Strain identifier

BacDive ID: 17698

Type strain: Yes

Species: Algoriphagus halophilus

Strain Designation: JC2051

Strain history: CIP <- 2004, J. Chun, Seoul, Korea: strain JC2051

NCBI tax ID(s): 226505 (species)

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General

@ref: 5830

BacDive-ID: 17698

DSM-Number: 15292

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

description: Algoriphagus halophilus JC2051 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample of getbol.

NCBI tax id

  • NCBI tax id: 226505
  • Matching level: species

strain history

@refhistory
5830<- J. Chun; JC2051
367172004, J. Chun, Seoul, Korea: strain JC2051
67771<- J Chun, Seoul Univ.
119812CIP <- 2004, J. Chun, Seoul, Korea: strain JC2051

doi: 10.13145/bacdive17698.20230509.8.1

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 halophilus
  • full scientific name: Algoriphagus halophilus (Yi and Chun 2004) Nedashkovskaya et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Hongiella halophila

@ref: 5830

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus halophilus

full scientific name: Algoriphagus halophilus (Yi and Chun 2004) Nedashkovskaya et al. 2004

strain designation: JC2051

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30033negative1-1.8 µm0.3-0.5 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.998
119812negativerod-shapedno

colony morphology

  • @ref: 119812

pigmentation

@refproductionname
30033yes
119812noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5830BACTO 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
36717Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119812CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5830positivegrowth35mesophilic
30033positiveoptimum35mesophilic
36717positivegrowth37mesophilic
67771positivegrowth35mesophilic
119812positivegrowth15-37
119812nogrowth5psychrophilic
119812nogrowth41thermophilic
119812nogrowth45thermophilic

culture pH

  • @ref: 30033
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30033aerobe
67771aerobe

spore formation

@refspore formationconfidence
30033no
69481no100
69480no99.915

halophily

@refsaltgrowthtested relationconcentration
30033NaClpositiveoptimum5 %
119812NaClnogrowth0 %
119812NaClnogrowth2 %
119812NaClnogrowth4 %
119812NaClnogrowth6 %
119812NaClnogrowth8 %
119812NaClnogrowth10 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3003328757fructose+carbon source
3003318257ornithine+carbon source
1198124853esculin+hydrolysis
119812606565hippurate+hydrolysis
11981217632nitrate-reduction
11981216301nitrite-reduction
11981215792malonate-assimilation

metabolite production

  • @ref: 119812
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11981215688acetoin-
11981217234glucose-

enzymes

@refvalueactivityec
30033catalase+1.11.1.6
30033gelatinase+
30033cytochrome oxidase+1.9.3.1
119812oxidase+
119812beta-galactosidase-3.2.1.23
119812alcohol dehydrogenase-1.1.1.1
119812gelatinase+/-
119812amylase-
119812DNase-
119812caseinase-3.4.21.50
119812catalase+1.11.1.6
119812tween esterase-
119812gamma-glutamyltransferase+2.3.2.2
119812lecithinase-
119812lipase-
119812lysine decarboxylase-4.1.1.18
119812ornithine decarboxylase-4.1.1.17
119812phenylalanine ammonia-lyase-4.3.1.24
119812tryptophan deaminase-
119812urease-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
119812-+++-++++++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
5830sediment sample of getbolKorea, Ganghwa islandRepublic of KoreaKORAsia
67771From tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia37.5922126.457
119812Environment, Sediment sample of getbolGanghwa islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_8271.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2463;97_3006;98_6024;99_8271&stattab=map
  • Last taxonomy: Algoriphagus
  • 16S sequence: AY264839
  • Sequence Identity:
  • Total samples: 420
  • soil counts: 82
  • aquatic counts: 282
  • animal counts: 32
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58301Risk group (German classification)
1198121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5830
  • description: Algoriphagus halophilus strain JC2051 16S ribosomal RNA gene, partial sequence
  • accession: AY264839
  • length: 1440
  • database: ena
  • NCBI tax ID: 226505

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus halophilus DSM 15292GCA_900129785scaffoldncbi226505
66792Algoriphagus halophilus strain DSM 15292226505.5wgspatric226505
66792Algoriphagus halophilus DSM 152922698536714draftimg226505

GC content

@refGC-content
3003337
6777137.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.091yes
flagellatedno96.973no
gram-positiveno98.224yes
anaerobicno98.773yes
aerobicyes90.238yes
halophileno71.431no
spore-formingno95.545yes
thermophileno98.721no
glucose-utilyes91.007no
glucose-fermentno89.378no

External links

@ref: 5830

culture collection no.: DSM 15292, IMSNU 14013, KCTC 12051, CIP 108304

straininfo link

  • @ref: 86689
  • straininfo: 97543

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14742474Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment.Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.02861-02004Bacteroides/classification, Carbohydrate Metabolism, Cytophaga/classification, Cytophagaceae/*classification/genetics/isolation & purification/ultrastructure, DNA, Ribosomal/genetics, Flavobacterium/classification, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny19648320Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment.Park S, Kang SJ, Oh KH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.012682-02009Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny22544791Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment.Kang H, Weerawongwiwat V, Jung MY, Myung SC, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.039214-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny26297134Algoriphagus aestuarii sp. nov., a member of the Cyclobacteriaceae isolated from a tidal-flat sediment of the Yellow Sea in Korea.Jung YT, Lee JS, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0004342015Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15292
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
30033Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2639628776041
36717Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5912
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86689Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97543.1StrainInfo: A central database for resolving microbial strain identifiers
119812Curators of the CIPCollection of Institut Pasteur (CIP 108304)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108304