Strain identifier

BacDive ID: 17708

Type strain: Yes

Species: Algoriphagus terrigena

Strain Designation: DS-44

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, South Korea: strain DS-44

NCBI tax ID(s): 1120967 (strain), 344884 (species)

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General

@ref: 16462

BacDive-ID: 17708

DSM-Number: 22685

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

description: Algoriphagus terrigena DS-44 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
344884species
1120967strain

strain history

@refhistory
16462<- CIP <- J. H. Yoon, KRIBB; DS-44
67771<- JH Yoon, KRIBB
123474CIP <- 2005, J. H. Yoon, KRIBB, Taejon, South Korea: strain DS-44

doi: 10.13145/bacdive17708.20240916.9.1

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 terrigena
  • full scientific name: Algoriphagus terrigena Yoon et al. 2006

@ref: 16462

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus terrigena

full scientific name: Algoriphagus terrigena Yoon et al. 2006 emend. Hahnke et al. 2016

strain designation: DS-44

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31708negative0.8-2.5 µm0.4-0.6 µmrod-shapedno
67771rod-shapedno
67771negative
123474negativeoval-shapedno
69480no90
69480negative97.5

pigmentation

  • @ref: 31708
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16462BACTO 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
38333Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123474CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
16462positivegrowth25
31708positivegrowth10-36
31708positiveoptimum25
38333positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepH
31708positivegrowth5.5-7.5
31708positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31708aerobe
67771aerobe

spore formation

  • @ref: 31708
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31708NaClpositivegrowth02-06 %
31708NaClpositiveoptimum2 %

observation

@refobservation
31708aggregates in chains
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170817057cellobiose+carbon source
3170828757fructose+carbon source
3170828260galactose+carbon source
3170817306maltose+carbon source
3170817814salicin+carbon source
3170817992sucrose+carbon source
3170827082trehalose+carbon source
3170818222xylose+carbon source
317084853esculin+hydrolysis
12347417632nitrate+reduction
12347416301nitrite-reduction

metabolite production

  • @ref: 123474
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123474oxidase+
123474alcohol dehydrogenase-1.1.1.1
123474catalase+1.11.1.6
123474lysine decarboxylase-4.1.1.18
123474ornithine decarboxylase-4.1.1.17
123474urease-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
123474-+-+-+--++++-+-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16462soilDokdoRepublic of KoreaKORAsia
67771From soilDokdoRepublic of KoreaKORAsia
123474Environment, SoilDokdo IslandRepublic of KoreaKORAsia2004

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2294.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_1239;97_1470;98_1792;99_2294&stattab=map
  • Last taxonomy: Algoriphagus terrigena
  • 16S sequence: DQ178979
  • Sequence Identity:
  • Total samples: 732
  • soil counts: 108
  • aquatic counts: 329
  • animal counts: 281
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164621Risk group (German classification)
1234741Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16462
  • description: Algoriphagus terrigena strain DS-44 16S ribosomal RNA gene, partial sequence
  • accession: DQ178979
  • length: 1479
  • database: nuccore
  • NCBI tax ID: 344884

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus terrigena DSM 22685GCA_000429445scaffoldncbi1120967
66792Algoriphagus terrigena DSM 226851120967.3wgspatric1120967
66792Algoriphagus terrigena DSM 226852523231064draftimg1120967

GC content

@refGC-contentmethod
1646249.0high performance liquid chromatography (HPLC)
3170849
1646247.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.985yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.825no
69480spore-formingspore-formingAbility to form endo- or exosporesno81.483yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.95yes
69480flagellatedmotile2+Ability to perform flagellated movementno90yes

External links

@ref: 16462

culture collection no.: DSM 22685, CIP 108837, KCTC 12545

straininfo link

  • @ref: 86699
  • straininfo: 290955

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585693Algoriphagus terrigena sp. nov., isolated from soil.Yoon JH, Lee MH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64092-02006Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, *Soil MicrobiologyGenetics
Phylogeny21460141Algoriphagus jejuensis sp. nov., isolated from seawater.Lee DH, Kahng HY, Lee SBInt J Syst Evol Microbiol10.1099/ijs.0.030106-02011Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16462Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22685)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22685
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
31708Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2798528776041
38333Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6511
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)
86699Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290955.1StrainInfo: A central database for resolving microbial strain identifiers
123474Curators of the CIPCollection of Institut Pasteur (CIP 108837)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108837