Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence

Miia Pasanen , Małgorzata Waleron , Thomas Schott , Ilse Cleenwerck , Agnieszka Misztak , Krzysztof Waleron , Leighton Pritchard , Ramadan Bakr , Yeshitila Degefu , Jan van der Wolf , Peter Vandamme , Minna Pirhonen


Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
Publication typeIn press (online first, early view)
Author Miia Pasanen
Miia Pasanen,,
, Małgorzata Waleron (IFB/IB/DBiotech)
Małgorzata Waleron,,
- Department of Biotechnology
, Thomas Schott
Thomas Schott,,
, Ilse Cleenwerck
Ilse Cleenwerck,,
, Agnieszka Misztak (IFB)
Agnieszka Misztak,,
- Intercollegiate Faculty of Biotechnology UG
, Krzysztof Waleron - [Medical Uniwersity of Gdańsk (GUMed)]
Krzysztof Waleron,,
- Gdański Uniwersytet Medyczny
, Leighton Pritchard
Leighton Pritchard,,
, Ramadan Bakr
Ramadan Bakr,,
, Yeshitila Degefu
Yeshitila Degefu,,
, Jan van der Wolf
Jan van der Wolf,,
et al.`
Journal seriesInternational Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, e-ISSN 1466-5034, (N/A 70 pkt)
Issue year2020
Noonline first
Publication size in sheets0.50
Keywords in EnglishPectobacterium, Pectobacterium parvum, Salmonella SPI-1 T3SS, potato, soft rot, virulence
ASJC Classification2700 General Medicine; 1105 Ecology, Evolution, Behavior and Systematics; 2404 Microbiology
Languageen angielski
LicenseOther; published final; Uznanie Autorstwa - Użycie Niekomercyjne (CC-BY-NC); with publication
Score (nominal)70
Score sourcejournalList
ScoreMinisterial score = 70.0, 11-03-2020, ArticleFromJournal
Publication indicators Scopus SNIP (Source Normalised Impact per Paper): 2018 = 1.028; WoS Impact Factor: 2018 = 2.166 (2) - 2018=2.212 (5)
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