Impact of cultivation and origin on the fruit microbiome of apples and blueberries

Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. While the gut microbiome is considered an integral environmental factor under the exposome concept, the influence of the environmental microbiota, including food microbiota, is not well understood. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland) and three fruit production methods (commercial, home-grown, and grown in the wild). It was found that the typical fruit microbiome consists of Gammaproteobacteria (Pseudomonadaceae, Burkholderiaceae and Enterobacteriaceae), Alphaproteobacteria (Sphingomonadaceae), and Cladosporiaceae. Microbial abundance, diversity and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (natural or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e. for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered as an important but relatively unexplored external exposomic factor.