Strain identifier

BacDive ID: 134288

Type strain: Yes

Species: Parapedobacter soli

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 416955 (species)

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General

@ref: 32278

BacDive-ID: 134288

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

description: Parapedobacter soli KCTC 12984 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 416955
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive134288.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Parapedobacter
  • species: Parapedobacter soli
  • full scientific name: Parapedobacter soli Kim et al. 2008

@ref: 32278

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Parapedobacter

species: Parapedobacter soli

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32278negativerod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 32278
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32278positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32278aerobe
67771aerobe

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3227822599arabinose+carbon source
3227817234glucose+carbon source
3227828087glycogen+carbon source
3227817306maltose+carbon source
3227829864mannitol+carbon source
3227837684mannose+carbon source
3227828053melibiose+carbon source
32278506227N-acetylglucosamine+carbon source
3227826546rhamnose+carbon source
3227833942ribose+carbon source
3227817814salicin+carbon source
3227830911sorbitol+carbon source
3227817992sucrose+carbon source

enzymes

@refvalueactivityec
32278acid phosphatase+3.1.3.2
32278alkaline phosphatase+3.1.3.1
32278alpha-galactosidase+3.2.1.22
32278catalase+1.11.1.6
32278cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
32278soil
67771From soil from ginseng fieldRepublic of KoreaKORAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 32278
  • description: Parapedobacter soli strain DCY14 16S ribosomal RNA gene, partial sequence
  • accession: EF151805
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 416955

Genome sequences

  • @ref: 66792
  • description: Parapedobacter soli KCTC 12984
  • accession: GCA_025460835
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 416955

GC content

  • @ref: 32278
  • GC-content: 50.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.287yes
flagellatedno97.035no
gram-positiveno96.148yes
anaerobicno98.534yes
aerobicyes77.615no
halophileno88.661no
spore-formingno94.54no
glucose-fermentno79.542no
thermophileno97.901yes
glucose-utilyes91.231yes

External links

@ref: 32278

culture collection no.: KCTC 12984, LMG 24069, DCY 14

straininfo link

  • @ref: 91872
  • straininfo: 302694

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218927Parapedobacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Kim YA, Kim YJ, Soung NK, Yi TH, Kim SY, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65249-02008Bacterial Typing Techniques, Bacteroidetes/classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Panax/*growth & development, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19767359Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost.Kim SJ, Weon HY, Kim YS, Yoo SH, Kim BY, Anandham R, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.013318-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gossypium/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, Waste Products/*analysisMetabolism
Phylogeny28895519Parapedobacter lycopersici sp. nov., isolated from the rhizosphere soil of tomato plants (Solanum lycopersicum L.).Kim JM, Lee SA, Cho H, Kim SJ, Joa JH, Kwon SW, Weon HYInt J Syst Evol Microbiol10.1099/ijsem.0.0021622017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
32278Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172851828776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
91872Reimer, 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-ID302694.1