Strain identifier

BacDive ID: 14113

Type strain: Yes

Species: Pedobacter agri

Strain Designation: PB92

Variant: Isotype of BacDive ID 132884

Strain history: <- ZX Quan, KAIST

NCBI tax ID(s): 454586 (species)

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General

@ref: 8114

BacDive-ID: 14113

DSM-Number: 19486

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

description: Pedobacter agri PB92 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 454586
  • Matching level: species

strain history

@refhistory
8114<- S. W. Roh, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); PB92
67770S. W. Roh PB92.
67771<- ZX Quan, KAIST

doi: 10.13145/bacdive14113.20230509.8.1

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 agri
  • full scientific name: Pedobacter agri Roh et al. 2008

@ref: 8114

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter agri

full scientific name: Pedobacter agri Roh et al. 2008

strain designation: PB92

variant: Isotype of BacDive ID 132884

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shape
32616negative3 µm0.7 µmrod-shaped
67771rod-shaped
67771negative

pigmentation

  • @ref: 32616
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8114
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8114positivegrowth28mesophilic
32616positivegrowth10-30
32616positiveoptimum25mesophilic
67770positivegrowth30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
32616positivegrowth06-08
32616positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32616aerobe
67771aerobe

spore formation

  • @ref: 32616
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32616NaClpositivegrowth0-2.5 %
32616NaClpositiveoptimum0-2.5 %

observation

  • @ref: 32616
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32616581435-dehydro-D-gluconate+carbon source
3261615963ribitol+carbon source
3261622599arabinose+carbon source
3261617057cellobiose+carbon source
3261628260galactose+carbon source
3261617234glucose+carbon source
3261628087glycogen+carbon source
3261617716lactose+carbon source
3261617306maltose+carbon source
3261637684mannose+carbon source
3261628053melibiose+carbon source
32616506227N-acetylglucosamine+carbon source
3261616634raffinose+carbon source
3261626546rhamnose+carbon source
3261617814salicin+carbon source
3261617992sucrose+carbon source
3261627082trehalose+carbon source
3261618222xylose+carbon source
326164853esculin+hydrolysis

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8114soilDaejeonRepublic of KoreaKORAsia
67770SoilDaejeonRepublic of KoreaKORAsia
67771From soilDaejeonRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 8114
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8114
  • description: Pedobacter agri PB92 16S ribosomal RNA gene, partial sequence
  • accession: EF660751
  • length: 1460
  • database: ena
  • NCBI tax ID: 1149865

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter agri PB921149865.7wgspatric1149865
66792Pedobacter agri PB922548876984draftimg1149865
67770Pedobacter agri PB92GCA_000258495contigncbi1149865

GC content

@refGC-contentmethod
811441.4
6777041.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.779no
gram-positiveno96.702no
anaerobicno99.445yes
aerobicyes89.418no
halophileno96.312no
spore-formingno95.116yes
flagellatedno97.323no
thermophileno99.238yes
glucose-utilyes88.599yes
glucose-fermentno89.665no

External links

@ref: 8114

culture collection no.: DSM 19486, KCTC 12511, JCM 15120

straininfo link

  • @ref: 83280
  • straininfo: 412334

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
Phylogeny31346824Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica.He RH, Liu ZW, Yu Y, Li HR, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-019-01305-42019Aerobiosis, Antarctic Regions, *Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Pedobacter/*classification/genetics/*isolation & purification/physiology, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8114Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19486)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19486
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
32616Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2882828776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
83280Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID412334.1StrainInfo: A central database for resolving microbial strain identifiers