The Virome of Cocoa Fermentation-Associated Microorganisms

Area of Science:

• Microbiology
• Virology
• Food Science
• Metagenomics

Background:

• Cocoa bean fermentation is crucial for chocolate flavor and color, influenced by microbial communities.
• Viruses can impact microbial diversity and fermentation quality by infecting key microorganisms.
• The viral communities associated with cocoa fermentation remain largely unexplored.

Purpose of the Study:

• To identify and characterize viruses present during cocoa bean fermentation.
• To explore the potential role of these viruses in the fermentation process and microbial dynamics.
• To investigate the evolutionary relationships of identified viruses.

Main Methods:

• Analysis of publicly available metatranscriptomic libraries from cocoa bean fermentation.
• Utilized a comprehensive bioinformatic pipeline for viral sequence identification.
• Applied Hidden Markov Models to analyze viral sequence characteristics and associations.

Main Results:

• Identified 68 viral sequences, including 62 new species and 6 known viruses across nine families.
• Discovered a significant abundance of ssRNA phages (Fiersviridae) and fungi-infecting viruses (Botourmiaviridae, Narnaviridae, Mitoviridae).
• Observed a general decline in virus-derived RNAs correlating with microbial dynamics, and identified novel segmented narnavirus-related elements.

Conclusions:

• Elucidated the complex virome associated with cocoa bean fermentation microbial consortia.
• The identified virome may influence microbial selection, metabolite production, and sensory characteristics of cocoa.
• This research highlights the importance of viruses in shaping fermentation outcomes and cocoa quality.