2021
DOI: 10.1016/j.cofs.2021.03.007
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Abstract: Bacteriophage ecology has raised an increasing attention over the last few years, thanks to the improvement and contributions of microscopy, comparative genomics and viral metagenomics methods. Fermented foods host dense and diverse microbial communities and, therefore, represent an ideal biotope for bacteriophages. If their occurrence in such environments has been demonstrated decades ago, data highlighting their impact on mixed communities and their ecological roles are scarce when compared to other microbia… Show more

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Cited by 8 publications
(5 citation statements)
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References 101 publications
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“…The development of new high-throughput approaches for the study of the metavirome in dairy products (see Zotta et al, 2021 for a recent review) combined with network science approaches is certainly promising in studying the evolution of bacteriophage-host relationships in natural starters and cheese in self-assembled communities (Canon et al, 2020) in cheese manufacture, like the many cheeses produced by using undefined starters reproduced by back-slopping (Zotta et al, 2021), in which dispersal, diversification, evolution and drift (Nemergut et al, 2013) all play a role in shaping the structure, dynamics and function of the cheese microbial communities, at least in early stages of cheese-making. Finally, beyond their role in regulating the structure of bacterial populations, bacteriophages (and prophages) of LAB may have other beneficial effects in microbial communities (induction of lysis, with release on nutrients for other members of the community; providing mechanisms for recombination and gene exchange; Paillet and Dugat-Bon, 2021). Use of the concepts and computational approaches of bipartite network analysis (available, for example in the R bipartite package; Dormann et al, 2008) may be of assistance to both scientists interested in studying the structure and evolution of PBINs in cheese and to starter companies seeking to develop phage rotation schemes by facilitating the identification of potential hub strains and the identification of modules of virulent phages and susceptible strains.…”
Section: A Short Note On Phage-bacteria Interaction Networkmentioning
confidence: 99%
“…The development of new high-throughput approaches for the study of the metavirome in dairy products (see Zotta et al, 2021 for a recent review) combined with network science approaches is certainly promising in studying the evolution of bacteriophage-host relationships in natural starters and cheese in self-assembled communities (Canon et al, 2020) in cheese manufacture, like the many cheeses produced by using undefined starters reproduced by back-slopping (Zotta et al, 2021), in which dispersal, diversification, evolution and drift (Nemergut et al, 2013) all play a role in shaping the structure, dynamics and function of the cheese microbial communities, at least in early stages of cheese-making. Finally, beyond their role in regulating the structure of bacterial populations, bacteriophages (and prophages) of LAB may have other beneficial effects in microbial communities (induction of lysis, with release on nutrients for other members of the community; providing mechanisms for recombination and gene exchange; Paillet and Dugat-Bon, 2021). Use of the concepts and computational approaches of bipartite network analysis (available, for example in the R bipartite package; Dormann et al, 2008) may be of assistance to both scientists interested in studying the structure and evolution of PBINs in cheese and to starter companies seeking to develop phage rotation schemes by facilitating the identification of potential hub strains and the identification of modules of virulent phages and susceptible strains.…”
Section: A Short Note On Phage-bacteria Interaction Networkmentioning
confidence: 99%
“…For example, after microbiota dysbiosis in mice caused by antibiotic treatment, commensal phage transplantations contributed to reshaping the microbial equilibria of the microbiota to a state close to that observed before the antibiotic treatment [ 9 ]. The role of phages in fermented foods and beverages is little described on the scale of microbial communities taking into account the interactions between phages and bacteria [ 36 , 37 ]. To our knowledge, the literature on model microbial communities integrating phages is not available for the study of microbial interactions in fermented foods and beverages.…”
Section: Discussionmentioning
confidence: 99%
“…Fermented foods can contain numerous phages that can have a substantial effect on the fermentation process and can lead to low quality or failed fermentations and fermented end products. Similarly, virome studies have significant potential in improving fermented food safety through the detection of foodborne viruses [ 208 , 209 ]. However, the sequencing of viruses in fermented foods can be problematic due to their low abundance and smaller genome size compared to bacterial and fungal populations present in the food.…”
Section: Applications Of Metagenomics In the Fermented Food Industrymentioning
confidence: 99%