Exploring viral diversity in fermented vegetables through viral metagenomics

Area of Science:

• Microbiology
• Virology
• Food Science

Background:

• Fermented vegetables rely on endogenous microorganisms, with bacterial and fungal communities well-studied.
• Viral communities (phages) in fermented vegetables remain largely unexplored, despite their potential ecological impact.

Purpose of the Study:

• To characterize the microbial and viral communities in fermented cabbage, carrot, and turnip.
• To identify the types of viruses present and their potential bacterial hosts.

Main Methods:

• Shotgun and viral metagenomic sequencing of twelve fermented vegetable samples.
• Epifluorescence microscopy for viral load estimation.
• Bioinformatic analysis of metagenome-assembled genomes (MAGs) to detect prophages.

Main Results:

• Microbiome dominated by lactic acid bacteria, varying by vegetable type.
• Detected 22 prophages, with 8 found as free viral particles (metaviromes).
• Viral load ranged from 5.28 to 7.57 log virus-like particles/gram.
• Viral communities primarily dsDNA viruses (bacteriophages), with some ssDNA and RNA viruses.
• Bacteriophages targeted Lactobacillaceae and Enterobacteriaceae families.

Conclusions:

• Fermented vegetables harbor complex and variable microbial and viral communities.
• Bacteriophage composition is influenced by the type of vegetable used.
• Further research is needed to understand viral impact on fermented food ecology and quality.