Abstract
BackgroundIn complex microbial ecosystems such as the marine environment, the gastrointestinal tract, but also in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community. Moreover, prophages or prophage-like elements are frequently identified in sequenced bacterial genomes. The mixed undefined starter cultures represent an ecosystem which is shaped by long term evolution under relatively defined environmental conditions and provides an interesting model to study co-evolution of phages and their hosts as well as the impact of diversity on microbial community stability.ResultsIn the present study we investigated the presence, identity and behaviour of prophages in lactococci being part of a complex cheese starter culture. Genome analysis of representative strains of the 7 genetic lineages of Lactococcus lactis constituting the culture indicated the presence of prophages in all strains. Exposure of potential lysogens to mitomycin C confirmed the release of ~ 1010·ml− 1 phage particles from all tested strains. Furthermore, phages were also released in substantial amounts due to spontaneous induction: more than 108·ml− 1 phage particles were present in cultures under non-inducing conditions. This observation suggests continuous release of phage particles by the lactococci. The released bacteriophages exhibited an unusual morphology. For most strains tested, tailless icosahedral phage heads were found. The competitive advantage of lysogens compared to their cured derivatives and their high abundance in the culture suggests that the released tailless bacteriophages play an important role in the ecosystem.ConclusionsThe results of this study indicate that chromosomal genetic elements are active participants in the stable complex microbial community of the starter culture. We show that prophages are abundant in such a community, are produced continuously in large amounts and, despite the huge metabolic burden imposed on the cells by phage particle production, provide a selective advantage to the host.
Highlights
In complex microbial ecosystems such as the marine environment, the gastrointestinal tract, and in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community
In silico analysis of potentially inducible prophage pool from a dairy mixed starter culture An in silico analysis of genomic sequence assemblies of the 7 representative Lactococcus lactis strains was carried out. Each of these strains are representatives of the 7 L. lactis genomic lineages found in the starter culture referred to as Ur [2]
Putative prophage DNA sequences were identified using manual genome browsing based on frequent homology of the ORFs in the chromosomal regions to known phage proteins as well as by using a Web-based prophage-predicting tool PHAST (Phage Search Tool, available at http://phast.wishartlab.com/) [21]
Summary
In complex microbial ecosystems such as the marine environment, the gastrointestinal tract, and in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community. Artisanal starter cultures for the production of cheese have a long history of use in a dairy environment and can be considered as domesticated cultures [1] For that reason, these cultures represent an interesting model ecosystem shaped by relatively defined environmental conditions. Alexeeva et al BMC Microbiology (2018) 18:120 of these domesticated lactic acid bacteria uncovered high incidence of lysogeny [5,6,7] This shows that prophages are rather common residents of lactic acid bacterial genomes. The prophages of L. lactis belong to the temperate P335 group of the Siphoviridae family, a taxon of the order of Caudovirales (tailed bacteriophages) They resemble lambdoid phages, are heterogeneous in nature and have genomes with a highly mosaic structure with functional modules exchangeable through homologous recombination [8,9,10]. Lysogenic strains rarely find their way to industrial processes [12], the beneficial side of lysogeny seems to be underestimated so far
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