Next time when you eat an apple for extra fibre, flavonoids, and flavour—remember that you are also gulping down about 100 million bacteria; and whether these are good or bad microbes may depend on how the apples were grown.

Most microbes are inside the apple but the strains depend on which bits you eat, and whether you go organic, say researchers—adding that organically-grown apples harbour more diverse and balanced bacteria which make them healthier and tastier than conventional apples.

“The bacteria, fungi, and viruses in our food transiently colonise our gut. Cooking kills most of these, so raw fruit and vegetable are particularly important sources of gut microbes,” said professor Gabriele Berg from Graz University of Technology in Austria.

The study, published in the journal Frontiers in Microbiology, compared the bacteria in conventional store-bought apples with those in visually-matched fresh organic ones.

Stem, peel, flesh, seeds, and calyx—the straggly bit at the bottom where the flower used to be—were analyzed separately. Overall, the organic and conventional apples were occupied by similar numbers of bacteria.

“Putting together the average for each apple component, we estimate a typical 240-gram apple contains roughly 100 million bacteria,” Berg stated. The majority of the bacteria are in the seeds, with the flesh accounting for most of the remainder. So, if you discard the core, your intake falls to nearer 10 million.

The question is: Are these bacteria good for you?

“Freshly harvested, organically-managed apples harbour a significantly more diverse, more even and distinct bacterial community, compared to conventional ones,” explained Berg. Specific groups of bacteria known for health-affecting potential also weighed in favour of organic apples.

“Escherichia-Shigella—a group of bacteria that includes known pathogens—was found in most of the conventional apple samples, but none from organic apples. For beneficial Lactobacilli—of probiotic fame—the reverse was true,” said the researchers.

Methylobacterium, known to enhance the biosynthesis of strawberry flavour compounds, was significantly more abundant in organic apples, “especially on peel and flesh samples, which in general had a more diverse microbiota than seeds, stem or calyx”, said the researchers.

The results also mirrored findings on fungal communities in apples. “Our results agree remarkably with a recent study on the apple fruit associated fungal community, which revealed specificity of fungal varieties to different tissues and management practices,” said Birgit Wasserman, lead author of the study.