Strain identifier

BacDive ID: 133768

Type strain: Yes

Species: Pedobacter ginsengiterrae

Strain history: D.-C. Yang DCY49.

NCBI tax ID(s): 871696 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 30449

BacDive-ID: 133768

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

description: Pedobacter ginsengiterrae KCTC 23317 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 871696
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-C. Yang DCY49.

doi: 10.13145/bacdive133768.20230509.8.1

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 ginsengiterrae
  • full scientific name: Pedobacter ginsengiterrae Hoang et al. 2013

@ref: 30449

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter ginsengiterrae

type strain: yes

Morphology

cell morphology

  • @ref: 30449
  • gram stain: negative
  • cell length: 2 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: gliding

pigmentation

  • @ref: 30449
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30449positivegrowth04-34
30449positiveoptimum28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30449positivegrowth4.5-10alkaliphile
30449positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30449
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30449NaClpositivegrowth0-3 %
30449NaClpositiveoptimum0.5 %

observation

@refobservation
30449aggregates in clumps
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3044922599arabinose+carbon source
3044917057cellobiose+carbon source
3044928260galactose+carbon source
3044917234glucose+carbon source
3044928087glycogen+carbon source
3044917716lactose+carbon source
3044917306maltose+carbon source
3044937684mannose+carbon source
3044928053melibiose+carbon source
30449506227N-acetylglucosamine+carbon source
3044916634raffinose+carbon source
3044926546rhamnose+carbon source
3044917814salicin+carbon source
3044917992sucrose+carbon source
3044927082trehalose+carbon source
304494853esculin+hydrolysis

enzymes

@refvalueactivityec
30449acid phosphatase+3.1.3.2
30449alkaline phosphatase+3.1.3.1
30449catalase+1.11.1.6
30449cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
30449soil
67770Soil of a ginseng field in a mountainous region of Chungbuk ProvinceRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_14225.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_3275;98_4120;99_14225&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: HM776704
  • Sequence Identity:
  • Total samples: 7612
  • soil counts: 2160
  • aquatic counts: 1652
  • animal counts: 1898
  • plant counts: 1902

Sequence information

16S sequences

  • @ref: 30449
  • description: Pedobacter ginsengiterrae strain DCY49 16S ribosomal RNA gene, partial sequence
  • accession: HM776704
  • length: 1410
  • database: nuccore
  • NCBI tax ID: 871696

GC content

@refGC-contentmethod
3044940.5
6777040.5high performance liquid chromatography (HPLC)

External links

@ref: 30449

culture collection no.: KCTC 23317, JCM 17338, DCY 49

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22771687Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field.Hoang VA, Kim YJ, Nguyen NL, Min JW, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.036376-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24573158Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter.Kook M, Park Y, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.058024-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pinus/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny35819898Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0054482022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

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
30449Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172678428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/