Assessing the functionality and genetic diversity of lactococcal prophages

Kelleher, Philip; Mahony, Jennifer; Schweinlin, Katharina; Neve, Horst; Franz, Charles M. A. P.; Sinderen, Douwe van

doi:10.1016/j.ijfoodmicro.2018.02.024

Cited by 26 publications

(38 citation statements)

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“…All other prophages were found to have experienced different levels of mutational decay. Moreover, it is also acknowledged that many genes in the defective prophages remain functional and contribute to various traits of the hosts, and that the prophage functions are a result of purifying selection in the bacterial chromosome (Bobay et al, 2014;Kelleher et al, 2018). Prophage genes encoding core phage-related functions, e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Maintenance of a temperate bacteriophage inside a bacterial chromosome in the form of prophage, also referred to as lysogeny, is a common phenomenon in L. lactis strains (Brondsted and Hammer, 2006;Kelleher et al, 2018). Nevertheless, lysogenic bacterial strains, carrying inducible prophages in the chromosome, usually do not find their way into commercial fermentation practice when it concerns a defined starter composition (Garneau and Moineau, 2011).…”

Section: Introductionmentioning

confidence: 99%

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

Alexeeva

Liu

Zhu

et al. 2020

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Background Our previous study on a model microbial community originating from artisanal cheese fermentation starter revealed that bacteriophages not only co-exist with bacteria but also are highly abundant. To gain more insight into the potential role of prophages in the microbial community, we analysed the genomic content of 6 phage crops released by different strains in the starter culture, performed comparative genome analysis, and demonstrated their roles in phage defence of respective hosts. Results 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, resulting in a 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 functional in protecting the host from foreign phage infection. Conclusion We suggest that the presumably defective prophages are a result of bacteria-phage coevolution and convey advantages to host bacteria; knowledge on the ecological role of such (defective) prophages may contribute to a refreshed look in strain selection criteria in (dairy) industry.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Alexeeva

Liu

Zhu

et al. 2020

Preprint

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“…Currently, 34 complete and 97 partially assembled lactococcal genomes are available in NCBI’s GenBank 1 . In each one, the genomes of temperate bacteriophages (complete prophages) and prophage remnants have been identified ( Chopin et al, 2001 ; Ventura et al, 2007 ; Kelleher et al, 2018 ). Prophage-related sequences encompass from 3 to 10% of the total genome, and represent a significant part of the observed genomic differences among L. lactis strains ( Kelleher et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

“…In each one, the genomes of temperate bacteriophages (complete prophages) and prophage remnants have been identified ( Chopin et al, 2001 ; Ventura et al, 2007 ; Kelleher et al, 2018 ). Prophage-related sequences encompass from 3 to 10% of the total genome, and represent a significant part of the observed genomic differences among L. lactis strains ( Kelleher et al, 2018 ). Genome sequence analyses of lactococcal prophages indicated that they are affiliated with the P335 group of phages, one of the three dominant phage species commonly found in dairy factories ( Deveau et al, 2006 ).…”

Section: Introductionmentioning

confidence: 99%

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Characterization of a Prophage-Free Derivative Strain of Lactococcus lactis ssp. lactis IL1403 Reveals the Importance of Prophages for Phenotypic Plasticity of the Host

et al. 2018

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Lactococcus lactis is a lactic acid bacterium of major importance for the dairy industry and for human health. Recent sequencing surveys of this species have provided evidence that all lactococcal genomes contain prophages and prophage-like elements. The prophage-related sequences encompass up to 10% of the bacterial chromosomes and thus contribute significantly to the genetic diversity of lactococci. However, the impact of these resident prophages on the physiology of L. lactis is presently unknown. The genome of the first sequenced prototype strain, L. lactis ssp. lactis IL1403, contains six prophage-like elements which together represent 6.7% of the IL1403 chromosome. Diverse prophage genes other than those encoding phage repressors have been shown to be expressed in lysogenic conditions, suggesting that prophage genes are indeed able to modulate the physiology of their host. To elucidate the effect of resident prophages on the behavior of L. lactis in different growth conditions, we constructed and characterized, for the first time, a derivative strain of IL1403 that is prophage-free. This strain provides unique experimental opportunities for the study of different aspects of lactococcal physiology using the well-defined genetic background of IL1403. Here, we show that resident prophages modify the growth and survival of the host strain to a considerable extent in different conditions, including in the gastrointestinal environment. They also may affect cellular autolytic properties and the host cells’ susceptibility to virulent bacteriophages and antimicrobial agents. It thus appears that prophages contribute significantly to lactococcal cell physiology and might play an important role in the adaptation of L. lactis to cultivation and environmental conditions.

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