Genomics of tailless bacteriophages in a complex lactic acid bacteria starter culture

Thijs R.H.M Kouwen,Svetlana Alexeeva,Tjakko Abee,Eddy J Smid,Joanna Kaczorowska,Jingjie Zhu,Yue Liu

doi:10.1016/j.idairyj.2020.104900

Thijs R.H.M Kouwen, Svetlana Alexeeva + Show 5 more

Open Access

https://doi.org/10.1016/j.idairyj.2020.104900

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Abstract

Our previous study on a model microbial community originating from an artisanal cheese fermentation starter revealed that bacteriophages not only co-exist with bacteria but also are highly abundant. Here we describe the genomic content of phage particles released by 6 different strains in the starter culture. The identified prophages belong to three different subgroups of the Siphoviridae P335 phage group. Remarkably, most analysed prophages show disruptions in different tail encoding genes, explaining the common tailless phenotype. Furthermore, a number of potentially beneficial features for the host carried by prophages were identified. The prophages carry up to 3 different phage defence systems per genome that are potentially functional in protecting the host from foreign phage infection. We suggest that the presumably defective prophages are a result of bacteria-phage coevolution and could convey advantages to host bacteria.

Highlights

Cells from all domains of life are susceptible to viral infections
Whole phage genome sequences were obtained for phage particles released by L. lactis strains TIFN1, TIFN2, TIFN4, TIFN5, TIFN6 and TIFN7 upon mitomycin C (MitC) induction
In our previous study we described morphologically tailless bacteriophages, abundantly and continuously released by all analysed L. lactis strains originating from a complex dairy starter culture Ur without showing obvious cell lysis (Alexeeva et al, 2018)

Summary

Introduction

Cells from all domains of life are susceptible to viral infections. Their viruses (bacteriophages or, phages), are estimated to be the most abundant biological entities on Earth. Total number of bacteriophages is estimated to be 1031 in the biosphere (Comeau et al, 2008). In complex microbial consortia such as those found in a marine environment, the gastrointestinal tract and in complex food fermentations, bacteriophages can alter the dynamics and diversity of microbial communities (Erkus et al, 2013; Smid et al, 2014; Spus et al, 2015; Stern & Sorek, 2011). Bacteriophages help to drive microbial evolution through phage-mediated gene transfer (Canchaya, Fournous, Chibani-Chennoufi, Dillmann, & Brüssow, 2003; Penades, Chen, Quiles-Puchalt, Carpena, & Novick, 2015)

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