High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community

Abstract

Endogenous starter cultures are used in the production of several cheeses around the world, such as Parmigiano Reggiano, in Italy, Epoisses, in France, and Canastra, in Brazil. These microbial communities are responsible for many of the intrinsic characteristics of each of these cheeses. Bacteriophages are ubiquitous around the world, well known to be involved in the modulation of complex microbiological processes. However, little is known about phage bacteria growth dynamics in cheese production systems, where phages are normally treated as problems, as the viral infections can negatively affect or even eliminate the starter culture during production. Furthermore, a recent metagenomic based meta-analysis has reported that cheeses contain a high abundance of phage-associated sequences. Here, we analyse the viral and bacterial metagenomes of Canastra cheese, a tradition artisanal cheese produced using an endogenous starter culture. We observe a very high phage diversity level, mostly composed of novel sequences. We detect several metagenomic assembled bacterial genomes at strain level resolution, and several putative phage-bacteria interactions, evidenced by the recovered viral and bacterial genomic signatures. We postulate that at least one bacterial strain detected could be endogenous to the Canastra region, in Brazil, and that its growth seems to be modulated by native phages present in this artisanal production system. This relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for all cheeses that employ similar production processes around the world.

A review of methods for the inference and experimental confirmation of microbial association networks in cheese

“…: Jacobs-Sera et al, 2020;Klyczek et al, 2017;de Melo et al, 2020) or Swiss-type cheese (Propionibacterium: Cheng et al, 2018) are also known and, in some cases might be responsible of defects in cheese. More recently, metavirome studies are being carried out in starter cultures and in cheeses (Colombo et al, 2018;Dugat-Bony et al, 2020;Frantzen and Holo, 2019;Muhammed et al, 2017;Queiroz et al, 2021) and are allowing the discovery of novel bacteriophage-host interactions relevant to cheese ecology and quality.…”

Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar

“…It has been observed that some viruses can positively influence the fermentation process of fermented foods [ 5 ]. Reports showed that, in some fermented food such as cocoa beans and milk cheese, viruses can regulate bacterial community succession during fermentation, and might have beneficial effects on the quality and sensory characteristics of fermented products [ 6 , 7 ]. Moreover, Pacini and Ruggiero [ 8 ] suggested that phages have potential probiotic properties in modern fermented foods and fermented milk supplemented with probiotics bacteriophage can improve the efficacy of probiotics in food.…”