oceanisphaera litoralis 16S rRNA gene, type strain DSM 15406
  • accession: AJ550470
  • length: 1506
  • database: ena
  • NCBI tax ID: 225144

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oceanisphaera litoralis DSM 15406GCA_016907015scaffoldncbi225144
66792Oceanisphaera litoralis strain DSM 15406225144.3wgspatric225144
66792Oceanisphaera litoralis DSM 154062861657729draftimg225144

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes81.896no
gram-positiveno98.855no
anaerobicno98.953no
aerobicyes89.97no
halophileyes59.001no
spore-formingno95.801no
thermophileno97.537yes
glucose-utilyes82.418no
motileyes90.26no
glucose-fermentyes53.429no

External links

@ref: 5796

culture collection no.: DSM 15406, CIP 108812, KCTC 23479, KMM 3654

straininfo link

  • @ref: 69973
  • straininfo: 97661

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657118Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments.Romanenko LA, Schumann P, Zhukova NV, Rohde M, Mikhailov VV, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02774-02003Aeromonadaceae/*classification/isolation & purification/physiology/ultrastructure, Geologic Sediments/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Seawater/*microbiologyGenetics
Phylogeny15830805Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.Ivanova EP, Onyshchenko OM, Christen R, Zhukova NV, Lysenko AM, Shevchenko LS, Buljan V, Hambly B, Kiprianova EASyst Appl Microbiol10.1016/j.syapm.2004.11.0022005Aeromonadaceae/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, UkraineGenetics
Phylogeny16585712Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea.Park SJ, Kang CH, Nam YD, Bae JW, Park YH, Quan ZX, Moon DS, Kim HJ, Roh DH, Rhee SKInt J Syst Evol Microbiol10.1099/ijs.0.64116-02006Aeromonadaceae/*classification/isolation & purification/physiology, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolismGenetics
Phylogeny21257693Oceanisphaera ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Oceanisphaera Romanenko et al. 2003.Choi WC, Kang SJ, Jung YT, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.029496-02011Aeromonadaceae/*classification/genetics/*isolation & purification/metabolism, Animals, Aquaculture, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Ostreidae/*growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiologyMetabolism
Phylogeny22003041Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera.Srinivas TNR, Reddy PVV, Begum Z, Manasa P, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.036475-02011Aeromonadaceae/*classification/genetics/isolation & purification, Arctic Regions, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25991663Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples.Zhou S, Wang H, Wang Y, Ma K, He M, Chen X, Kong D, Guo X, Ruan Z, Zhao BInt J Syst Evol Microbiol10.1099/ijs.0.0003312015Aeromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Temperature, Ubiquinone/chemistryGenetics
Phylogeny35590019Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus.Xue JH, Shi LF, Zhang BN, Wu WJ, Gao Y, Zhu Q, Zhao LHArch Microbiol10.1007/s00203-022-02928-42022Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestines, *Perciformes, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5796Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15406)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15406
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
36410Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6482
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)
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
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
69973Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97661.1StrainInfo: A central database for resolving microbial strain identifiers
120633Curators of the CIPCollection of Institut Pasteur (CIP 108812)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108812