Strain identifier
BacDive ID: 4404
Type strain: 
Species: Erwinia piriflorinigrans
Strain history: <- CECT <- M.M. López, Instituto Valenciano de Investigaciones Agrarias, Spain
NCBI tax ID(s): 1161919 (strain), 665097 (species)
version 8.1 (current version)
General
@ref: 18178
BacDive-ID: 4404
DSM-Number: 26166
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen
description: Erwinia piriflorinigrans DSM 26166 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from necrotic pear blossoms.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1161919 | strain |
| 665097 | species |
strain history
- @ref: 18178
- history: <- CECT <- M.M. López, Instituto Valenciano de Investigaciones Agrarias, Spain
doi: 10.13145/bacdive4404.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Erwiniaceae
- genus: Erwinia
- species: Erwinia piriflorinigrans
- full scientific name: Erwinia piriflorinigrans López et al. 2011
@ref: 18178
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Erwiniaceae
genus: Erwinia
species: Erwinia piriflorinigrans
full scientific name: Erwinia piriflorinigrans López et al. 2011
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 29771 | negative | rod-shaped | yes | |
| 69480 | yes | 97.997 | ||
| 69480 | negative | 99.973 |
multimedia
- @ref: 18178
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26166.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 18178
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 18178 | positive | growth | 28 | mesophilic |
| 29771 | positive | growth | 25-30 | mesophilic |
| 29771 | positive | optimum | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 29771
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29771 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.923 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29771 | 15963 | ribitol | + | carbon source |
| 29771 | 16449 | alanine | + | carbon source |
| 29771 | 22599 | arabinose | + | carbon source |
| 29771 | 28757 | fructose | + | carbon source |
| 29771 | 33984 | fucose | + | carbon source |
| 29771 | 28260 | galactose | + | carbon source |
| 29771 | 17234 | glucose | + | carbon source |
| 29771 | 25115 | malate | + | carbon source |
| 29771 | 29864 | mannitol | + | carbon source |
| 29771 | 28053 | melibiose | + | carbon source |
| 29771 | 17268 | myo-inositol | + | carbon source |
| 29771 | 506227 | N-acetylglucosamine | + | carbon source |
| 29771 | 26271 | proline | + | carbon source |
| 29771 | 16634 | raffinose | + | carbon source |
| 29771 | 33942 | ribose | + | carbon source |
| 29771 | 17822 | serine | + | carbon source |
| 29771 | 30031 | succinate | + | carbon source |
| 29771 | 17992 | sucrose | + | carbon source |
| 29771 | 27082 | trehalose | + | carbon source |
| 29771 | 53424 | tween 20 | + | carbon source |
| 29771 | 18222 | xylose | + | carbon source |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | + | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29771 | catalase | + | 1.11.1.6 |
| 68369 | cytochrome oxidase | - | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 18178 | - | - | + | - | - | + | - | + | + | + | - | + | + | - | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 18178
- sample type: necrotic pear blossoms
- geographic location: Valencia
- country: Spain
- origin.country: ESP
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Inflammation | |
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Flower |
taxonmaps
- @ref: 69479
- File name: preview.99_118173.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_502;98_576;99_118173&stattab=map
- Last taxonomy: Erwinia piriflorinigrans
- 16S sequence: GQ405202
- Sequence Identity:
- Total samples: 58
- soil counts: 1
- aquatic counts: 1
- animal counts: 47
- plant counts: 9
Safety information
risk assessment
- @ref: 18178
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18178
- description: Erwinia piriflorinigrans CFBP 5888 strain CECT 7348 16S ribosomal RNA gene, partial sequence
- accession: GQ405202
- length: 1350
- database: ena
- NCBI tax ID: 1161919
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Erwinia piriflorinigrans CFBP 5888 | GCA_001050515 | contig | ncbi | 1161919 |
| 66792 | Erwinia piriflorinigrans CFBP 5888 | 1161919.3 | wgs | patric | 1161919 |
| 66792 | Erwinia piriflorinigrans CFBP 5888 | 2630968383 | draft | img | 1161919 |
GC content
- @ref: 18178
- GC-content: 51.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.892 | yes |
| gram-positive | no | 98.092 | yes |
| anaerobic | no | 98.18 | no |
| aerobic | no | 58.613 | yes |
| halophile | no | 82.973 | no |
| spore-forming | no | 94.48 | yes |
| flagellated | no | 56.837 | no |
| thermophile | no | 98.693 | yes |
| glucose-util | yes | 95.524 | no |
| glucose-ferment | yes | 89.436 | yes |
External links
@ref: 18178
culture collection no.: DSM 26166, CECT 7348, CFBP 5888, IVIA 2057.5
straininfo link
- @ref: 73895
- straininfo: 320313
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20382791 | Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms. | Lopez MM, Rosello M, Llop P, Ferrer S, Christen R, Gardan L | Int J Syst Evol Microbiol | 10.1099/ijs.0.020479-0 | 2010 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Erwinia/*classification/genetics/*isolation & purification, Genotype, Molecular Sequence Data, Molecular Typing, Nucleic Acid Hybridization, Phylogeny, Plant Diseases/*microbiology, Plasmids/analysis, Polymerase Chain Reaction, Pyrus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain | Genetics |
| Genetics | 23726521 | Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. | Smits TH, Rezzonico F, Lopez MM, Blom J, Goesmann A, Frey JE, Duffy B | Syst Appl Microbiol | 10.1016/j.syapm.2013.04.003 | 2013 | Base Sequence, Cluster Analysis, DNA, Bacterial/*chemistry/*genetics, Erwinia/*classification/*genetics/isolation & purification/pathogenicity, Flowers/microbiology, *Genome, Bacterial, Molecular Sequence Data, *Phylogeny, Plant Diseases/microbiology, Plasmids, Pyrus/microbiology, Sequence Analysis, DNA, Spain, Virulence Factors/*genetics | Phylogeny |
| Phylogeny | 31675291 | Mixta tenebrionis sp. nov., isolated from the gut of the plastic-eating mealworm Tenebrio molitor L. | Xia M, Wang J, Huo YX, Yang Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003826 | 2020 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Gastrointestinal Tract/*microbiology, Nucleic Acid Hybridization, *Phylogeny, *Plastics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tenebrio/*microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18178 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26166) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26166 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29771 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26151 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 69479 | João 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 73895 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID320313.1 | StrainInfo: A central database for resolving microbial strain identifiers |