A dataset on habitat-associated changes in the fecal microbiota of Drosophila melanogaster.

Drosophila melanogaster is a flagship model for studying animal-microbe interactions. In nature, its larvae develop on ephemeral plant substrates, where growth depends on the presence and metabolic activity of bacterial and fungal symbionts. Yet, microbial communities associated with natural breeding sites differ markedly from those maintained in laboratory cultures on artificial media. Most research on Drosophila-microbe interactions has been conducted under controlled but artificial conditions, limiting our understanding of the ecological and evolutionary dynamics of these associations. To bridge this gap, we re-associated laboratory fly cultures with field-exposed plant substrates, establishing semi-natural microcosms that harbor diverse, substrate-specific microbiota. Microcosms were sustained by fly-mediated transfer of microbial communities through fecal deposition onto new plant substrates. We present a comprehensive metabarcoding dataset of D. melanogaster fecal microbiota, including both bacterial (16S V3-V4) and fungal (ITS2) communities. To capture temporal dynamics, six plant substrate-based microcosms - apple, tomato, lemon, grape, onion, and plum - were sampled three times over five months, providing strain-level resolution of symbiont community composition.