Strain identifier

BacDive ID: 134221

Type strain: Yes

Species: Parapedobacter koreensis

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 332977 (species)

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General

@ref: 31935

BacDive-ID: 134221

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

description: Parapedobacter koreensis KCTC 12643 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from From soil.

NCBI tax id

  • NCBI tax id: 332977
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- ST Lee, KAIST

doi: 10.13145/bacdive134221.20230509.8.1

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 koreensis
  • full scientific name: Parapedobacter koreensis Kim et al. 2007

@ref: 31935

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Parapedobacter

species: Parapedobacter koreensis

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31935negativerod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 31935
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31935positivegrowth04-42
31935positiveoptimum37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31935aerobe
67771aerobe

spore formation

  • @ref: 31935
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31935NaClpositivegrowth03-04 %
31935NaClpositiveoptimum3.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3193533984fucose+carbon source
3193517234glucose+carbon source
3193517306maltose+carbon source
3193529864mannitol+carbon source
3193537684mannose+carbon source
31935506227N-acetylglucosamine+carbon source
3193533942ribose+carbon source
3193517814salicin+carbon source
3193517822serine+carbon source
3193530911sorbitol+carbon source
3193517992sucrose+carbon source

enzymes

@refvalueactivityec
31935catalase+1.11.1.6
31935cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 67771
  • sample type: From soil
  • geographic location: KAIST
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_184813.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_2374;97_65978;98_120271;99_184813&stattab=map
  • Last taxonomy: Parapedobacter koreensis subclade
  • 16S sequence: DQ680836
  • Sequence Identity:
  • Total samples: 82
  • soil counts: 33
  • aquatic counts: 15
  • animal counts: 29
  • plant counts: 5

Sequence information

16S sequences

  • @ref: 31935
  • description: Parapedobacter koreensis strain Jip14 16S ribosomal RNA gene, partial sequence
  • accession: DQ680836
  • length: 1481
  • database: nuccore
  • NCBI tax ID: 332977

GC content

@refGC-content
3193545.6
6777145.56

External links

@ref: 31935

culture collection no.: KCTC 12643, LMG 23493, Jip 14

straininfo link

  • @ref: 91815
  • straininfo: 290304

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551054Parapedobacter koreensis gen. nov., sp. nov.Kim MK, Na JR, Cho DH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64677-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, BacterialGenetics
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
Phylogeny25298380Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil.Kumar R, Dwivedi V, Nayyar N, Verma H, Singh AK, Rani P, Rao DLN, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.069104-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hexachlorocyclohexane/analysis, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/analysis, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
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
31935Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172819228776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91815Reimer, 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-ID290304.1