Strain identifier

BacDive ID: 134222

Type strain: Yes

Species: Pedobacter panaciterrae

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363849 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 31944

BacDive-ID: 134222

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped

description: Pedobacter panaciterrae KCTC 12594 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 363849
  • Matching level: species

strain history

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

doi: 10.13145/bacdive134222.20230509.8.1

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 panaciterrae
  • full scientific name: Pedobacter panaciterrae Yoon et al. 2007

@ref: 31944

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter panaciterrae

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31944negative2 µm0.75 µmrod-shapedno
67771rod-shapedno
67771negative

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31944positivegrowth04-30
31944positiveoptimum25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31944positivegrowth5.5-8.5alkaliphile
31944positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31944facultative anaerobe
67771aerobe

spore formation

@refspore formation
31944no
67771no

halophily

  • @ref: 31944
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3194422599arabinose+carbon source
3194417057cellobiose+carbon source
3194417234glucose+carbon source
3194417754glycerol+carbon source
3194417716lactose+carbon source
3194417306maltose+carbon source
3194437684mannose+carbon source
3194428053melibiose+carbon source
31944506227N-acetylglucosamine+carbon source
3194416634raffinose+carbon source
3194417814salicin+carbon source
3194417992sucrose+carbon source
3194427082trehalose+carbon source
3194418222xylose+carbon source

enzymes

@refvalueactivityec
31944catalase+1.11.1.6
31944cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
31944soil
67771From soil of the ginseng fieldRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6274.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3973;99_6274&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: AB245368
  • Sequence Identity:
  • Total samples: 780
  • soil counts: 523
  • aquatic counts: 50
  • animal counts: 111
  • plant counts: 96

Sequence information

16S sequences

  • @ref: 31944
  • description: Pedobacter panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 042
  • accession: AB245368
  • length: 1463
  • database: nuccore
  • NCBI tax ID: 363849

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter panaciterrae LMG 23400GCA_013204795contigncbi363849
66792Pedobacter panaciterrae strain LMG 23400363849.11wgspatric363849

GC content

  • @ref: 31944
  • GC-content: 44.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.976yes
anaerobicno99.606yes
halophileno96.214no
spore-formingno94.207yes
glucose-utilyes89.986yes
aerobicyes87.005no
flagellatedno96.114yes
thermophileno99.065yes
motileno90.079yes
glucose-fermentno90.811no

External links

@ref: 31944

culture collection no.: KCTC 12594, LMG 23400, Gsoil 042

straininfo link

  • @ref: 91816
  • straininfo: 289682

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267983Pedobacter panaciterrae sp. nov., isolated from soil in South Korea.Yoon MH, Ten LN, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64693-02007Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Gelatinases/analysis, Genes, rRNA, Hydrogen Sulfide/metabolism, Indoles/metabolism, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil MicrobiologyMetabolism
Phylogeny24425748Pedobacter nutrimenti sp. nov., isolated from chilled food.Derichs J, Kampfer P, Lipski AInt J Syst Evol Microbiol10.1099/ijs.0.058677-02014Animals, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Swine, Vitamin K 2/analogs & derivatives/chemistryBiotechnology
Phylogeny27032079Pedobacter humi sp. nov., isolated from a playground soil.Trinh H, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0010322016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902181Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0015322016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33502299Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana.Qi SS, Cnockaert M, Carlier A, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0046672021

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
31944Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172820028776041
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
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/
91816Reimer, 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-ID289682.1