The impact of an apple a day in keeping the doctor away may be partly down to the beneficial bacteria it carries and their subsequent colonisation of your gut, according to scientists.

A study has found that a typical apple carries more than 100m bacteria. Some of these microbes are important in maintaining a healthy gut environment, or microbiome, says Prof Gabriele Berg from Graz University of Technology, Austria, one of the authors of the research.

“The bacteria, fungi and viruses in our food transiently colonise our gut,” she said. “Cooking kills most of these, so raw fruit and veg are particularly important sources of gut microbes.”

The researchers compared the bacteria in shop-bought apples with those in visually matched organic ones. The apple’s stem, peel, flesh, seeds and calyx – the straggly bit at the bottom where the flower used to be – were all analysed separately.

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Although organic and conventional apples were occupied by similar numbers of bacteria, the researchers found organic apples harboured a more diverse and balanced bacterial community, which they said could make them healthier and tastier than conventional apples.

Variety in the microbiome is thought to be key to a healthy gut and the researchers said there appeared to be more microbial diversity in organic apples.

“Freshly harvested, organically managed apples harbour a significantly more diverse, more even and distinct bacterial community, compared to conventional ones,” explained Berg. “This variety and balance would be expected to limit overgrowth of any one species, and previous studies have reported a negative correlation between human pathogen abundance and microbiome diversity of fresh produce.” In other words, the more varied your diet, the fewer harmful bacteria are found.

The research may also vindicate the people who claim to be able to taste the difference between organic and ordinary produce, say the researchers. A microbe known as methylobacterium, which is known to boost strawberry-flavoured compounds, was significantly more abundant in organic apples, Berg said.

Birgit Wassermann, also at Graz University of Technology and the lead author of the study, said the next step would be “to confirm to what extent diversity in the food microbiome translates to gut microbial diversity and improved health outcomes”.

She also suggested that this information might one day appear on supermarket food labels. “The microbiome and antioxidant profiles of fresh produce may one day become standard nutritional information, displayed alongside macronutrients, vitamins and minerals to guide consumers,” she added.

The research was published in the journal Frontiers in Microbiology.