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There are numerous benefits we have derived from our microbial co-inhabitants on planet Earth over millions of years. It starts with the realization that we humans wouldn’t be here if microbes living in the planet’s oceans had not developed the sophisticated language that ultimately was adopted by our nervous system and made our brains the most powerful computational devices in the universe. Equally important was the fact that microbes developed and continue to synergize with our metabolic machinery that keeps all of our cells alive.

This body of wisdom has been stored in hundreds of millions of genes and handed down during evolution over several billion years. Even though only partially understood, this microbe-based wisdom still helps us to adapt to the many challenges we are faced in a rapidly evolving world.

“The majority of our adult gut microbiome develops early on in life through vertical transmission from our mothers.”

Fast forwarding to the arrival of humans some 1 million years ago, and particularly to the present, the best-known benefits of living in harmony with our gut microbes come from the interactions of these trillions of microbes, and the rest of our body, including the brain. Research has shown that lifelong diversity and richness of this largely stable gut microbiome is associated with a lower prevalence of many if not most chronic non-transmissible diseases.

The majority of our adult gut microbiome develops early on in life through vertical transmission from our mothers. However, there are several environmental influences on our gut microbial ecosystem, including our diet, and microbes transmitted from household members, pets, and exposure to greenspaces.

Another influence comes from a group of microbes that we add to our stable gut microbiota when we regularly consume a variety of naturally fermented foods. As shown in a recent study published by the Sonnenburg Lab at Stanford University, the consumption of a diet rich in a number of naturally fermented foods, is able to increase the diversity of the gut microbiome, even more than eating a fiber rich diet.

And interestingly, this food-related transfer of microbes into our gut is not limited to fermented foods. Professor Gabriele Berg from Graz University of Technology in Austria has studied this question in great detail and has published some little-known aspects about the health benefits of consuming organically grown apples. In 2019, her group published a research article in the journal Frontiers in Microbiology, in which they compared the bacteria in conventional store-bought apples with those in visually matched organic ones. Stem, peel, flesh, seeds, and calyx – the straggly bit at the bottom where the flower used to be – were analyzed separately.

“…the data showed that freshly harvested, organically managed apples harbored a significantly more diverse, and distinct bacterial community, compared to conventional ones.”

Overall, the organic and conventional apples were occupied by similar numbers of bacteria. According to Berg, “Putting together the averages for each apple component, it has been estimated that a typical 240g apple contains roughly 100 million bacteria.” Organically managed apples harbored a significantly more diverse, and distinct bacterial community, compared to conventional ones.

There are some major caveats to this study, including the fact that the conventionally grown apples were packaged and refrigerated for days before analysis. In contrast, the organic apples were analyzed immediately following harvest, and were grown on a different farm in Austria.

Despite these methodological limitations, the study confirms previous results, showing that the majority of the bacteria found in apples were located in the seeds, with the flesh and skin accounting for most of the remainder. So, if you discard the core, as most apple consumers do – your intake falls to closer to 10 million!

“Considering that 83 million tons of apples were grown in 2018, this source of ingested microbes is quite substantial.”

Matthew Prior, science writer for the Frontiers journals stated wisely: “To the heroes among you who eat the whole apple: besides extra fiber, flavonoids and flavor, you’re also quaffing 10 times as many bacteria per fruit as your core-discarding counterparts.” Considering that 83 million tons of apples were grown in 2018, this source of ingested microbes is quite substantial.

There is general evidence that the more diverse microbial ecosystem protects the apple against harmful bacteria and fungi, just like a diverse gut microbiome protects us against enteric infections. But does eating these apple-associated microbes provide any health benefits for us? Do the treatments that some apples go through before coming to your market, like spraying with insecticides, irradiating them to destroy harmful bacteria and covering them with a thin layer of wax to make them look more attractive have a negative effect on the apple’s microbial ecosystem? Certainly, the absence of these treatments could be one reason for the observed differences of the organically grown apples.

While the final answers to these questions have not been shown in well controlled studies, based on Berg’s exciting research and studies looking into other health benefits of apples, one can make some well-informed speculations:

1. Organically grown and treated apples are likely to contain a more diverse and health promoting microbiome, and when consumed on a regular basis – ideally including the apple core, seeds, and skin – will add to the health and diversity of our gut microbiome, just like the consumption of naturally fermented foods do.
2. In addition to being an excellent source of beneficial microbes, apples contain the highest amounts of flavanols, the same compound contained in cocoa beans. Flavonoids are not only metabolized into absorbable small molecules by our gut microbes, but they also have a beneficial effect on the diversity and relative abundance of beneficial gut microbes. A recent study in a large, placebo controlled clinical trial has shown that regular consumption of 1000 mg of flavanols reduces cardiovascular morbidity and improves cognitive function.
3. As the polyphenol content of plants grown in regenerative organic soil seems to be higher than of plants grown conventionally, the greatest health benefits both from ingested apple-associated microbes and flavanol content would be expected to come from apples grown in regenerative organic agriculture.

Birgit Wasserman, Berg protégé and co-author of the study, suggested that “The microbiome and antioxidant profiles of fresh produce may one day become standard nutritional information, displayed alongside macronutrients, vitamins, and minerals to guide consumers … another key step will be to confirm to what extent diversity in the food microbiome [and flavanol content] translates to gut microbial diversity and improved health outcomes.”