Strain identifier
BacDive ID: 133801
Type strain:
Species: Phyllobacterium endophyticum
Strain Designation: PEPV15
NCBI tax ID(s): 1149773 (species)
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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
30551 | negative | rod-shaped | yes | |
69480 | yes | 92.344 | ||
69480 | negative | 99.989 |
pigmentation
- @ref: 30551
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30551 | positive | growth | 05-39 | |
30551 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30551 | positive | growth | 06-08 |
30551 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30551
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30551 | no | |
69481 | no | 100 |
69480 | no | 99.992 |
halophily
- @ref: 30551
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30551 | 37054 | 3-hydroxybutyrate | + | carbon source |
30551 | 16449 | alanine | + | carbon source |
30551 | 22599 | arabinose | + | carbon source |
30551 | 33984 | fucose | + | carbon source |
30551 | 17234 | glucose | + | carbon source |
30551 | 24996 | lactate | + | carbon source |
30551 | 25115 | malate | + | carbon source |
30551 | 29864 | mannitol | + | carbon source |
30551 | 37684 | mannose | + | carbon source |
30551 | 506227 | N-acetylglucosamine | + | carbon source |
30551 | 26271 | proline | + | carbon source |
30551 | 26546 | rhamnose | + | carbon source |
30551 | 33942 | ribose | + | carbon source |
30551 | 30911 | sorbitol | + | carbon source |
30551 | 4853 | esculin | + | hydrolysis |
30551 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
- @ref: 30551
- sample type: plant associated
isolation source categories
- Cat1: #Host
- Cat2: #Plants
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Phyllobacterium endophyticum PEPV15 | GCA_003010935 | contig | ncbi | 1149773 |
66792 | Phyllobacterium endophyticum CECT 7949 | GCA_014192255 | scaffold | ncbi | 1149773 |
66792 | Phyllobacterium endophyticum PEPV15 | GCA_008180215 | scaffold | ncbi | 1149773 |
66792 | Phyllobacterium endophyticum strain CECT 7949 | 1149773.6 | wgs | patric | 1149773 |
66792 | Phyllobacterium endophyticum strain PEPV15 | 1149773.3 | wgs | patric | 1149773 |
66792 | Phyllobacterium endophyticum PEPV15 | 2839993093 | draft | img | 1149773 |
66792 | Phyllobacterium endophyticum CECT 7949 | 2824427252 | draft | img | 1149773 |
GC content
- @ref: 30551
- GC-content: 52
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 82.414 | no |
gram-positive | no | 97.837 | yes |
anaerobic | no | 99.092 | yes |
aerobic | yes | 94.826 | no |
halophile | no | 92.31 | no |
spore-forming | no | 96.255 | no |
glucose-util | yes | 89.989 | yes |
thermophile | no | 97.677 | no |
motile | yes | 88.369 | yes |
glucose-ferment | no | 90.182 | no |
External links
@ref: 30551
culture collection no.: LMG 26470, CECT 7949
straininfo link
- @ref: 91598
- straininfo: 377657
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22611197 | Phyllobacterium 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 R | Int J Syst Evol Microbiol | 10.1099/ijs.0.038497-0 | 2012 | Bacterial 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, Spain | Genetics |
Phylogeny | 25376850 | Phyllobacterium 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 WF | Int J Syst Evol Microbiol | 10.1099/ijs.0.067017-0 | 2014 | Bacterial 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/chemistry | Genetics |
Phylogeny | 29620492 | Phyllobacterium 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 IA | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002722 | 2018 | Bacterial 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, Symbiosis | Transcriptome |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
30551 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26882 | 28776041 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||
91598 | Reimer, 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 identifiers | 10.60712/SI-ID377657.1 |