Strain identifier

BacDive ID: 14104

Type strain: Yes

Species: Pedobacter insulae

Strain Designation: DS-139, DS-39

Strain history: CIP <- 2007, KCTC <- J.H. Yoon, KRIBB, Teajon, Korea: strain DS-139

NCBI tax ID(s): 414048 (species)

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General

@ref: 7658

BacDive-ID: 14104

DSM-Number: 18684

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

description: Pedobacter insulae DS-139 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 414048
  • Matching level: species

strain history

@refhistory
7658<- J.-H. Yoon, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); DS-39 <- J.-H. Yoon et al.
67771<- JH Yoon, KRIBB
120140CIP <- 2007, KCTC <- J.H. Yoon, KRIBB, Teajon, Korea: strain DS-139

doi: 10.13145/bacdive14104.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter insulae
  • full scientific name: Pedobacter insulae Yoon et al. 2007

@ref: 7658

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter insulae

full scientific name: Pedobacter insulae Yoon et al. 2007

strain designation: DS-139, DS-39

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32115negative3.35 µm0.4 µmrod-shapedno
67771rod-shapedno
67771negative
120140negativerod-shapedyes
69480negative97.5
69480no90.345

pigmentation

  • @ref: 32115
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7658TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
37832MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120140CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7658positivegrowth25
32115positivegrowth04-31
32115positiveoptimum30
37832positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepHPH range
32115positivegrowth06-10alkaliphile
32115positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32115aerobe
67771aerobe
120140obligate aerobe

spore formation

@refspore formationconfidence
32115no
69481no100

halophily

@refsaltgrowthtested relationconcentration
32115NaClpositivegrowth<2 %
32115NaClpositiveoptimum0.25 %

observation

@refobservation
32115aggregates in clumps
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3211515963ribitol+carbon source
3211522599arabinose+carbon source
3211517057cellobiose+carbon source
3211517234glucose+carbon source
3211517754glycerol+carbon source
3211528087glycogen+carbon source
3211517716lactose+carbon source
3211517306maltose+carbon source
3211537684mannose+carbon source
3211528053melibiose+carbon source
32115506227N-acetylglucosamine+carbon source
3211526546rhamnose+carbon source
3211517814salicin+carbon source
3211517992sucrose+carbon source
3211527082trehalose+carbon source
3211518222xylose+carbon source
321154853esculin+hydrolysis
12014017632nitrate-reduction
12014016301nitrite-reduction

metabolite production

  • @ref: 120140
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32115acid phosphatase+3.1.3.2
32115catalase+1.11.1.6
32115cytochrome oxidase+1.9.3.1
120140oxidase-
120140catalase-1.11.1.6
120140urease-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
120140-+++++++-+++--+++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7658soil sampleDokdo island (37° 14' 12'' N 131° 52' 07'' E)Republic of KoreaKORAsia37.2367131.869
67771From soilDokdoRepublic of KoreaKORAsia
120140Environment, Soil sampleDokdo IslandRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76581Risk group (German classification)
1201401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7658
  • description: Pedobacter insulae strain DS-139 16S ribosomal RNA gene, partial sequence
  • accession: EF100697
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 414048

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter insulae DSM 18684GCA_900113525contigncbi414048
66792Pedobacter insulae strain DSM 18684414048.7wgspatric414048
66792Pedobacter insulae DSM 186842634166297draftimg414048

GC content

@refGC-contentmethod
765839.4high performance liquid chromatography (HPLC)
3211539.4

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.349yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.036yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.386yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.761yes
69480flagellatedmotile2+Ability to perform flagellated movementno90.345no

External links

@ref: 7658

culture collection no.: DSM 18684, KCTC 12820, CIP 109748

straininfo link

  • @ref: 83271
  • straininfo: 309551

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766862Pedobacter insulae sp. nov., isolated from soil.Yoon JH, Kang SJ, Oh HW, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64986-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/*isolation & purification/physiology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Locomotion/physiology, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Phylogeny21257683Pedobacter boryungensis sp. nov., isolated from soil.Jung YT, Lee SY, Choi WC, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.028183-02011Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny25613852Pedobacter lotistagni sp. nov. isolated from lotus pond water.Singh H, Du J, Ngo HT, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0387-52015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, Lotus/growth & development, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7658Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18684
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
32115Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2836028776041
37832Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7526
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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
83271Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309551.1StrainInfo: A central database for resolving microbial strain identifiers
120140Curators of the CIPCollection of Institut Pasteur (CIP 109748)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109748