Strain identifier

BacDive ID: 17704

Type strain: Yes

Species: Algoriphagus aquimarinus

Strain history: CIP <- 2004, CCUG <- 2002, KMM

NCBI tax ID(s): 237018 (species)

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General

@ref: 16841

BacDive-ID: 17704

DSM-Number: 23399

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

description: Algoriphagus aquimarinus DSM 23399 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea-water sample.

NCBI tax id

  • NCBI tax id: 237018
  • Matching level: species

strain history

@refhistory
16841<- CCUG <- O. Nedashkovskaya, KMM
116455CIP <- 2004, CCUG <- 2002, KMM

doi: 10.13145/bacdive17704.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Algoriphagus
  • species: Algoriphagus aquimarinus
  • full scientific name: Algoriphagus aquimarinus Nedashkovskaya et al. 2004

@ref: 16841

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus aquimarinus

full scientific name: Algoriphagus aquimarinus Nedashkovskaya et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30078negative6 µm0.6 µmrod-shapedno
69480no93.163
69480negative99.975
116455negativerod-shapedno

colony morphology

  • @ref: 116455

pigmentation

  • @ref: 30078
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16841BACTO 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
36749Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116455CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16841positivegrowth28mesophilic
30078positivegrowth04-34
30078positiveoptimum24psychrophilic
36749positivegrowth30mesophilic
57508positivegrowth30mesophilic
116455positivegrowth15-30
116455nogrowth5psychrophilic
116455nogrowth37mesophilic
116455nogrowth41thermophilic
116455nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30078aerobe
57508aerobe
116455facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30078NaClpositivegrowth0-10 %
30078NaClpositiveoptimum5 %
116455NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3007822599arabinose+carbon source
3007817057cellobiose+carbon source
3007833984fucose+carbon source
300785291gelatin+carbon source
3007817234glucose+carbon source
3007817716lactose+carbon source
3007829864mannitol+carbon source
3007837684mannose+carbon source
3007828053melibiose+carbon source
30078506227N-acetylglucosamine+carbon source
3007826546rhamnose+carbon source
3007817992sucrose+carbon source
3007853424tween 20+carbon source
3007853423tween 40+carbon source
3007853426tween 80+carbon source
3007818222xylose+carbon source
300784853esculin+hydrolysis
1164554853esculin-hydrolysis
116455606565hippurate+hydrolysis
11645517632nitrate+reduction
11645516301nitrite-reduction
11645515792malonate-assimilation
11645517632nitrate+respiration

metabolite production

  • @ref: 116455
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11645515688acetoin+
11645517234glucose+

enzymes

@refvalueactivityec
30078alkaline phosphatase+3.1.3.1
30078catalase+1.11.1.6
30078gelatinase+
30078cytochrome oxidase+1.9.3.1
116455oxidase+
116455beta-galactosidase+3.2.1.23
116455alcohol dehydrogenase+1.1.1.1
116455gelatinase+
116455amylase-
116455caseinase+3.4.21.50
116455catalase+1.11.1.6
116455tween esterase+
116455gamma-glutamyltransferase-2.3.2.2
116455lecithinase-
116455lipase-
116455lysine decarboxylase-4.1.1.18
116455ornithine decarboxylase-4.1.1.17
116455phenylalanine ammonia-lyase-4.3.1.24
116455protease+
116455tryptophan deaminase-
116455urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116455-+++-+++--++++-++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116455-------------+----+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountry
16841sea-water sampleSea of Japan, Amursky Bay
57508SeawaterSea of Japan,Amursky Bay2000-06-01Pacific Ocean
116455Environment, Sea waterPacific OceanSea of Japan

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_65987.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2082;97_5333;98_16596;99_65987&stattab=map
  • Last taxonomy: Algoriphagus
  • 16S sequence: AJ575264
  • Sequence Identity:
  • Total samples: 197
  • soil counts: 16
  • aquatic counts: 141
  • animal counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
168411Risk group (German classification)
1164551Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16841
  • description: Rhodovirga aquimarina 16S rRNA gene, strain LMG 21971
  • accession: AJ575264
  • length: 1473
  • database: ena
  • NCBI tax ID: 237018

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus aquimarinus DSM 23399GCA_900112005scaffoldncbi237018
66792Algoriphagus aquimarinus strain DSM 23399237018.6wgspatric237018
66792Algoriphagus aquimarinus DSM 233992634166319draftimg237018

GC content

@refGC-content
1684141.0
3007841

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.397yes
flagellatedno96.837yes
gram-positiveno97.608no
anaerobicno99.1yes
aerobicyes90.042yes
halophileno62.989no
spore-formingno94.964no
glucose-fermentno90.014no
thermophileno99.474yes
glucose-utilyes90.363yes

External links

@ref: 16841

culture collection no.: DSM 23399, CCUG 47101, KMM 3958, LMG 21971, CIP 108555

straininfo link

  • @ref: 86695
  • straininfo: 93524

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388741
  • title: Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004.
  • authors: Nedashkovskaya OI, Vancanneyt M, Van Trappen S, Vandemeulebroecke K, Lysenko AM, Rohde M, Falsen E, Frolova GM, Mikhailov VV, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02915-0
  • year: 2004
  • mesh: Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Eukaryota/*microbiology, Fatty Acids/analysis, Genes, rRNA, Growth Inhibitors/pharmacology, Japan, Microbial Sensitivity Tests, Molecular Sequence Data, Movement, Nitrates/metabolism, Oxidation-Reduction, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16841Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23399)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23399
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
30078Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2643528776041
36749Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6190
57508Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47101)https://www.ccug.se/strain?id=47101
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
86695Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93524.1StrainInfo: A central database for resolving microbial strain identifiers
116455Curators of the CIPCollection of Institut Pasteur (CIP 108555)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108555