Strain identifier

BacDive ID: 133801

Type strain: Yes

Species: Phyllobacterium endophyticum

Strain Designation: PEPV15

NCBI tax ID(s): 1149773 (species)

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: 30551

BacDive-ID: 133801

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

description: Phyllobacterium endophyticum PEPV15 is an aerobe, Gram-negative, motile bacterium that was isolated from plant associated.

NCBI tax id

  • NCBI tax id: 1149773
  • Matching level: species

doi: 10.13145/bacdive133801.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Phyllobacterium
  • species: Phyllobacterium endophyticum
  • full scientific name: Phyllobacterium endophyticum Flores-Félix et al. 2013

@ref: 30551

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Phyllobacterium

species: Phyllobacterium endophyticum

strain designation: PEPV15

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30551negativerod-shapedyes
69480yes92.344
69480negative99.989

pigmentation

  • @ref: 30551
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30551positivegrowth05-39
30551positiveoptimum28mesophilic

culture pH

@refabilitytypepH
30551positivegrowth06-08
30551positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30551
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30551no
69481no100
69480no99.992

halophily

  • @ref: 30551
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30551370543-hydroxybutyrate+carbon source
3055116449alanine+carbon source
3055122599arabinose+carbon source
3055133984fucose+carbon source
3055117234glucose+carbon source
3055124996lactate+carbon source
3055125115malate+carbon source
3055129864mannitol+carbon source
3055137684mannose+carbon source
30551506227N-acetylglucosamine+carbon source
3055126271proline+carbon source
3055126546rhamnose+carbon source
3055133942ribose+carbon source
3055130911sorbitol+carbon source
305514853esculin+hydrolysis
3055117632nitrate+reduction

Isolation, sampling and environmental information

isolation

  • @ref: 30551
  • sample type: plant associated

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phyllobacterium endophyticum PEPV15GCA_003010935contigncbi1149773
66792Phyllobacterium endophyticum CECT 7949GCA_014192255scaffoldncbi1149773
66792Phyllobacterium endophyticum PEPV15GCA_008180215scaffoldncbi1149773
66792Phyllobacterium endophyticum strain CECT 79491149773.6wgspatric1149773
66792Phyllobacterium endophyticum strain PEPV151149773.3wgspatric1149773
66792Phyllobacterium endophyticum PEPV152839993093draftimg1149773
66792Phyllobacterium endophyticum CECT 79492824427252draftimg1149773

GC content

  • @ref: 30551
  • GC-content: 52

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno82.414no
gram-positiveno97.837yes
anaerobicno99.092yes
aerobicyes94.826no
halophileno92.31no
spore-formingno96.255no
glucose-utilyes89.989yes
thermophileno97.677no
motileyes88.369yes
glucose-fermentno90.182no

External links

@ref: 30551

culture collection no.: LMG 26470, CECT 7949

straininfo link

  • @ref: 91598
  • straininfo: 377657

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22611197Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris.Flores-Felix JD, Carro L, Velazquez E, Valverde A, Cerda-Castillo E, Garcia-Fraile P, Rivas RInt J Syst Evol Microbiol10.1099/ijs.0.038497-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phaseolus/*microbiology, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SpainGenetics
Phylogeny25376850Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens.Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH, Zhang XX, Wang ET, Chen WX, Chen WFInt J Syst Evol Microbiol10.1099/ijs.0.067017-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Sophora/*microbiology, *Symbiosis, Ubiquinone/chemistryGenetics
Phylogeny29620492Phyllobacterium zundukense sp. nov., a novel species of rhizobia isolated from root nodules of the legume species Oxytropis triphylla (Pall.) Pers.Safronova VI, Sazanova AL, Kuznetsova IG, Belimov AA, Andronov EE, Chirak ER, Popova JP, Verkhozina AV, Willems A, Tikhonovich IAInt J Syst Evol Microbiol10.1099/ijsem.0.0027222018Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Oxytropis/*microbiology, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Russia, Sequence Analysis, DNA, SymbiosisTranscriptome

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
30551Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172688228776041
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91598Reimer, 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-ID377657.1