Distinct microbial communities associated with health-relevant wild berries

Lingonberries (Vaccinium vitis-idaea L.), rowanberries (Sorbus aucuparia L.) and rosehips (Rosa canina L.) positively affect human health due to their healing properties, determined by a high content of bioactive compounds. The consumption of unprocessed wild berries is relevant and encouraged, making their in-depth microbiological characterization essential for food safety. This study presents the first high-throughput sequencing analysis of bacterial and fungal communities distributed on the surface of lingonberries, rowanberries and rosehips. Significant plant-defined differences in the taxonomic composition of prokaryotic and eukaryotic microbiota were observed. The bacterial community on rosehips was shown to be prevalent by Enterobacteriaceae, lingonberries by Methylobacteriaceae and rowanberries by Sphingomonadaceae representatives. Among the fungal microbiota, Dothioraceae dominated on rosehips and Exobasidiaceae on lingonberries; meanwhile, rowanberries were inhabited by a similar level of a broad spectrum of fungal families. Cultivable yeast profiling revealed that lingonberries were distinguished by the lowest amount and most distinct yeast populations. Potentially pathogenic to humans or plants, as well as beneficial and relevant biocontrol microorganisms, were identified on tested berries. The combination of metagenomics and a cultivation-based approach highlighted the wild berries-associated microbial communities and contributed to uncovering their potential in plant health, food and human safety.