Archive BacDiveID:10.13145/bacdive4408.20221219.7.1

Strain identifier

BacDive ID: 4408

Type strain:

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.

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

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
30177	negative	02-04 µm	0.7-0.8 µm	rod-shaped	yes
69480					yes	69.431
69480	negative					99.064

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

@ref	growth	type	temperature	range
16458	positive	growth	28	mesophilic
30177	positive	optimum	22-36

Physiology and metabolism

oxygen tolerance

@ref: 30177
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
30177	no
69480	no	97.6

halophily

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

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30177	22599	arabinose	+	carbon source
30177	28757	fructose	+	carbon source
30177	28260	galactose	+	carbon source
30177	17234	glucose	+	carbon source
30177	15792	malonate	+	carbon source
30177	29864	mannitol	+	carbon source
30177	37684	mannose	+	carbon source
30177	506227	N-acetylglucosamine	+	carbon source
30177	33942	ribose	+	carbon source
30177	27082	trehalose	+	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

Cat1	Cat2	Cat3
#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

@ref	GC-content	method
16458	49.1	high performance liquid chromatography (HPLC)
30177	49.1

External links

@ref: 16458

culture collection no.: DSM 22678, LMG 25347

straininfo link

@ref	passport
20218	http://www.straininfo.net/strains/869857
20218	http://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

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
16458	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22678)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22678
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
26526			10.1099/ijs.0.030304-0			21669921
30177	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		28776041	26526
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)