Modulation of food microbiome by processing of apple fruits

Fruits, vegetables and berries are key components of a healthy human diet. The role of the indigenous microbiome as a source for beneficial gut microbes, especially during food processing, is largely unknown. Therefore, we investigated the apple fruit microbiome before and after processing using functional assays, advanced microscopic as well as sequencing technologies. Apple fruits carried a high abundance (1.8 x 105 16S rRNA copies per g of apple pulp) and diverse microbiome (H'=2.5). We found severe expected effects of heat and mechanical treatment on the fruit's microbiota following a declining gradient of abundance and diversity from shredded > boiled > puree > preserved > dried apples. Betaproteobacteriales and Enterobacteriales were the two dominant bacterial orders (51.3%, 20.4% of total reads) in the unprocessed apple. Boiling and air drying reduces the microbial load, but an unexpected, substantial fraction of 1/3 of the microbiota survived. Boiling and air drying shifted the microbiota leading to a relative increase in low abundant taxa such as Pseudomonas and Ralstonia (>2 log2 fold change), while others such as Bacillus decrease. Bacillus spp., frequently found in raw fruits, were shown to have specific traits i.e. antagonist activity against opportunistic pathogens, biosurfactant production, and bile salt resistance indicating a probiotic potential. Our findings provide novel insights into food microbial changes during processing, and demonstrate that food microbiome studies need a combined methodological approach. Food inhabiting microbes, currently considered being a risk factor for food safety, are a key exposome and potential resource for human gut microbes.