Strain identifier

BacDive ID: 134185

Type strain: Yes

Species: Pedobacter sandarakinus

Strain Designation: DS-27

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-27

NCBI tax ID(s): 353156 (species)

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General

@ref: 31736

BacDive-ID: 134185

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

description: Pedobacter sandarakinus DS-27 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from From soil.

NCBI tax id

  • NCBI tax id: 353156
  • Matching level: species

strain history

@refhistory
67771<- JH Yoon, KRIBB
122414CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-27

doi: 10.13145/bacdive134185.20230509.8.1

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 sandarakinus
  • full scientific name: Pedobacter sandarakinus Yoon et al. 2006

@ref: 31736

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter sandarakinus

strain designation: DS-27

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31736negative0.7-4 µm0.3-0.5 µmrod-shapedno
67771rod-shaped
67771negative
122414negativerod-shapedno

pigmentation

  • @ref: 31736
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40052MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
122414CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
31736positivegrowth04-33
31736positiveoptimum30mesophilic
40052positivegrowth25mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31736positivegrowth5.5-7.5
31736positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31736aerobe
67771aerobe
122414obligate aerobe

spore formation

@refspore formation
31736no
67771no

halophily

@refsaltgrowthtested relationconcentration
31736NaClpositivegrowth0-2 %
31736NaClpositiveoptimum0-0.5 %

observation

@refobservation
31736aggregates in chains
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31736581435-dehydro-D-gluconate+carbon source
3173617057cellobiose+carbon source
3173628260galactose+carbon source
3173628087glycogen+carbon source
3173617306maltose+carbon source
3173617814salicin+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12241417632nitrate-reduction
12241416301nitrite-reduction

metabolite production

  • @ref: 122414
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122414oxidase+
122414catalase+1.11.1.6
122414urease-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
122414-+++-++-+-++-++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122414---------+/-+/--+/----------+/--+/-+/-+/-+/-+/-+/-+/-----+/-+/--+/-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
67771From soilDokdoRepublic of KoreaKORAsia
122414Environment, SoilDokdo IslandRepublic of KoreaKORAsia2004

Safety information

risk assessment

  • @ref: 122414
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31736
  • description: Pedobacter sandarakinus strain DS-27 16S ribosomal RNA gene, partial sequence
  • accession: DQ235228
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 353156

GC content

  • @ref: 31736
  • GC-content: 39.7

External links

@ref: 31736

culture collection no.: KCTC 12559, CIP 108922

straininfo link

  • @ref: 91782
  • straininfo: 297287

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738103Pedobacter sandarakinus sp. nov., isolated from soil.Yoon JH, Lee MH, Kang SJ, Park SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64148-02006Culture Media, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/growth & development/*isolation & purificationCultivation
Phylogeny17329772Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris).Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ, Kwon JS, Kim WG, Weon HYInt J Syst Evol Microbiol10.1099/ijs.0.64196-02007Brassica/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purificationGenetics
Phylogeny18599709Pedobacter agri sp. nov., from soil.Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH, Kim MK, Im WT, Jin L, Kim SH, Lee ST, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65783-02008Bacteroidetes/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Phylogeny22990491Pedobacter kyungheensis sp. nov., with ginsenoside converting activity.Yang JE, Shin JY, Park SY, T Mavlonov G, Yi EJ, Lee EH, Lee JM, Yi THJ Gen Appl Microbiol10.2323/jgam.58.3092012Aerobiosis, Bacterial Typing Techniques, Base Composition, Biotransformation, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Pedobacter/*classification/*isolation & purification/metabolism/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, beta-Glucosidase/metabolismMetabolism
Phylogeny23456708Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW, Seong CN, Ka JOJ Microbiol10.1007/s12275-013-2231-92013Aerobiosis, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Brassica/growth & development, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, TemperatureGenetics
Phylogeny27498823Pedobacterpsychrotolerans sp. nov., isolated from soil.Manandhar P, Zhang G, Lama A, Hu Y, Gao FInt J Syst Evol Microbiol10.1099/ijsem.0.0013912016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34296986Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila.Peng Y, Jiang L, Seo J, Li Z, Choe H, Jeong JC, Kim SW, Kim YM, Kim CY, Lee JInt J Syst Evol Microbiol10.1099/ijsem.0.0049152021Bacterial Typing Techniques, Base Composition, Carex Plant/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pedobacter/*classification/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34590995Pedobacter riviphilus sp. nov., isolated from stream sediment.Im HS, Joung Y, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0049892021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Pedobacter/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2Transcriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31736Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172801228776041
40052Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6606
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
91782Reimer, 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-ID297287.1
122414Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108922Collection of Institut Pasteur (CIP 108922)