Abstract The invasive fly Drosophila suzukii is a pest that can infest a diverse range of intact, ripening fruits, using its serrated ovipositor. This constitutes a different niche compared to the rotting fruits its ancestors use, especially because these intact fruits have limited quantities of microbes and soluble nutrients for the developing larvae. To investigate the potential role of microbial associations in the niche expansion of this invasive fly, we characterized the bacterial and fungal communities of D. suzukii and various wild fruits from which they developed. To assess cross-generational microbial associations, we also lab-reared fly populations and characterized their microbial communities. Diversity metrics of microbial communities differed significantly between flies and fruits. Different fruit types varied substantially in microbial composition, while flies showed relatively uniform bacterial communities, irrespective of the fruit source they developed on. After approximately ten generations of lab-rearing, bacterial communities still showed considerable overlap with those of wild flies. Fungal communities of flies and fruits showed larger resemblance, with a substantial overlap between wild flies and the fruits on which they had developed. Our study thus reports that the fungal community structure in these pests largely reflects those on the breeding substrates, while these flies might have formed more persistent associations with some bacteria and transmit these across generations.
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