Comparison of physical preservation strategies for accurate characterization of the coffee fruit microbiome

Abstract

The method used to preserve samples prior to DNA extraction is crucial for the accurate characterization of microbial diversity. This study evaluated the effects of different storage conditions on microbial DNA preservation in Coffea arabica fruit samples. Coffee cherries were harvested directly from plants, placed in plastic tubes, and stored at 4 °C before being subjected to four treatments: lyophilization, cryopreservation at − 80 °C, and refrigeration at 4 °C. Samples were stored for 3 and 13 days. Microbial communities were characterized by next-generation sequencing. Lyophilization retained more than 80% of the ASVs shared between days 3 and 13 of storage, whereas refrigeration at 4 °C retained less than 50%. These findings demonstrate that preservation method significantly affects the integrity of bacterial and fungal microbiomes in C. arabica beans. The absence of a time-zero control, chemical preservative comparisons, and the study’s limited scope (single variety, location, and short storage period) warrant cautious interpretation of the findings. Although lyophilization was the best-performing physical preservation strategy evaluated here, broader validation across coffee cultivars, environments, and storage durations is still required before it can be considered a standard preservation protocol for preserving microbial materials derived from coffee samples.

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