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

Abstract

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.

Specific Integration of Temperate Phage Decreases the Pathogenicity of Host Bacteria

“…However, it is well-known that prophages can switch to the lytic life cycle, in which the prophage DNA is excised from the host genome. Although such process often accompanied by lysis of the host cells, curing of prophages from host bacteria was reported in some bacteria (Euler et al, 2016;Aucouturier et al, 2018). Therefore, it is necessary to ensure there is no spontaneous release of prophage before using a lysogenized bacterium as a live attenuated vaccine.…”

Lactococcus Ceduovirus Phages Isolated from Industrial Dairy Plants—From Physiological to Genomic Analyses

“…Phages E1, and p6/4 exhibited poor lysis (turbid, small plaques, low titer compared to their reference strains) of the IL1403 strain, while the cremoris type strains (MG1363 and NZ9000) were fully resistant to these phages. Recently, it has been shown that resident prophages may influence host susceptibility and the phage plaquing efficiency [60]. This effect may be due to a yet undermined prophage-encoded anti-Ceduovirus defense mechanism, similar to the described super-infection exclusion (Sie) phenomenon against Skunavirus phages.…”

Lysogenization of a Lactococcal Host with Three Distinct Temperate Phages Provides Homologous and Heterologous Phage Resistance

“…In previous studies, antimicrobial susceptibility was observed in general to be higher in the presence of resident prophages than in prophage-cured derivatives [9]. In the present study, a complementary approach was taken whereby lysogens were generated and evaluated for antimicrobial susceptibility where newly acquired prophages have been integrated in the host chromosome.…”

“…The susceptibility of L. lactis 3107 and its lysogenized derivatives 3107-TPlys, -Dublys, and -LC3lys to antimicrobials was determined using the method described by Aucouturier et al (2018). Briefly, overnight cultures of 3107 and its derivative strains were diluted 10-fold in Ringer's solution (Sigma, St. Louis, MO, USA).…”

“…Detailed characterization of the model lactococcal strain IL1403 and its prophage-cured derivatives demonstrated the higher susceptibility of the prophage-carrying derivatives to cell wall-targeting and anti-microbial compounds, such as nisin and lysozyme, compared to the prophage-cured version(s). However, the stationary phase survival at 30 • C and thermal stability (at 37 • C) was observed to be higher in the parent strain relative to the prophage-cured derivatives [9]. Therefore, prophage carriage in IL1403 has both positive and negative connotations for the host with important implications for the industrial application of prophage-carrying lactococcal strains.…”