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, mesophilic, Gram-negative, rod-shaped

description: Algoriphagus terrigena DS-44 is an aerobe, mesophilic, Gram-negative 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/bacdive17708.20250331.9.3

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
125438no90
125438negative97.5
125439negative99.8
123474negativeoval-shapedno

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

@refspore formationconfidence
31708no
125439no99.6

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
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
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
68382alpha-mannosidase+3.2.1.24
68382alpha-galactosidase-3.2.1.22
68382lipase (C 14)-

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe69.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetmotilityAbility to perform movementno54.1
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.985yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.825no
125438spore-formingspore-formingAbility to form endo- or exosporesno81.483yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.95yes
125438motile2+flagellatedAbility 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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1