When comparing the microbiota of organic and non-organic apples, you might as well be comparing apples and oranges. Well, perhaps the differences aren’t quite as stark as that, but they are significant.
All parts of an apple contain bacteria and we consume about 114 million bacterial cells with every
Apples grown organically, however, had a more diverse community of bacteria, which included Lactobacillus and other bacteria frequently used in probiotics. The apples grown non-organically, on the other hand, had significantly greater abundance of Enterobacteriales, which can be responsible for food-borne outbreaks. The scientists conclude that “the highly diverse microbiome of organically managed apples might probably limit or hamper the abundance of human pathogens, simply by outcompeting them; negative correlations between human pathogen abundance and the natural microbiome of fresh produce has already been described.”
Source: B Wassermann, H Müller and G Berg. 2019. An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? Frontiers in Microbiology. Volume 10. July. Article 1629. Pages 1-13.