Year: 2026
Type: data-paper
Abstract: 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.
Source: Scientific Data
Authors: Elisabeth K. Riedel, Marko Rohlfs
Institution: University of Bremen
Language: English
Subfield: Insect Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,490
Funder: Universität Bremen
OpenAlex ID: W7166674292