Strain identifier

BacDive ID: 138458

Type strain: Yes

Species: Isoptericola dokdonensis

Strain Designation: DS-3

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-3

NCBI tax ID(s): 372663 (species)

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General

@ref: 39794

BacDive-ID: 138458

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Isoptericola dokdonensis DS-3 is an aerobe, mesophilic, Gram-positive bacterium of the family Promicromonosporaceae.

NCBI tax id

  • NCBI tax id: 372663
  • Matching level: species

strain history

@refhistory
67770CIP 108921 <-- J.-H. Yoon DS-3.
67771<- JH Yoon, KRIBB
39794CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-3

doi: 10.13145/bacdive138458.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Isoptericola
  • species: Isoptericola dokdonensis
  • full scientific name: Isoptericola dokdonensis Yoon et al. 2006

@ref: 39794

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Promicromonosporaceae

genus: Isoptericola

species: Isoptericola dokdonensis

strain designation: DS-3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
39794positivecoccus-shapedno

colony morphology

  • @ref: 39794

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39794MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
39794CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
39794positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
39794nitrate+reduction17632
39794nitrite-reduction16301

metabolite production

  • @ref: 39794
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
39794oxidase+
39794alcohol dehydrogenase-1.1.1.1
39794lysine decarboxylase-4.1.1.18
39794ornithine decarboxylase-4.1.1.17
39794urease-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
39794-+++++----++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39794+--+-+--+/-++++-+/--------+/-++++++/--++---++-++------+-+

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
39794Dokdo islandRepublic of KoreaKORAsia
67770Soil
67771DokdoRepublic of KoreaKORAsiaFrom soil
39794Dokdo IslandRepublic of KoreaKORAsiaEnvironment, Soil2004

taxonmaps

  • @ref: 69479
  • File name: preview.99_7019.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_2608;99_7019&stattab=map
  • Last taxonomy: Isoptericola
  • 16S sequence: DQ387860
  • Sequence Identity:
  • Total samples: 195
  • soil counts: 82
  • aquatic counts: 31
  • animal counts: 53
  • plant counts: 29

Safety information

risk assessment

  • @ref: 39794
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67771
  • description: Isoptericola dokdonensis strain DS-3 16S ribosomal RNA gene, partial sequence
  • accession: DQ387860
  • length: 1474
  • database: ena
  • NCBI tax ID: 372663

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Isoptericola dokdonensis DS-3GCA_001636295completencbi1300344
66792Isoptericola dokdonensis DS-31300344.3completepatric1300344
66792Isoptericola dokdonensis DS-32687453494completeimg1300344

GC content

  • @ref: 67770
  • GC-content: 74.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.826no
gram-positiveyes87.987yes
anaerobicno99.487yes
aerobicyes91.11yes
halophileno85.561no
spore-formingno83.571no
thermophileno98.669no
glucose-utilyes89.191no
motileno93.006no
glucose-fermentno75.719no

External links

@ref: 39794

culture collection no.: CIP 108921, KCTC 19128, JCM 15137

straininfo link

  • @ref: 95181
  • straininfo: 297246

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158994Isoptericola dokdonensis sp. nov., isolated from soil.Yoon JH, Schumann P, Kang SJ, Jung SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64430-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny19661504Isoptericola jiangsuensis sp. nov., a chitin-degrading bacterium.Wu Y, Li WJ, Tian W, Zhang LP, Xu L, Shen QR, Shen BInt J Syst Evol Microbiol10.1099/ijs.0.012864-02009Actinomycetales/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, *Bathing Beaches, China, Chitin/*metabolism, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Species SpecificityGenetics
Phylogeny34724179Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola.Bae Y, Lee S, Kim K, Lee HK, Kwon SK, Kim JFJ Microbiol10.1007/s12275-021-1452-62021Actinobacteria/classification/*enzymology/*genetics/isolation & purification, Bacterial Proteins/genetics/*metabolism, Cellulase/genetics/*metabolism, Cellulose/metabolism, Genome, Bacterial, Genomics, Multigene Family, Phylogeny, Republic of Korea, *Soil MicrobiologyGenetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
39794Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108921Collection of Institut Pasteur (CIP 108921)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
95181Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID297246.1