Strain identifier

BacDive ID: 17700

Type strain: Yes

Species: Algoriphagus mannitolivorans

Strain Designation: JC2050

Strain history: CIP <- 2004, J. Chun, Seoul, Korea: strain JC2050

NCBI tax ID(s): 1120965 (strain), 226504 (species)

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General

@ref: 5835

BacDive-ID: 17700

DSM-Number: 15301

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

description: Algoriphagus mannitolivorans JC2050 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample of getbol.

NCBI tax id

NCBI tax idMatching level
226504species
1120965strain

strain history

@refhistory
5835<- J. Chun; JC2050
339372004, J. Chun, Seoul, Korea: strain JC2050
67771<- J Chun, Seoul Nat. Univ.
120781CIP <- 2004, J. Chun, Seoul, Korea: strain JC2050

doi: 10.13145/bacdive17700.20230509.8.1

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 mannitolivorans
  • full scientific name: Algoriphagus mannitolivorans (Yi and Chun 2004) Nedashkovskaya et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Hongiella mannitolivorans

@ref: 5835

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus mannitolivorans

full scientific name: Algoriphagus mannitolivorans (Yi and Chun 2004) Nedashkovskaya et al. 2007 emend. Shahina et al. 2014

strain designation: JC2050

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30033negative1.1-1.7 µm0.4-0.5 µmrod-shapedno
67771rod-shapedno
67771negative
69480no94.124
69480negative99.99
120781negativerod-shapedno

colony morphology

  • @ref: 120781

pigmentation

  • @ref: 30033
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5835BACTO 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
33937Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120781CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5835positivegrowth37mesophilic
30033positivegrowth35-40
30033positiveoptimum37.5mesophilic
33937positivegrowth37mesophilic
67771positivegrowth35-40
120781positivegrowth15-41
120781nogrowth5psychrophilic
120781nogrowth45thermophilic

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
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
30033NaClpositiveoptimum1 %
120781NaClnogrowth0 %
120781NaClnogrowth2 %
120781NaClnogrowth4 %
120781NaClnogrowth6 %
120781NaClnogrowth8 %
120781NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3003329864mannitol+carbon source
3003317632nitrate+reduction
1207814853esculin+hydrolysis
120781606565hippurate+hydrolysis
12078117632nitrate+reduction
12078116301nitrite-reduction
12078115792malonate-assimilation
12078117632nitrate-respiration

antibiotic resistance

  • @ref: 120781
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120781
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12078115688acetoin-
12078117234glucose-

enzymes

@refvalueactivityec
30033catalase+1.11.1.6
30033gelatinase+
30033cytochrome oxidase+1.9.3.1
120781oxidase+
120781beta-galactosidase+3.2.1.23
120781alcohol dehydrogenase-1.1.1.1
120781gelatinase+/-
120781amylase+
120781caseinase+3.4.21.50
120781catalase+1.11.1.6
120781tween esterase-
120781gamma-glutamyltransferase+2.3.2.2
120781lecithinase-
120781lipase-
120781lysine decarboxylase-4.1.1.18
120781ornithine decarboxylase-4.1.1.17
120781phenylalanine ammonia-lyase-4.3.1.24
120781protease-
120781tryptophan deaminase-
120781urease-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
120781-+++-+++++++++-++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120781-------------+----+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
5835sediment sample of getbolKorea, Ganghwa islandRepublic of KoreaKORAsia
67771From tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia37.5922126.457
120781Environment, Sample of tidal flat sediment from Ganghwa IslandGanghwa IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4179.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2115;97_2548;98_3154;99_4179&stattab=map
  • Last taxonomy: Algoriphagus mannitolivorans
  • 16S sequence: AY264838
  • Sequence Identity:
  • Total samples: 44
  • soil counts: 12
  • aquatic counts: 24
  • animal counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58351Risk group (German classification)
1207811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5835
  • description: Algoriphagus mannitolivorans strain JC2050 16S ribosomal RNA gene, partial sequence
  • accession: AY264838
  • length: 1446
  • database: ena
  • NCBI tax ID: 226504

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus mannitolivorans DSM 15301GCA_000429425scaffoldncbi1120965
66792Algoriphagus mannitolivorans DSM 153011120965.3wgspatric1120965
66792Algoriphagus mannitolivorans DSM 153012523533553draftimg1120965

GC content

@refGC-content
3003342
6777142.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.155yes
flagellatedno98.177yes
gram-positiveno97.324no
anaerobicno98.798yes
aerobicyes85.728yes
halophileno87.771yes
spore-formingno95.256yes
thermophileno96.662no
glucose-utilyes88.263no
glucose-fermentno86.685no

External links

@ref: 5835

culture collection no.: DSM 15301, IMSNU 14012, KCTC 12050, CIP 108302

straininfo link

  • @ref: 86691
  • straininfo: 97542

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
Phylogeny19542135Algoriphagus aquatilis sp. nov., isolated from a freshwater lake.Liu Y, Li H, Jiang JT, Liu YH, Song XF, Xu CJ, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.005215-02009Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny23332681Algoriphagus shivajiensis sp. nov., isolated from Cochin back water, India.Kumar PA, Bhumika V, Ritika C, Bhaskar YV, Priyashanth P, Aravind R, Bindu E, Srinivas TNSyst Appl Microbiol10.1016/j.syapm.2012.11.0062013Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gelatin/metabolism, Hydrolysis, India, Molecular Sequence Data, Oxidoreductases/metabolism, Phospholipids/metabolism, Phylogeny, Pigments, Biological/metabolism, Polysorbates/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyMetabolism
Phylogeny25213549Description of Algoriphagus taiwanensis sp. nov., a xylanolytic bacterium isolated from surface seawater, and emended descriptions of Algoriphagus mannitolivorans, Algoriphagus olei, Algoriphagus aquatilis and Algoriphagus ratkowskyi.Shahina M, Hameed A, Lin SY, Lai WA, Hsu YH, Young CCAntonie Van Leeuwenhoek10.1007/s10482-014-0272-72014Aerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analysis, Xylans/*metabolismMetabolism
Phylogeny31663498Algoriphagus sanaruensis sp. nov., a member of the family Cyclobacteriaceae, isolated from a brackish lake in Hamamatsu, Japan.Maejima Y, Iino T, Muraguchi Y, Ohkuma M, Kimbara K, Shintani MInt J Syst Evol Microbiol10.1099/ijsem.0.0034472019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5835Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15301)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15301
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
33937Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5910
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
86691Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97542.1StrainInfo: A central database for resolving microbial strain identifiers
120781Curators of the CIPCollection of Institut Pasteur (CIP 108302)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108302