A Simple Method for Assessing Diversity and Dynamics of Microbial Community: Comparison of Dairy Phages from Industrial and Spontaneous Fermentation

Abstract

Background: The dairy industry heavily relies on fermentation processes driven in high proportion by Lactococcus lactis. The fermentation process can be perturbed or even stopped by bacteriophage activity, leading to complete loss of fermentation batch or decreased quality product. The monitoring of the phage diversity and dynamics in the process allows implementing protective measures (e.g., starter rotation) to maintain unperturbed production. Methods: Universal primers were used to amplify sequences of the 936, c2, and P335 Lactococcus phage types. The amplicons were sequenced with the Sanger method and obtained degenerate sequences were analyzed using a simple bioinformatic pipeline in the R environment. Results: The most prevalent phage type is 936, followed by P335, whereas the c2 type is less frequent. Conclusions: Curd cheeses prepared on non-pasteurized milk based on native milk microbiota had a higher diversity of phages distinct from those found in dairy plants. Sanger sequencing of heterogenous amplicons generated on metagenome DNA can be used to assess low-complexity microbiota diversity.