Project name: The apple fruit microbiome

Description: Apples are the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple fruit microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds and calyx), which provide niches for distinct bacterial communities. Interestingly fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approx. 108 16S rRNA bacterial gene copy numbers were determined in each g apple. While abundances were not influenced by the management practice, we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. The general structure of the apple microbiota was similar and dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%) and Firmicutes (3%) but significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Taken together, our results suggest that we consume about 115 million bacteria with one apple. Although this amount is the same, the bacterial composition is significantly different in conventionally and organically produced apples.

Data type: Other

Sample scope: Monoisolate

Last updated: 2019-08-19