Strain identifier

BacDive ID: 17706

Type strain: Yes

Species: Algoriphagus yeomjeoni

Strain Designation: MSS-160

Strain history: CIP <- 2005, JCM <- J. H. Yoon, KRIBB: strain MSS-160

NCBI tax ID(s): 291403 (species)

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General

@ref: 17214

BacDive-ID: 17706

DSM-Number: 23446

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

description: Algoriphagus yeomjeoni MSS-160 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine solar saltern.

NCBI tax id

  • NCBI tax id: 291403
  • Matching level: species

strain history

@refhistory
17214<- KCTC; KCTC 12309 <- ; MSS-160
67770J.-H. Yoon MSS-160.
67771<- JH Yoon, KRIBB
124015CIP <- 2005, JCM <- J. H. Yoon, KRIBB: strain MSS-160

doi: 10.13145/bacdive17706.20230509.8.1

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 yeomjeoni
  • full scientific name: Algoriphagus yeomjeoni Yoon et al. 2005

@ref: 17214

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus yeomjeoni

full scientific name: Algoriphagus yeomjeoni Yoon et al. 2005

strain designation: MSS-160

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31404negative2 µm0.55 µmrod-shapedno
67771rod-shapedno
67771negative
69480no94.915
69480negative99.989
124015negativerod-shapedno

colony morphology

  • @ref: 124015

pigmentation

  • @ref: 31404
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17214BACTO 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
40057Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
124015CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
17214positivegrowth28mesophilic
31404positivegrowth25-30mesophilic
31404positiveoptimum27.5mesophilic
40057positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth25-30mesophilic
124015positivegrowth30mesophilic
124015nogrowth37mesophilic
124015nogrowth41thermophilic

culture pH

@refabilitytypepH
31404positivegrowth05-08
31404positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31404aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
31404NaClpositivegrowth<9 %
31404NaClpositiveoptimum4.5 %

observation

@refobservation
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3140417057cellobiose+carbon source
3140428757fructose+carbon source
3140428260galactose+carbon source
314045291gelatin+carbon source
3140417234glucose+carbon source
3140417716lactose+carbon source
3140417306maltose+carbon source
3140428053melibiose+carbon source
3140416634raffinose+carbon source
3140426546rhamnose+carbon source
3140417814salicin+carbon source
3140417992sucrose+carbon source
3140427082trehalose+carbon source
3140453424tween 20+carbon source
3140453423tween 40+carbon source
3140453425tween 60+carbon source
3140453426tween 80+carbon source
314044853esculin+hydrolysis
12401517632nitrate-reduction
12401516301nitrite-reduction

enzymes

@refvalueactivityec
31404cytochrome oxidase+1.9.3.1
124015oxidase+
124015alcohol dehydrogenase-1.1.1.1
124015catalase+1.11.1.6
124015lysine decarboxylase-4.1.1.18
124015ornithine decarboxylase-4.1.1.17
124015urease-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
124015-+++-++++++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17214marine solar salternYellow SeaRepublic of KoreaKORAsia
67770Marine solar saltern in the Yellow SeaRepublic of KoreaKORAsia
67771From marine solar saltern in the Yellow SeaRepublic of KoreaKORAsia
124015Marine solar salternYellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Condition#Saline
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_9174.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2082;97_5333;98_6743;99_9174&stattab=map
  • Last taxonomy: Algoriphagus
  • 16S sequence: AY699794
  • Sequence Identity:
  • Total samples: 368
  • soil counts: 18
  • aquatic counts: 307
  • animal counts: 38
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172141Risk group (German classification)
1240151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17214
  • description: Algoriphagus yeomjeoni strain MSS-160 16S ribosomal RNA gene, partial sequence
  • accession: AY699794
  • length: 1476
  • database: ena
  • NCBI tax ID: 291403

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus yeomjeoni DSM 23446GCA_003259505scaffoldncbi291403
66792Algoriphagus yeomjeoni strain DSM 23446291403.6wgspatric291403
66792Algoriphagus yeomjeoni DSM 234462593339292draftimg291403

GC content

@refGC-contentmethod
3140441
6777041high performance liquid chromatography (HPLC)
6777141.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.609yes
flagellatedno97.284yes
gram-positiveno97.796yes
anaerobicno98.645yes
aerobicyes87.906no
halophileno64.022yes
spore-formingno95.087no
glucose-utilyes90.061yes
thermophileno98.833no
glucose-fermentno89.443no

External links

@ref: 17214

culture collection no.: DSM 23446, CIP 108748, JCM 12598, KCTC 12309

straininfo link

  • @ref: 86697
  • straininfo: 137990

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774676Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern in the Yellow Sea, Korea.Yoon JH, Kang SJ, Jung SY, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63479-02005Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium ChlorideGenetics
Phylogeny34623951Penaeicolahalotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond.Ali S, Xie J, Chen Y, Cai R, Juventus AJ, Hu Z, Zhang Y, Wang HInt J Syst Evol Microbiol10.1099/ijsem.0.0050472021Aquaculture, Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Ponds, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17214Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23446)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23446
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
31404Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2771328776041
40057Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6411
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86697Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137990.1StrainInfo: A central database for resolving microbial strain identifiers
124015Curators of the CIPCollection of Institut Pasteur (CIP 108748)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108748