Strain identifier

BacDive ID: 134171

Type strain: Yes

Species: Pedobacter roseus

Strain Designation: CL-GP80

Strain history: B. C. Cho CL-GP80.

NCBI tax ID(s): 336820 (species)

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General

@ref: 31681

BacDive-ID: 134171

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

description: Pedobacter roseus CL-GP80 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hypertrophic pond.

NCBI tax id

  • NCBI tax id: 336820
  • Matching level: species

strain history

  • @ref: 67770
  • history: B. C. Cho CL-GP80.

doi: 10.13145/bacdive134171.20230509.8.1

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 roseus
  • full scientific name: Pedobacter roseus Hwang et al. 2006

@ref: 31681

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter roseus

strain designation: CL-GP80

type strain: yes

Morphology

cell morphology

  • @ref: 31681
  • gram stain: negative
  • cell length: 0.8-1.1 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 31681
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31681positivegrowth05-33
31681positiveoptimum25-30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31681positivegrowth06-08
31681positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31681
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31681
  • spore formation: no

halophily

  • @ref: 31681
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

observation

@refobservation
31681aggregates in chains
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3168122599arabinose+carbon source
3168117057cellobiose+carbon source
3168128757fructose+carbon source
3168128260galactose+carbon source
3168129987glutamate+carbon source
3168128087glycogen+carbon source
3168117716lactose+carbon source
3168117306maltose+carbon source
3168137684mannose+carbon source
31681506227N-acetylglucosamine+carbon source
3168115361pyruvate+carbon source
3168116634raffinose+carbon source
3168126546rhamnose+carbon source
3168117814salicin+carbon source
3168130031succinate+carbon source
3168117992sucrose+carbon source
3168127082trehalose+carbon source
3168118222xylose+carbon source
316814853esculin+hydrolysis

enzymes

@refvalueactivityec
31681acid phosphatase+3.1.3.2
31681alkaline phosphatase+3.1.3.1
31681catalase+1.11.1.6
31681gelatinase+
31681cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
31681hypertrophic pond
67770Hypertrophic pond in SeoulRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Pond (small)

Sequence information

16S sequences

  • @ref: 31681
  • description: Pedobacter roseus strain CL-GP80 16S ribosomal RNA gene, partial sequence
  • accession: DQ112353
  • length: 1381
  • database: nuccore
  • NCBI tax ID: 336820

GC content

@refGC-contentmethod
3168141.3
6777041.3high performance liquid chromatography (HPLC)

External links

@ref: 31681

culture collection no.: KCCM 42272, JCM 13399, LMG 31320, NCIMB 14494

straininfo link

  • @ref: 91769
  • straininfo: 297286

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902016Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter.Hwang CY, Choi DH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.64045-02006Bacteroides/*classification/isolation & purification/physiology, DNA, Bacterial/genetics, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Temperature, *Water MicrobiologyGenetics
Phylogeny17329772Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris).Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ, Kwon JS, Kim WG, Weon HYInt J Syst Evol Microbiol10.1099/ijs.0.64196-02007Brassica/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purificationGenetics
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
Phylogeny21257686Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HYInt J Syst Evol Microbiol10.1099/ijs.0.026781-02011Base Composition, Brassica/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Pedobacter/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Soil MicrobiologyMetabolism
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
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
31681Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172795828776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
91769Reimer, 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-ID297286.1