Strain identifier

BacDive ID: 17703

Type strain: Yes

Species: Algoriphagus ratkowskyi

Strain Designation: IC025

Strain history: CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain IC025

NCBI tax ID(s): 57028 (species)

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General

@ref: 16463

BacDive-ID: 17703

DSM-Number: 22686

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Algoriphagus ratkowskyi IC025 is a mesophilic bacterium that was isolated from sea-ice algal assemblage.

NCBI tax id

  • NCBI tax id: 57028
  • Matching level: species

strain history

@refhistory
16463<- CIP <- J. Bowman, Univ. Tasmania, Australia
338002002, J. Bowman, Tasmania Univ., Tasmania, Australie: strain IC025
122142CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain IC025

doi: 10.13145/bacdive17703.20230509.8.1

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 ratkowskyi
  • full scientific name: Algoriphagus ratkowskyi Bowman et al. 2003

@ref: 16463

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus ratkowskyi

full scientific name: Algoriphagus ratkowskyi Bowman et al. 2003 emend. Shahina et al. 2014

strain designation: IC025

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.765
6948099.983negative
122142nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16463BACTO 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
33800Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122142CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16463positivegrowth28mesophilic
33800positivegrowth10psychrophilic
122142positivegrowth10psychrophilic
122142nogrowth25mesophilic
122142nogrowth30mesophilic
122142nogrowth37mesophilic
122142nogrowth41thermophilic
122142nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
122142NaClpositivegrowth0-8 %
122142NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12214216947citrate-carbon source
1221424853esculin+hydrolysis
122142606565hippurate+hydrolysis
12214217632nitrate-reduction
12214216301nitrite+reduction
12214217632nitrate-respiration

metabolite production

  • @ref: 122142
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12214215688acetoin-
12214217234glucose-

enzymes

@refvalueactivityec
122142oxidase+
122142beta-galactosidase+3.2.1.23
122142alcohol dehydrogenase-1.1.1.1
122142gelatinase+/-
122142amylase-
122142caseinase+3.4.21.50
122142catalase+1.11.1.6
122142tween esterase+
122142gamma-glutamyltransferase+2.3.2.2
122142lecithinase-
122142lipase-
122142lysine decarboxylase-4.1.1.18
122142ornithine decarboxylase-4.1.1.17
122142phenylalanine ammonia-lyase-4.3.1.24
122142protease-
122142tryptophan deaminase-
122142urease-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
122142-+++-++--+++++--+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122142------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
16463sea-ice algal assemblagePrdyz BayAustralia and Oceania
122142Environment, Sea iceAntarcticaAntarcticaATA1996

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Aquatic#Marine
#Host#Algae

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164631Risk group (German classification)
1221421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16463Algoriphagus ratkowskyi 16S rRNA gene, type strain LMG 21435AJ6086411436ena57028
16463Marine psychrophile IC025 16S ribosomal RNA gene, partial sequenceU858911484ena57028

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus ratkowskyi DSM 22686GCA_003254355scaffoldncbi57028
66792Algoriphagus ratkowskyi DSM 22686GCA_002150505contigncbi57028
66792Algoriphagus ratkowskyi strain DSM 2268657028.4wgspatric57028
66792Algoriphagus ratkowskyi strain DSM 2268657028.6wgspatric57028
66792Algoriphagus ratkowskyi DSM 226862593339288draftimg57028

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.47no
gram-positiveno98.123no
anaerobicno98.888no
halophileno65.758no
spore-formingno95.568no
aerobicyes90.134no
glucose-utilyes89.273no
thermophileno99.11no
motileno91.106no
glucose-fermentno91.344no

External links

@ref: 16463

culture collection no.: DSM 22686, ACAM 646, CIP 107452, LMG 21435

straininfo link

  • @ref: 86694
  • straininfo: 86445

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/urltitle
16463Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22686)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22686
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
33800Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4889
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
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
86694Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86445.1StrainInfo: A central database for resolving microbial strain identifiers
122142Curators of the CIPCollection of Institut Pasteur (CIP 107452)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107452