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Strain identifier

BacDive ID: 4408

Type strain: Yes

Species: Erwinia typographi

Strain Designation: Y1

Strain history: <- V. Skrodenyte-Arbaciauskiene, Inst. Ecology, Vilnius Univ., Lithuania; Y1

NCBI tax ID(s): 371042 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16458

BacDive-ID: 4408

DSM-Number: 22678

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

description: Erwinia typographi Y1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of adult bark beetle Ips typographus.

NCBI tax id

  • NCBI tax id: 371042
  • Matching level: species

strain history: <- V. Skrodenyte-Arbaciauskiene, Inst. Ecology, Vilnius Univ., Lithuania; Y1

doi: 10.13145/bacdive4408.20221219.7.1

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 typographi
  • full scientific name: Erwinia typographi Skrodenyt?-Arba?iauskien? et al. 2012

@ref: 16458

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia typographi

full scientific name: Erwinia typographi Skrodenyt?-Arba?iauskien? et al. 2012

strain designation: Y1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30177negative02-04 µm0.7-0.8 µmrod-shapedyes
69480yes69.431
69480negative99.064

pigmentation

  • @ref: 30177
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16458
  • 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

@refgrowthtypetemperaturerange
16458positivegrowth28mesophilic
30177positiveoptimum22-36

Physiology and metabolism

oxygen tolerance

  • @ref: 30177
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
30177no
69480no97.6

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 94.006

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3017722599arabinose+carbon source
3017728757fructose+carbon source
3017728260galactose+carbon source
3017717234glucose+carbon source
3017715792malonate+carbon source
3017729864mannitol+carbon source
3017737684mannose+carbon source
30177506227N-acetylglucosamine+carbon source
3017733942ribose+carbon source
3017727082trehalose+carbon source

enzymes

  • @ref: 30177
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 16458
  • sample type: gut of adult bark beetle Ips typographus
  • host species: Ips typographus
  • country: Lithuania
  • origin.country: LTU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract#Stomach

Safety information

risk assessment

  • @ref: 16458
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16458
  • description: Erwinia typographi strain Y1 16S ribosomal RNA gene, partial sequence
  • accession: GU166291
  • length: 1406
  • database: ena
  • NCBI tax ID: 371042

GC content

@refGC-contentmethod
1645849.1high performance liquid chromatography (HPLC)
3017749.1

External links

@ref: 16458

culture collection no.: DSM 22678, LMG 25347

straininfo link

@refpassport
20218http://www.straininfo.net/strains/869857
20218http://www.straininfo.net/strains/842542

literature

  • topic: Phylogeny
  • Pubmed-ID: 21669921
  • title: Erwinia typographi sp. nov., isolated from bark beetle (Ips typographus) gut.
  • authors: Skrodenyte-Arbaciauskiene V, Radziute S, Stunzenas V, Buda V
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.030304-0
  • year: 2011
  • mesh: Acyclic Monoterpenes, Alkenes/chemistry, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Erwinia/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Gastrointestinal Tract/microbiology, Genes, Bacterial, Lithuania, Molecular Sequence Data, Monoterpenes/chemistry, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Picea, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Weevils/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16458Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22678)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22678
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2652610.1099/ijs.0.030304-021669921
30177Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126526
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)