Bacteriophages on dairy foods.

This review focuses on the impact of bacteriophages on the manufacture of dairy foods. Firstly, the impact of phages of lactic acid bacteria in the dairy industry, where they are considered enemies, is discussed. The sources of phage contamination in dairy plants are detailed, with special emphasis on the rise of phage infections related to the growing use of cheese whey as ingredient. Other topics include traditional and new methods of phage detection, quantification and monitoring, and strategies of phage control in dairy plants, either of physical, chemical or biological nature. Finally, the use of phages or purified phage enzymes as allies to control pathogenic bacteria in the food industry is reviewed.

Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community.

Fermented foods are considered as an integral part of the global human diet. Fermented foods also have unique microbial communities such as bacteria, archaea, fungi, and viruses that are essential to the fermentation process and affect final product characteristics. Despite the ecological importance of virus, little is known about the diversity and ecological role of virus in the food ecosystem. In this study, the viral and host bacterial communities from 10 representative samples of Korean and Chinese kimchi were analyzed in triplicate using next-generation sequencing technology. The overall structures of bacterial and viral communities were dominated by lactic acid bacteria in phylum Firmicutes and bacteriophages in order Caudovirales, respectively. For the single-stranded DNA (ssDNA) viruses, bacteriophage in family Microviridae were dominant in Korean kimchi. After correction for multiple comparisons using false discovery rate (FDR, P < 0.05), the relative abundances of 6 bacterial taxa and 33 viral host taxa at the genus level were significantly different between Korean and Chinese kimchi. Notably, in beta-diversity analysis, viral communities were much more clearly separated according to their geographical origin (PERMANOVA pseudo-F = 11.57, P < 0.001 in Bray-Curtis PCoA) than bacterial communities (pseudo-F = 4.75, P < 0.001 in unweighted UniFrac PCoA). Thus, viral metagenomics represents a potentially useful in-depth analytical method for determining the geographical origins of fermented foods.

Genome Engineering of Virulent Lactococcal Phages Using CRISPR-Cas9.

Phages are biological entities found in every ecosystem. Although much has been learned about them in past decades, significant knowledge gaps remain. Manipulating virulent phage genomes is challenging. To date, no efficient gene-editing tools exist for engineering virulent lactococcal phages. Lactococcus lactis is a bacterium extensively used as a starter culture in various milk fermentation processes, and its phage sensitivity poses a constant risk to the cheese industry. The lactococcal phage p2 is one of the best-studied models for these virulent phages. Despite its importance, almost half of its genes have no functional assignment. CRISPR-Cas9 genome editing technology, which is derived from a natural prokaryotic defense mechanism, offers new strategies for phage research. Here, the well-known Streptococcus pyogenes CRISPR-Cas9 was used in a heterologous host to modify the genome of a strictly lytic phage. Implementation of our adapted CRISPR-Cas9 tool in the prototype phage-sensitive host L. lactis MG1363 allowed us to modify the genome of phage p2. A simple, reproducible technique to generate precise mutations that allow the study of lytic phage genes and their encoded proteins in vivo is described.

Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria.

Cheese production is a global biotechnological practice that is reliant on robust and technologically appropriate starter and adjunct starter cultures to acidify the milk and impart particular flavor and textural properties to specific cheeses. To this end, lactic acid bacteria, including Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus and Leuconostoc spp., are routinely employed. However, these bacteria are susceptible to infection by (bacterio)phages. Over the past decade in particular, significant advances have been achieved in defining the receptor molecules presented by lactococcal host bacteria and in the structural analysis of corresponding phage-encoded receptor-binding proteins. These lactococcal model systems are expanding toward understanding phage-host interactions of other LAB species. Ultimately, such scientific efforts will uncover the mechanistic (dis)similarities among these phages and define how these phages recognize and infect their hosts. This review presents the current status of the LAB-phage interactome, highlighting the most recent and significant developments in this active research field.

Phages of lactic acid bacteria: the role of genetics in understanding phage-host interactions and their co-evolutionary processes.

Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

Bacteriophages of lactic acid bacteria and their impact on milk fermentations.

Every biotechnology process that relies on the use of bacteria to make a product or to overproduce a molecule may, at some time, struggle with the presence of virulent phages. For example, phages are the primary cause of fermentation failure in the milk transformation industry. This review focuses on the recent scientific advances in the field of lactic acid bacteria phage research. Three specific topics, namely, the sources of contamination, the detection methods and the control procedures will be discussed.