Microbial community induced by host genotype in Coffea canephora: from field to fermentation

The microbial community during coffee processing results from the interaction among host genetics, chemical composition, and post-harvest environmental selective pressures; however, the relative contribution of each factor remains poorly understood. In this study, we investigated how two genetically distinct Coffea canephora genotypes modulate bacterial and fungal communities from freshly harvested fruits to spontaneous and Saccharomyces cerevisiae -induced fermentations. Using high-throughput sequencing, beta diversity metrics, and variance decomposition by ASCA, we quantified the effects of genotype, processing, and their interaction. Processing acted as the main driver of microbial restructuring, clearly separating natural fruits from fermented samples, while genotype maintained a consistent influence on microbial community composition. ASCA models confirmed that processing explained the largest proportion of variance, followed by genotype and the genotype × process interaction. Taxonomic analyses revealed bacterial convergence toward profiles dominated by the genus Weissella , whereas fungal communities remained more genotype-dependent, including differences in the establishment capacity of S. cerevisiae . These patterns indicate that environmental factors and host-mediated selection jointly shape microbial profiles in C. canephora . Moreover, the genetic diversity of C. canephora supports distinct ecological responses during fermentation, providing a foundation for targeted fermentation strategies integrating plant genetics and microbial ecology.