Strain identifier

BacDive ID: 14101

Type strain: Yes

Species: Pedobacter suwonensis

Strain Designation: 15-52

Strain history: CIP <- 2007, DSMZ <- KACC <- H.Y. Weon, RDA, Suwon, Korea: strain 15-52

NCBI tax ID(s): 332999 (species)

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General

@ref: 7400

BacDive-ID: 14101

DSM-Number: 18130

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

description: Pedobacter suwonensis 15-52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil of Chinese cabbage .

NCBI tax id

  • NCBI tax id: 332999
  • Matching level: species

strain history

@refhistory
7400<- S.-W. Kwon, KACC <- H.-Y. Weon et al.; 15-52
123391CIP <- 2007, DSMZ <- KACC <- H.Y. Weon, RDA, Suwon, Korea: strain 15-52

doi: 10.13145/bacdive14101.20230509.8.1

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 suwonensis
  • full scientific name: Pedobacter suwonensis Kwon et al. 2007

@ref: 7400

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter suwonensis

full scientific name: Pedobacter suwonensis Kwon et al. 2007

strain designation: 15-52

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31756negative2.3 µm0.65 µmrod-shapedno
123391negativerod-shapedno

pigmentation

  • @ref: 31756
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7400TRYPTONE 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
37773MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123391CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7400positivegrowth30mesophilic
31756positivegrowth01-37
31756positiveoptimum34mesophilic
37773positivegrowth30mesophilic

culture pH

@refabilitytypepH
31756positivegrowth5.0-8.0
31756positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31756aerobe
123391obligate aerobe

spore formation

  • @ref: 31756
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31756NaClpositivegrowth0-3 %
31756NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3175622599arabinose+carbon source
3175617057cellobiose+carbon source
3175628757fructose+carbon source
3175628260galactose+carbon source
3175617234glucose+carbon source
3175628087glycogen+carbon source
3175617716lactose+carbon source
3175617306maltose+carbon source
3175637684mannose+carbon source
3175628053melibiose+carbon source
3175637657methyl D-glucoside+carbon source
31756506227N-acetylglucosamine+carbon source
3175616634raffinose+carbon source
3175626546rhamnose+carbon source
3175617814salicin+carbon source
3175617992sucrose+carbon source
3175627082trehalose+carbon source
3175618222xylose+carbon source
317564853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837115443inulin-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
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12339117632nitrate-reduction
12339116301nitrite-reduction

metabolite production

  • @ref: 123391
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31756acid phosphatase+3.1.3.2
31756alkaline phosphatase+3.1.3.1
31756catalase+1.11.1.6
31756gelatinase+
31756cytochrome oxidase+1.9.3.1
123391oxidase+
123391catalase+1.11.1.6
123391urease-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
123391-+++-++++-++++-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123391--+/-+/--+/----+/-+/--+/--------+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/-+/---+/-+/----+/-----+/-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
7400rhizosphere soil of Chinese cabbage (Brassica campestris)Brassica campestrisRepublic of KoreaKORAsia
123391Environment, Rhizosphere soil, Chinese cabbage Brassica campestrisRepublic of KoreaKORAsiaSuwon

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_8774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_3423;99_8774&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: DQ097274
  • Sequence Identity:
  • Total samples: 565
  • soil counts: 113
  • aquatic counts: 64
  • animal counts: 279
  • plant counts: 109

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74001Risk group (German classification)
1233911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7400
  • description: Pedobacter suwonensis strain 15-52 16S ribosomal RNA gene, partial sequence
  • accession: DQ097274
  • length: 1444
  • database: ena
  • NCBI tax ID: 332999

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter suwonensis DSM 18130GCA_900111825scaffoldncbi332999
66792Pedobacter suwonensis strain DSM 18130332999.8wgspatric332999
66792Pedobacter suwonensis DSM 181302622736524draftimg332999

GC content

  • @ref: 7400
  • GC-content: 44.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno88.741yes
flagellatedno95.75no
gram-positiveno97.19yes
anaerobicno99.46no
aerobicyes88.072no
halophileno95.961yes
spore-formingno93.034no
glucose-fermentno88.905no
thermophileno98.832no
glucose-utilyes88.557no

External links

@ref: 7400

culture collection no.: DSM 18130, CIP 109582, KACC 11317

straininfo link

  • @ref: 83269
  • straininfo: 297288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny21257686Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HYInt J Syst Evol Microbiol10.1099/ijs.0.026781-02011Base Composition, Brassica/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Pedobacter/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Soil MicrobiologyMetabolism
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
Phylogeny27600161Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0014802016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Vanadium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902277Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JGInt J Syst Evol Microbiol10.1099/ijsem.0.0016032017Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyEnzymology
Phylogeny29047421Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil.Chaudhary DK, Lee SD, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0024282017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/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

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7400Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18130
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
31756Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2802928776041
37773Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7341
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83269Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297288.1StrainInfo: A central database for resolving microbial strain identifiers
123391Curators of the CIPCollection of Institut Pasteur (CIP 109582)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109582