Novel Podoviridae Family Bacteriophage Infecting Weissella cibaria Isolated from Kimchi

Abstract

bThe first complete genome sequence of a phage infecting Weissella cibaria (Weissella kimchii) is presented. The bacteriophage YS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, YS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that YS61 resembles Podoviridae of the subfamily Picovirinae. Within the subfamily Picovirinae, the 29-like phages have been extensively studied, and their terminal protein-primed DNA replication is well characterized. Our data strongly suggest that YS61 also replicates by a protein-primed mechanism. Weissella phage YS61 is, however, markedly different from members of the Picovirinae with respect to genome size and morphology. Picovirinae are characterized by small (approximately 20-kb) genomes which contrasts with the 33,594-bp genome of YS61. Based on electron microscopy analysis, YS61 was classified as a member of the Podoviridae of morphotype C2, similar to the 29-like phages, but its capsid dimensions are significantly larger than those reported for these phages. The novelty of YS61 was also emphasized by the low number of open reading frames (ORFs) showing significant similarity to database sequences. We propose that the bacteriophage YS61 should represent a new subfamily within the family Podoviridae. Kimchi, a traditional Korean dish, is manufactured by fermentation of vegetables such as Chinese cabbage and radish. Hundreds of kimchi varieties are produced by the addition of different seasonings, such as scallions, powdered chili peppers, garlic, ginger, and fermented seafood. Lactic acid produced during fermentation contributes to preservation and gives kimchi its characteristic sour taste. Proper ripening and preservation are ensured by a 2 to 5% (wt/vol) salt content and anaerobic fermentation at low temperatures. Kimchi is traditionally prepared by spontaneous fermentation by lactic acid bacteria (LAB) indigenous to the vegetable ingredients. However, starter cultures have been developed in order to better control the fermentation and thus improve quality, safety, and shelf life of the fermented product (15,16,20,24). Several LAB species have been identified as likely contributors in kimchi fermentations, including species of the genera Leuconostoc, Lactobacillus, Lactococcus, Pediococcus, and Weissella (6,18,19,32,35,36,[38][39][40][41]51,53,57). Weissella species isolated from kimchi include Weissella confusa, Weissella kimchii, and Weissella koreensis. These bacteria are abundant late in the fermentation process and can continue to grow during storage at low temperatures (Ϫ1°C). Weissella species have thus been associated with the excessive acidic taste of overripened kimchi products. The species Weissella kimchii, first described in 2002 (19), was reclassified as Weissella cibaria in 2004 (9, 23).The kimchi fermentation process is ch...

Nuclear localization signals in phage terminal proteins provide a novel gene delivery tool in mammalian cells

“…Moreover, after the latter work was accepted we noticed that the TP of the recently discovered phage YS61, 10 which has been proposed to constitute a new independent subfamily within the Podoviridae virus family, also contains a putative NLS in its sequence (residues 126–155, according to NLStradamus 11 prediction), which further confirms the widespread presence of NLSs in TPs.…”

Why Are Weissella spp. Not Used as Commercial Starter Cultures for Food Fermentation?

“…Only a few studies reported phages infecting Weissella spp. Bacteriophage Φ22 from W. cibaria N22 was isolated from Nham, a Thai fermented pork sausage [212]. Both Φ22 and ΦYS61 belong to the Podoviridae phage family and harbor size genome of 29 Kb and 33.6 Kb, respectively.…”

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

“…The abundance of green alga in the Ofunato Bay was substantially high at the time of sampling ( Supplementary Table S3), and we observed a positive correlation between Prasinovirus abundance and green alga (data not shown). In the WGS library, a small number of unclassified Myoviridae, Podoviridae and Siphoviridae were detected that infect bacteria and Archaea, including highly abundant Synechococcus in the Ofunato Bay (Lavigne et al, 2009;Ghai et al, 2012;Kleppen et al, 2012;Bebeacua et al 2013).…”